EcoliWiki - User contributions [en]

PMID:19706412

2013-07-08T20:25:33Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="M50ad199107b8a" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Peters, JM, Mooney, RA, Kuan, PF, Rowland, JL, Keles, S and Landick, R''' (2009) Rho directs widespread termination of intragenic and stable RNA transcription.''Proc. Natl. Acad. Sci. U.S.A.'' '''106''':15406-11
|-
!align=left |Abstract
||
The transcription termination factor Rho is a global regulator of RNA polymerase (RNAP). Although individual Rho-dependent terminators have been studied extensively, less is known about the sites of RNAP regulation by Rho on a genome-wide scale. Using chromatin immunoprecipitation and microarrays (ChIP-chip), we examined changes in the distribution of Escherichia coli RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM). We found approximately 200 Rho-terminated loci that were divided evenly into 2 classes: intergenic (at the ends of genes) and intragenic (within genes). The intergenic class contained noncoding RNAs such as small RNAs (sRNAs) and transfer RNAs (tRNAs), establishing a previously unappreciated role of Rho in termination of stable RNA synthesis. The intragenic class of terminators included a previously uncharacterized set of short antisense transcripts, as judged by a shift in the distribution of RNAP in BCM-treated cells that was opposite to the direction of the corresponding gene. These Rho-terminated antisense transcripts point to a role of noncoding transcription in E. coli gene regulation that may resemble the ubiquitous noncoding transcription recently found to play myriad roles in eukaryotic gene regulation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19706412 PubMed]
Online version:[http://dx.doi.org/10.1073/pnas.0903846106 10.1073/pnas.0903846106]
|-
!align=left |Keywords
||
Bicyclo Compounds, Heterocyclic; Chromatin Immunoprecipitation; DNA-Directed RNA Polymerases; Escherichia coli; Genes, Bacterial; Microarray Analysis; RNA; Transcription, Genetic; rho GTP-Binding Proteins

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.M50ad199107b8a&page=182751&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="O50ad19913835a" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.O50ad19913835a&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z519f8d526b29b" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
RpoC
RNAP beta prime

|
RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=94828 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.3.gff +BCM (19M gff)]

|-
|
MG1655
|
ChIP-chip
|
RpoB RNAP beta

|
RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=3428302 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.1.gff +BCM, (20M gff)]

|-
|
MG1655
|
ChIP-chip
|
RpoB RNAP beta
|
Untreated
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=3427302 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.2.gff untreated (20M gff)]
|-
|
MG1655
|
ChIP-chip
|
RpoC RNAP beta prime
|
Untreated
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=100040 Gbrowse]

*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.4.gff untreated (19M gff)]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.Z519f8d526b29b&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]
[[Category:RNA_polymerase_tracks]]

PMID:19706412

2013-07-08T18:35:23Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="M50ad199107b8a" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Peters, JM, Mooney, RA, Kuan, PF, Rowland, JL, Keles, S and Landick, R''' (2009) Rho directs widespread termination of intragenic and stable RNA transcription.''Proc. Natl. Acad. Sci. U.S.A.'' '''106''':15406-11
|-
!align=left |Abstract
||
The transcription termination factor Rho is a global regulator of RNA polymerase (RNAP). Although individual Rho-dependent terminators have been studied extensively, less is known about the sites of RNAP regulation by Rho on a genome-wide scale. Using chromatin immunoprecipitation and microarrays (ChIP-chip), we examined changes in the distribution of Escherichia coli RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM). We found approximately 200 Rho-terminated loci that were divided evenly into 2 classes: intergenic (at the ends of genes) and intragenic (within genes). The intergenic class contained noncoding RNAs such as small RNAs (sRNAs) and transfer RNAs (tRNAs), establishing a previously unappreciated role of Rho in termination of stable RNA synthesis. The intragenic class of terminators included a previously uncharacterized set of short antisense transcripts, as judged by a shift in the distribution of RNAP in BCM-treated cells that was opposite to the direction of the corresponding gene. These Rho-terminated antisense transcripts point to a role of noncoding transcription in E. coli gene regulation that may resemble the ubiquitous noncoding transcription recently found to play myriad roles in eukaryotic gene regulation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19706412 PubMed]
Online version:[http://dx.doi.org/10.1073/pnas.0903846106 10.1073/pnas.0903846106]
|-
!align=left |Keywords
||
Bicyclo Compounds, Heterocyclic; Chromatin Immunoprecipitation; DNA-Directed RNA Polymerases; Escherichia coli; Genes, Bacterial; Microarray Analysis; RNA; Transcription, Genetic; rho GTP-Binding Proteins

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.M50ad199107b8a&page=182751&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="O50ad19913835a" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.O50ad19913835a&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z519f8d526b29b" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
RpoC
RNAP beta prime

|
RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=94828 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.3.gff +BCM (19M gff)]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.4.gff untreated (19M gff)]
|-
|
MG1655
|
ChIP-chip
|
RpoB RNAP beta

|
RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=3428302 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.1.gff +BCM, (20M gff)]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.2.gff untreated (20M gff)]
|-
|
MG1655
|
ChIP-chip
|
RpoB RNAP beta
|
Untreated
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=3427302 Gbrowse]
|-
|
MG1655
|
ChIP-chip
|
RpoC RNAP beta prime
|
Untreated
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=100040 Gbrowse]

*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.4.gff untreated (19M gff)]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.Z519f8d526b29b&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]
[[Category:RNA_polymerase_tracks]]

PMID:19706412

2013-07-05T21:10:22Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="M50ad199107b8a" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Peters, JM, Mooney, RA, Kuan, PF, Rowland, JL, Keles, S and Landick, R''' (2009) Rho directs widespread termination of intragenic and stable RNA transcription.''Proc. Natl. Acad. Sci. U.S.A.'' '''106''':15406-11
|-
!align=left |Abstract
||
The transcription termination factor Rho is a global regulator of RNA polymerase (RNAP). Although individual Rho-dependent terminators have been studied extensively, less is known about the sites of RNAP regulation by Rho on a genome-wide scale. Using chromatin immunoprecipitation and microarrays (ChIP-chip), we examined changes in the distribution of Escherichia coli RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM). We found approximately 200 Rho-terminated loci that were divided evenly into 2 classes: intergenic (at the ends of genes) and intragenic (within genes). The intergenic class contained noncoding RNAs such as small RNAs (sRNAs) and transfer RNAs (tRNAs), establishing a previously unappreciated role of Rho in termination of stable RNA synthesis. The intragenic class of terminators included a previously uncharacterized set of short antisense transcripts, as judged by a shift in the distribution of RNAP in BCM-treated cells that was opposite to the direction of the corresponding gene. These Rho-terminated antisense transcripts point to a role of noncoding transcription in E. coli gene regulation that may resemble the ubiquitous noncoding transcription recently found to play myriad roles in eukaryotic gene regulation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19706412 PubMed]
Online version:[http://dx.doi.org/10.1073/pnas.0903846106 10.1073/pnas.0903846106]
|-
!align=left |Keywords
||
Bicyclo Compounds, Heterocyclic; Chromatin Immunoprecipitation; DNA-Directed RNA Polymerases; Escherichia coli; Genes, Bacterial; Microarray Analysis; RNA; Transcription, Genetic; rho GTP-Binding Proteins

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.M50ad199107b8a&page=182751&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="O50ad19913835a" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.O50ad19913835a&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z519f8d526b29b" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
RpoC
RNAP beta prime

|
RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=94828 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.3.gff +BCM (19M gff)]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.4.gff untreated (19M gff)]
|-
|
MG1655
|
ChIP-chip
|
RpoB RNAP beta

|
RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=3428302 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.1.gff +BCM, (20M gff)]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.2.gff untreated (20M gff)]
|-
|
MG1655
|
ChIP-chip
|
RpoB RNAP beta
|
Untreated
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=3427302 Gbrowse]
|-
|
MG1655
|
ChIP-chip
|
RpoC RNAP beta prime
|
Untreated
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=100040 Gbrowse]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.Z519f8d526b29b&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]
[[Category:RNA_polymerase_tracks]]

PMID:19706412

2013-07-05T20:58:15Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="M50ad199107b8a" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Peters, JM, Mooney, RA, Kuan, PF, Rowland, JL, Keles, S and Landick, R''' (2009) Rho directs widespread termination of intragenic and stable RNA transcription.''Proc. Natl. Acad. Sci. U.S.A.'' '''106''':15406-11
|-
!align=left |Abstract
||
The transcription termination factor Rho is a global regulator of RNA polymerase (RNAP). Although individual Rho-dependent terminators have been studied extensively, less is known about the sites of RNAP regulation by Rho on a genome-wide scale. Using chromatin immunoprecipitation and microarrays (ChIP-chip), we examined changes in the distribution of Escherichia coli RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM). We found approximately 200 Rho-terminated loci that were divided evenly into 2 classes: intergenic (at the ends of genes) and intragenic (within genes). The intergenic class contained noncoding RNAs such as small RNAs (sRNAs) and transfer RNAs (tRNAs), establishing a previously unappreciated role of Rho in termination of stable RNA synthesis. The intragenic class of terminators included a previously uncharacterized set of short antisense transcripts, as judged by a shift in the distribution of RNAP in BCM-treated cells that was opposite to the direction of the corresponding gene. These Rho-terminated antisense transcripts point to a role of noncoding transcription in E. coli gene regulation that may resemble the ubiquitous noncoding transcription recently found to play myriad roles in eukaryotic gene regulation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19706412 PubMed]
Online version:[http://dx.doi.org/10.1073/pnas.0903846106 10.1073/pnas.0903846106]
|-
!align=left |Keywords
||
Bicyclo Compounds, Heterocyclic; Chromatin Immunoprecipitation; DNA-Directed RNA Polymerases; Escherichia coli; Genes, Bacterial; Microarray Analysis; RNA; Transcription, Genetic; rho GTP-Binding Proteins

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.M50ad199107b8a&page=182751&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="O50ad19913835a" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.O50ad19913835a&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z519f8d526b29b" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
RpoC
RNAP beta prime

|
RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=94828 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.3.gff +BCM (19M gff)]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.4.gff untreated (19M gff)]
|-
|
MG1655
|
ChIP-chip
|
RpoB RNAP beta

|
RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=3428302 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.1.gff +BCM, (20M gff)]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.2.gff untreated (20M gff)]
|-
|
MG1655
|
ChIP-chip
|
RpoB RNAP beta
|
Untreated
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=3427302 Gbrowse]
|-
|
MG1655
|
ChIP-chip
|
RpoC RNAP beta prime
|
Untreated
|

|

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.Z519f8d526b29b&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]
[[Category:RNA_polymerase_tracks]]

PMID:19706412

2013-07-05T20:45:25Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="M50ad199107b8a" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Peters, JM, Mooney, RA, Kuan, PF, Rowland, JL, Keles, S and Landick, R''' (2009) Rho directs widespread termination of intragenic and stable RNA transcription.''Proc. Natl. Acad. Sci. U.S.A.'' '''106''':15406-11
|-
!align=left |Abstract
||
The transcription termination factor Rho is a global regulator of RNA polymerase (RNAP). Although individual Rho-dependent terminators have been studied extensively, less is known about the sites of RNAP regulation by Rho on a genome-wide scale. Using chromatin immunoprecipitation and microarrays (ChIP-chip), we examined changes in the distribution of Escherichia coli RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM). We found approximately 200 Rho-terminated loci that were divided evenly into 2 classes: intergenic (at the ends of genes) and intragenic (within genes). The intergenic class contained noncoding RNAs such as small RNAs (sRNAs) and transfer RNAs (tRNAs), establishing a previously unappreciated role of Rho in termination of stable RNA synthesis. The intragenic class of terminators included a previously uncharacterized set of short antisense transcripts, as judged by a shift in the distribution of RNAP in BCM-treated cells that was opposite to the direction of the corresponding gene. These Rho-terminated antisense transcripts point to a role of noncoding transcription in E. coli gene regulation that may resemble the ubiquitous noncoding transcription recently found to play myriad roles in eukaryotic gene regulation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19706412 PubMed]
Online version:[http://dx.doi.org/10.1073/pnas.0903846106 10.1073/pnas.0903846106]
|-
!align=left |Keywords
||
Bicyclo Compounds, Heterocyclic; Chromatin Immunoprecipitation; DNA-Directed RNA Polymerases; Escherichia coli; Genes, Bacterial; Microarray Analysis; RNA; Transcription, Genetic; rho GTP-Binding Proteins

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.M50ad199107b8a&page=182751&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="O50ad19913835a" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.O50ad19913835a&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z519f8d526b29b" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
RpoC
RNAP beta prime

|
RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=94828 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.3.gff +BCM (19M gff)]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.4.gff untreated (19M gff)]
|-
|
MG1655
|
ChIP-chip
|
RpoB RNAP beta

|
RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=3428302 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.1.gff +BCM, (20M gff)]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.2.gff untreated (20M gff)]
|-
|
MG1655
|
ChIP-chip
|
RpoB RNAP beta
|
Untreated
|

|

|-
|
MG1655
|
ChIP-chip
|
RpoC RNAP beta prime
|
Untreated
|

|

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.Z519f8d526b29b&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]
[[Category:RNA_polymerase_tracks]]

PMID:19706412

2013-07-05T20:36:46Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="M50ad199107b8a" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Peters, JM, Mooney, RA, Kuan, PF, Rowland, JL, Keles, S and Landick, R''' (2009) Rho directs widespread termination of intragenic and stable RNA transcription.''Proc. Natl. Acad. Sci. U.S.A.'' '''106''':15406-11
|-
!align=left |Abstract
||
The transcription termination factor Rho is a global regulator of RNA polymerase (RNAP). Although individual Rho-dependent terminators have been studied extensively, less is known about the sites of RNAP regulation by Rho on a genome-wide scale. Using chromatin immunoprecipitation and microarrays (ChIP-chip), we examined changes in the distribution of Escherichia coli RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM). We found approximately 200 Rho-terminated loci that were divided evenly into 2 classes: intergenic (at the ends of genes) and intragenic (within genes). The intergenic class contained noncoding RNAs such as small RNAs (sRNAs) and transfer RNAs (tRNAs), establishing a previously unappreciated role of Rho in termination of stable RNA synthesis. The intragenic class of terminators included a previously uncharacterized set of short antisense transcripts, as judged by a shift in the distribution of RNAP in BCM-treated cells that was opposite to the direction of the corresponding gene. These Rho-terminated antisense transcripts point to a role of noncoding transcription in E. coli gene regulation that may resemble the ubiquitous noncoding transcription recently found to play myriad roles in eukaryotic gene regulation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19706412 PubMed]
Online version:[http://dx.doi.org/10.1073/pnas.0903846106 10.1073/pnas.0903846106]
|-
!align=left |Keywords
||
Bicyclo Compounds, Heterocyclic; Chromatin Immunoprecipitation; DNA-Directed RNA Polymerases; Escherichia coli; Genes, Bacterial; Microarray Analysis; RNA; Transcription, Genetic; rho GTP-Binding Proteins

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.M50ad199107b8a&page=182751&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="O50ad19913835a" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.O50ad19913835a&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z519f8d526b29b" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
RpoC
RNAP beta prime

|
RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=3428302 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.3.gff +BCM (19M gff)]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.4.gff untreated (19M gff)]
|-
|
MG1655
|
ChIP-chip
|
RpoB RNAP beta

|
RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=3428302&t=3427302 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.1.gff +BCM, (20M gff)]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/19706412.2.gff untreated (20M gff)]
|-
|
MG1655
|
ChIP-chip
|
RpoB RNAP beta
|
Untreated
|

|

|-
|
MG1655
|
ChIP-chip
|
RpoC RNAP beta prime
|
Untreated
|

|

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.Z519f8d526b29b&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]
[[Category:RNA_polymerase_tracks]]

PMID:21239586

2013-06-18T19:26:48Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="U514a0fc63f622" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Yamamoto, K , Ishihama, A , Busby, SJ and Grainger, DC ''' (2011) The Escherichia coli K-12 MntR miniregulon includes dps, which encodes the major stationary-phase DNA-binding protein. ''J. Bacteriol.'' '''193''':1477-80
|-
!align=left |Abstract
||
Escherichia coli MntR protein is the Mn(2+)-responsive transcriptional repressor of the MntH manganese transporter. We have used chromatin immunoprecipitation to determine the distribution of Mn(2+)-MntR across the entire E. coli chromosome in vivo, and we report that MntR binds to only four targets, adjacent to the mntH, mntR, yebN, and dps genes. Unexpectedly, we found that dps expression is directly repressed by Mn(2+)-MntR.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21239586 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3067631 PMC3067631]
Online version:[http://dx.doi.org/10.1128/JB.01230-10 10.1128/JB.01230-10]
|-
!align=left |Keywords
||
Bacterial Outer Membrane Proteins/biosynthesis; Chromatin Immunoprecipitation; Chromosomes, Bacterial; DNA, Bacterial/metabolism; Escherichia coli K12/genetics; Escherichia coli K12/physiology; Escherichia coli Proteins/biosynthesis; Escherichia coli Proteins/metabolism; Gene Expression Regulation, Bacterial; Protein Binding; Regulon; Repressor Proteins/metabolism

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182959.U514a0fc63f622&page=182959&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}
IMPORTANT!: This track is for E. coli strain BW25113 but is found under MG1655 since the array used was intended for MG1655!

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="S514a0fc652d61" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182959.S514a0fc652d61&page=182959&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

== Data ==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="F51a449b0a54fd" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
BW25113
|
ChIP-chip
|
MntR
|

|
This track is for E. coli strain BW25113 but is found under MG1655 since the array used was intended for MG1655.
|
* [http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=MntR Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/21239586/21239586.Supplementary_Table_1_16_12_2010.bw BigWig]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182959.F51a449b0a54fd&page=182959&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]

PMID:21239586

2013-06-18T19:26:05Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="U514a0fc63f622" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Yamamoto, K , Ishihama, A , Busby, SJ and Grainger, DC ''' (2011) The Escherichia coli K-12 MntR miniregulon includes dps, which encodes the major stationary-phase DNA-binding protein. ''J. Bacteriol.'' '''193''':1477-80
|-
!align=left |Abstract
||
Escherichia coli MntR protein is the Mn(2+)-responsive transcriptional repressor of the MntH manganese transporter. We have used chromatin immunoprecipitation to determine the distribution of Mn(2+)-MntR across the entire E. coli chromosome in vivo, and we report that MntR binds to only four targets, adjacent to the mntH, mntR, yebN, and dps genes. Unexpectedly, we found that dps expression is directly repressed by Mn(2+)-MntR.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21239586 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3067631 PMC3067631]
Online version:[http://dx.doi.org/10.1128/JB.01230-10 10.1128/JB.01230-10]
|-
!align=left |Keywords
||
Bacterial Outer Membrane Proteins/biosynthesis; Chromatin Immunoprecipitation; Chromosomes, Bacterial; DNA, Bacterial/metabolism; Escherichia coli K12/genetics; Escherichia coli K12/physiology; Escherichia coli Proteins/biosynthesis; Escherichia coli Proteins/metabolism; Gene Expression Regulation, Bacterial; Protein Binding; Regulon; Repressor Proteins/metabolism

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182959.U514a0fc63f622&page=182959&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}
IMPORTANT!: This track is for E. coli strain BW25113 but is found under MG1655 since the array used was intended for MG1655!

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="S514a0fc652d61" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182959.S514a0fc652d61&page=182959&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

== Data ==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="F51a449b0a54fd" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
BW25113
|
ChIP-chip
|
MntR
|

|
This track is for E. coli strain BW25113 but is found under MG1655 since the array used was intended for MG1655.
|
* [http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=MntR Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/1/21239586/21239586.Supplementary_Table_1_16_12_2010.bw BigWig]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182959.F51a449b0a54fd&page=182959&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]

PMID:21321206

2013-06-18T18:59:49Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="U51a4ec9fc71f9" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Cho, H, McManus, HR, Dove, SL and Bernhardt, TG''' (2011) Nucleoid occlusion factor SlmA is a DNA-activated FtsZ polymerization antagonist. ''Proc. Natl. Acad. Sci. U.S.A.'' '''108''':3773-8
|-
!align=left |Abstract
||
The tubulin-like FtsZ protein initiates assembly of the bacterial cytokinetic machinery by polymerizing into a ring structure, the Z ring, at the prospective site of division. To block Z-ring formation over the nucleoid and help coordinate cell division with chromosome segregation, Escherichia coli employs the nucleoid-associated division inhibitor, SlmA. Here, we investigate the mechanism by which SlmA regulates FtsZ assembly. We show that SlmA disassembles FtsZ polymers in vitro. In addition, using chromatin immunoprecipitation (ChIP), we identified 24 SlmA-binding sequences (SBSs) on the chromosome. Remarkably, SlmA binding to SBSs dramatically enhanced its ability to interfere with FtsZ polymerization, and ChIP studies indicate that SlmA regulates FtsZ assembly at these sites in vivo. Because of the dynamic and highly organized nature of the chromosome, coupling SlmA activation to specific DNA binding provides a mechanism for the precise spatiotemporal control of its anti-FtsZ activity within the cell.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21321206 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048121 PMC3048121]
Online version:[http://dx.doi.org/10.1073/pnas.1018674108 10.1073/pnas.1018674108]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183199.U51a4ec9fc71f9&page=183199&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="B51a4eca008efb" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183199.B51a4eca008efb&page=183199&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="X51a4edafde310" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
SlmA
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SlmA&t=SlmA_density Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/21321206/SlmA/21321206.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/21321206/SlmA/21321206.SlmA.bw BigWig]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183199.X51a4edafde310&page=183199&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[Category:Papers_with_tracks_in_Gbrowse]]

PMID:20689753

2013-06-18T17:11:29Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="O5110505532e46" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Sánchez-Romero, MA , Busby, SJ , Dyer, NP , Ott, S , Millard, AD and Grainger, DC ''' (2010) Dynamic distribution of seqa protein across the chromosome of escherichia coli K-12. ''MBio'' '''1'''
|-
!align=left |Abstract
||
The bacterial SeqA protein binds to hemi-methylated GATC sequences that arise in newly synthesized DNA upon passage of the replication machinery. In Escherichia coli K-12, the single replication origin oriC is a well-characterized target for SeqA, which binds to multiple hemi-methylated GATC sequences immediately after replication has initiated. This sequesters oriC, thereby preventing reinitiation of replication. However, the genome-wide DNA binding properties of SeqA are unknown, and hence, here, we describe a study of the binding of SeqA across the entire Escherichia coli K-12 chromosome, using chromatin immunoprecipitation in combination with DNA microarrays. Our data show that SeqA binding correlates with the frequency and spacing of GATC sequences across the entire genome. Less SeqA is found in highly transcribed regions, as well as in the ter macrodomain. Using synchronized cultures, we show that SeqA distribution differs with the cell cycle. SeqA remains bound to some targets after replication has ceased, and these targets locate to genes encoding factors involved in nucleotide metabolism, chromosome replication, and methyl transfer.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20689753 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912659 PMC2912659]
Online version:[http://dx.doi.org/10.1128/mBio.00012-10 10.1128/mBio.00012-10]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.O5110505532e46&page=182904&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="O5110505579ecb" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.O5110505579ecb&page=182904&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="N519f9885e1384" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
SeqA
|
dnaC(ts) at 30°ree;C
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SeqA_Bigwig_density&t=SeqA_Bigwig Gbrowse time?]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/SeqA/20689753.seqA.tA.gff timeA gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/SeqA/20689753.SeqAtimeA.bw timeA BigWig]
|-
|
MG1655
|
ChIP-chip
|
SeqA
|
dnaC(ts) at 42°ree;C for 1 hour; replication ceased
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SeqA_Bigwig_density&t=SeqA_Bigwig Gbrowse time?]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/SeqA/20689753.seqA.tB.gff timeB gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/SeqA/20689753.SeqAtimeB.bw timeB BigWig]
|-
|
MG1655
|
ChIP-chip
|
SeqA
|
dnaC(ts) at 42°ree;C for 1 hour; shifted back to 30°ree;C for 6 min; synchronized initiation of replication
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SeqA_Bigwig_density&t=SeqA_Bigwig Gbrowse time?]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/SeqA/20689753.seqA.tC.gff timeC gff]
|-
|
MG1655
|
ChIP-chip
|
RNAP
|
dnaC(ts) at 30°C for 1 hour; shifted back to 30°C for 6 min; synchronized initiation of replication
|

|

*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/RNAp/20689753.rnap.tC.gff timeC gff]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.N519f9885e1384&page=182904&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[Category:Papers with tracks in Gbrowse]]
[[Category:High-Throughput Papers]]
[[Category:RNA_polymerase_tracks]]

PMID:20689753

2013-06-18T16:55:41Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="O5110505532e46" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Sánchez-Romero, MA , Busby, SJ , Dyer, NP , Ott, S , Millard, AD and Grainger, DC ''' (2010) Dynamic distribution of seqa protein across the chromosome of escherichia coli K-12. ''MBio'' '''1'''
|-
!align=left |Abstract
||
The bacterial SeqA protein binds to hemi-methylated GATC sequences that arise in newly synthesized DNA upon passage of the replication machinery. In Escherichia coli K-12, the single replication origin oriC is a well-characterized target for SeqA, which binds to multiple hemi-methylated GATC sequences immediately after replication has initiated. This sequesters oriC, thereby preventing reinitiation of replication. However, the genome-wide DNA binding properties of SeqA are unknown, and hence, here, we describe a study of the binding of SeqA across the entire Escherichia coli K-12 chromosome, using chromatin immunoprecipitation in combination with DNA microarrays. Our data show that SeqA binding correlates with the frequency and spacing of GATC sequences across the entire genome. Less SeqA is found in highly transcribed regions, as well as in the ter macrodomain. Using synchronized cultures, we show that SeqA distribution differs with the cell cycle. SeqA remains bound to some targets after replication has ceased, and these targets locate to genes encoding factors involved in nucleotide metabolism, chromosome replication, and methyl transfer.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20689753 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912659 PMC2912659]
Online version:[http://dx.doi.org/10.1128/mBio.00012-10 10.1128/mBio.00012-10]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.O5110505532e46&page=182904&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="O5110505579ecb" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.O5110505579ecb&page=182904&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="N519f9885e1384" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
SeqA
|
dnaC(ts) at 30°ree;C
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SeqA_Bigwig_density&t=SeqA_Bigwig Gbrowse time?]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/SeqA/20689753.seqA.tA.gff timeA gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/SeqA/20689753.SeqAtimeA.bw timeA BigWig]
|-
|
MG1655
|
ChIP-chip
|
SeqA
|
dnaC(ts) at 42&degree;C for 1 hour; replication ceased
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SeqA_Bigwig_density&t=SeqA_Bigwig Gbrowse time?]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/SeqA/20689753.seqA.tB.gff timeB gff]

|-
|
MG1655
|
ChIP-chip
|
SeqA
|
dnaC(ts) at 42°ree;C for 1 hour; shifted back to 30°ree;C for 6 min; synchronized initiation of replication
|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SeqA_Bigwig_density&t=SeqA_Bigwig Gbrowse time?]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/SeqA/20689753.seqA.tC.gff timeC gff]
|-
|
MG1655
|
ChIP-chip
|
RNAP
|
dnaC(ts) at 30°C for 1 hour; shifted back to 30°C for 6 min; synchronized initiation of replication
|

|

*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/RNAp/20689753.rnap.tC.gff timeC gff]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.N519f9885e1384&page=182904&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[Category:Papers with tracks in Gbrowse]]
[[Category:High-Throughput Papers]]
[[Category:RNA_polymerase_tracks]]

PMID:19150431

2013-06-12T18:01:00Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="R51a429996fc2e" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Mooney, RA, Davis, SE, Peters, JM, Rowland, JL, Ansari, AZ and Landick, R''' (2009) Regulator trafficking on bacterial transcription units in vivo. ''Mol. Cell'' '''33''':97-108
|-
!align=left |Abstract
||
The trafficking patterns of the bacterial regulators of transcript elongation sigma(70), rho, NusA, and NusG on genes in vivo and the explanation for promoter-proximal peaks of RNA polymerase (RNAP) are unknown. Genome-wide, E. coli ChIP-chip revealed distinct association patterns of regulators as RNAP transcribes away from promoters (rho first, then NusA, then NusG). However, the interactions of elongating complexes with these regulators did not differ significantly among most transcription units. A modest variation of NusG signal among genes reflected increased NusG interaction as transcription progresses, rather than functional specialization of elongating complexes. Promoter-proximal RNAP peaks were offset from sigma(70) peaks in the direction of transcription and co-occurred with NusA and rho peaks, suggesting that the RNAP peaks reflected elongating, rather than initiating, complexes. However, inhibition of rho did not increase RNAP levels within genes downstream from the RNAP peaks, suggesting the peaks are caused by a mechanism other than rho-dependent attenuation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19150431 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747249 PMC2747249]
Online version:[http://dx.doi.org/10.1016/j.molcel.2008.12.021 10.1016/j.molcel.2008.12.021]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183193.R51a429996fc2e&page=183193&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Brief Description==
This paper uses ChIP-chip methods to investigate the occupancy of 5 proteins along the ''E. coli'' chromosome:
* the RNA Polymerase (RNAP)
* [[nusA|NusA]]
* [[nusG|NusG]]
* [[:Category:Complex:RNA_polymerase_sigma70|σ70]]
* [[rho|ρ]]

== Main Points ==
* There is not a one-to-one relationship between the (observed) occupancy of [[:Category:Complex:RNA_polymerase_sigma70|σ70]] and [[RNA Polymerase|RNAP]].
* Evidence sustaining the idea that [[nusA|NusA]] displaces σ70 during transcript elongation. (Previously reported in <ref name='PMID:6263495'/>)
* Elongating RNAPs do not exhibit transcription-unit specific variations in affinities for σ70, NusA, NusG or ρ. This suggests these proteins are ''general'' elongation regulators and not ''specific'' regulators (as in the case of [[rfaH]].)
* σ70 binds almost exclusively to the promoter regions.
* NusG is associated with elongation complexes more slowly than NusA (on most transcription units.)
* ρ binding is most evident between the σ70 and RNAP signals near the promoter. This suggests ρ may associate with the nascent transcripts soon after transcription initiation.

==Methods and Calculations==

; High Quality TUs
: 109 "high-quality" transciption units were identified in which overlap from adjacent transcription units did not obscure the patterns. (Fig 1D & Table S1)

; RNA Polymerase Control
: 170 regions of the genome (greater than 1kb in length) were identified as similar in transcript level to the cryptic gene ''[[bglB]]''. This gave a non-specific background - see Fig 1B & 1C.

; Apparent Occupancy
: The Occapp was defined by linearly scaling the signals for each protein between 0 (basal level of RNAP) and 1 (the average of the 10 3-probe clusters with highest average value).

* IP samples were compared to control samples of input DNA (recovered from cell extract immediately prior to IP.)
* The microarray contains two copies of 187,204 Tm-matched ≥45bp oligos.
** This tiled the chromosome with an average of 24.5bp separation.

===EcoliWiki data manipulation===
In order to show the results of this paper across the entire genome, we first downloaded the data-sets ([http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13938 GSE13938]) from the [[Gene Expression Omnibus (GEO)]].

Tracks for the PortEco GBrowse were added for
*
*
*
*
[Category:GBrowse]

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="Y4b8d6b9bd9a1a" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.171538.Y4b8d6b9bd9a1a&page=171538&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z51a42a9f1c63c" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
NusA
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=NusA Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusA/19150431.nusA.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusA/19150431.NusA.bw BigWig]
|-
|
MG1655
|
ChIP-chip
|
NusG
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=NusG Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusG/19150431.nusG.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusG/19150431.NusG.bw BigWig]
|-
|
MG1655
|
ChIP-chip
|
Rho
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Rho Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/Rho/19150431.rho.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/Rho/19150431.Rho.bw BigWig]
|-
|
MG1655
|
ChIP-chip
|
RNAP
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=RNAp Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/RNAP/19150431.RNAp.bw BigWig]
|-
|
MG1655
|
ChIP-chip
|
RpoD (Sigma70)
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Sigma70 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/Sigma70/19150431.rpoD.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/Sigma70/19150431.Sigma70.bw BigWig]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183193.Z51a42a9f1c63c&page=183193&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==
* Information about [http://openwetware.org/wiki/ChIP-Chip_E._coli ChIP-chip for E. coli] at OpenWetWare
* Wikipedia article about [http://en.wikipedia.org/wiki/ChIP-on-chip ChIP-chip]

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]
[[Category:High-Throughput Papers]]
[[Category:RNA_polymerase_tracks]]

PMID:19150431

2013-06-12T17:59:13Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="R51a429996fc2e" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Mooney, RA, Davis, SE, Peters, JM, Rowland, JL, Ansari, AZ and Landick, R''' (2009) Regulator trafficking on bacterial transcription units in vivo. ''Mol. Cell'' '''33''':97-108
|-
!align=left |Abstract
||
The trafficking patterns of the bacterial regulators of transcript elongation sigma(70), rho, NusA, and NusG on genes in vivo and the explanation for promoter-proximal peaks of RNA polymerase (RNAP) are unknown. Genome-wide, E. coli ChIP-chip revealed distinct association patterns of regulators as RNAP transcribes away from promoters (rho first, then NusA, then NusG). However, the interactions of elongating complexes with these regulators did not differ significantly among most transcription units. A modest variation of NusG signal among genes reflected increased NusG interaction as transcription progresses, rather than functional specialization of elongating complexes. Promoter-proximal RNAP peaks were offset from sigma(70) peaks in the direction of transcription and co-occurred with NusA and rho peaks, suggesting that the RNAP peaks reflected elongating, rather than initiating, complexes. However, inhibition of rho did not increase RNAP levels within genes downstream from the RNAP peaks, suggesting the peaks are caused by a mechanism other than rho-dependent attenuation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19150431 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747249 PMC2747249]
Online version:[http://dx.doi.org/10.1016/j.molcel.2008.12.021 10.1016/j.molcel.2008.12.021]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183193.R51a429996fc2e&page=183193&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Brief Description==
This paper uses ChIP-chip methods to investigate the occupancy of 5 proteins along the ''E. coli'' chromosome:
* the RNA Polymerase (RNAP)
* [[nusA|NusA]]
* [[nusG|NusG]]
* [[:Category:Complex:RNA_polymerase_sigma70|σ70]]
* [[rho|ρ]]

== Main Points ==
* There is not a one-to-one relationship between the (observed) occupancy of [[:Category:Complex:RNA_polymerase_sigma70|σ70]] and [[RNA Polymerase|RNAP]].
* Evidence sustaining the idea that [[nusA|NusA]] displaces σ70 during transcript elongation. (Previously reported in <ref name='PMID:6263495'/>)
* Elongating RNAPs do not exhibit transcription-unit specific variations in affinities for σ70, NusA, NusG or ρ. This suggests these proteins are ''general'' elongation regulators and not ''specific'' regulators (as in the case of [[rfaH]].)
* σ70 binds almost exclusively to the promoter regions.
* NusG is associated with elongation complexes more slowly than NusA (on most transcription units.)
* ρ binding is most evident between the σ70 and RNAP signals near the promoter. This suggests ρ may associate with the nascent transcripts soon after transcription initiation.

==Methods and Calculations==

; High Quality TUs
: 109 "high-quality" transciption units were identified in which overlap from adjacent transcription units did not obscure the patterns. (Fig 1D & Table S1)

; RNA Polymerase Control
: 170 regions of the genome (greater than 1kb in length) were identified as similar in transcript level to the cryptic gene ''[[bglB]]''. This gave a non-specific background - see Fig 1B & 1C.

; Apparent Occupancy
: The Occapp was defined by linearly scaling the signals for each protein between 0 (basal level of RNAP) and 1 (the average of the 10 3-probe clusters with highest average value).

* IP samples were compared to control samples of input DNA (recovered from cell extract immediately prior to IP.)
* The microarray contains two copies of 187,204 Tm-matched ≥45bp oligos.
** This tiled the chromosome with an average of 24.5bp separation.

===EcoliWiki data manipulation===
In order to show the results of this paper across the entire genome, we first downloaded the data-sets ([http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13938 GSE13938]) from the [[Gene Expression Omnibus (GEO)]].

Tracks for the PortEco GBrowse were added for
*
*
*
*
[Category:GBrowse]

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="Y4b8d6b9bd9a1a" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.171538.Y4b8d6b9bd9a1a&page=171538&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z51a42a9f1c63c" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
NusA
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=NusA Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusA/19150431.nusA.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusA/19150431.NusA.bw BigWig]
|-
|
MG1655
|
ChIP-chip
|
NusG
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=NusG Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusG/19150431.nusG.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusG/19150431.NusG.bw BigWig]
|-
|
MG1655
|
ChIP-chip
|
Rho
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Rho Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/Rho/19150431.rho.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/Rho/19150431.Rho.bw BigWig]
|-
|
MG1655
|
ChIP-chip
|
RNAP
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=RNAp Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/RNAP/19150431.RNAp.bw BigWig]
|-
|
MG1655
|
ChIP-chip
|
RpoD (Sigma70)
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Sigma70 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/Sigma70/19150431.rpoD.gff gff]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183193.Z51a42a9f1c63c&page=183193&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==
* Information about [http://openwetware.org/wiki/ChIP-Chip_E._coli ChIP-chip for E. coli] at OpenWetWare
* Wikipedia article about [http://en.wikipedia.org/wiki/ChIP-on-chip ChIP-chip]

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]
[[Category:High-Throughput Papers]]
[[Category:RNA_polymerase_tracks]]

PMID:19150431

2013-06-12T17:47:51Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="R51a429996fc2e" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Mooney, RA, Davis, SE, Peters, JM, Rowland, JL, Ansari, AZ and Landick, R''' (2009) Regulator trafficking on bacterial transcription units in vivo. ''Mol. Cell'' '''33''':97-108
|-
!align=left |Abstract
||
The trafficking patterns of the bacterial regulators of transcript elongation sigma(70), rho, NusA, and NusG on genes in vivo and the explanation for promoter-proximal peaks of RNA polymerase (RNAP) are unknown. Genome-wide, E. coli ChIP-chip revealed distinct association patterns of regulators as RNAP transcribes away from promoters (rho first, then NusA, then NusG). However, the interactions of elongating complexes with these regulators did not differ significantly among most transcription units. A modest variation of NusG signal among genes reflected increased NusG interaction as transcription progresses, rather than functional specialization of elongating complexes. Promoter-proximal RNAP peaks were offset from sigma(70) peaks in the direction of transcription and co-occurred with NusA and rho peaks, suggesting that the RNAP peaks reflected elongating, rather than initiating, complexes. However, inhibition of rho did not increase RNAP levels within genes downstream from the RNAP peaks, suggesting the peaks are caused by a mechanism other than rho-dependent attenuation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19150431 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747249 PMC2747249]
Online version:[http://dx.doi.org/10.1016/j.molcel.2008.12.021 10.1016/j.molcel.2008.12.021]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183193.R51a429996fc2e&page=183193&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Brief Description==
This paper uses ChIP-chip methods to investigate the occupancy of 5 proteins along the ''E. coli'' chromosome:
* the RNA Polymerase (RNAP)
* [[nusA|NusA]]
* [[nusG|NusG]]
* [[:Category:Complex:RNA_polymerase_sigma70|σ70]]
* [[rho|ρ]]

== Main Points ==
* There is not a one-to-one relationship between the (observed) occupancy of [[:Category:Complex:RNA_polymerase_sigma70|σ70]] and [[RNA Polymerase|RNAP]].
* Evidence sustaining the idea that [[nusA|NusA]] displaces σ70 during transcript elongation. (Previously reported in <ref name='PMID:6263495'/>)
* Elongating RNAPs do not exhibit transcription-unit specific variations in affinities for σ70, NusA, NusG or ρ. This suggests these proteins are ''general'' elongation regulators and not ''specific'' regulators (as in the case of [[rfaH]].)
* σ70 binds almost exclusively to the promoter regions.
* NusG is associated with elongation complexes more slowly than NusA (on most transcription units.)
* ρ binding is most evident between the σ70 and RNAP signals near the promoter. This suggests ρ may associate with the nascent transcripts soon after transcription initiation.

==Methods and Calculations==

; High Quality TUs
: 109 "high-quality" transciption units were identified in which overlap from adjacent transcription units did not obscure the patterns. (Fig 1D & Table S1)

; RNA Polymerase Control
: 170 regions of the genome (greater than 1kb in length) were identified as similar in transcript level to the cryptic gene ''[[bglB]]''. This gave a non-specific background - see Fig 1B & 1C.

; Apparent Occupancy
: The Occapp was defined by linearly scaling the signals for each protein between 0 (basal level of RNAP) and 1 (the average of the 10 3-probe clusters with highest average value).

* IP samples were compared to control samples of input DNA (recovered from cell extract immediately prior to IP.)
* The microarray contains two copies of 187,204 Tm-matched ≥45bp oligos.
** This tiled the chromosome with an average of 24.5bp separation.

===EcoliWiki data manipulation===
In order to show the results of this paper across the entire genome, we first downloaded the data-sets ([http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13938 GSE13938]) from the [[Gene Expression Omnibus (GEO)]].

Tracks for the PortEco GBrowse were added for
*
*
*
*
[Category:GBrowse]

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="Y4b8d6b9bd9a1a" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.171538.Y4b8d6b9bd9a1a&page=171538&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z51a42a9f1c63c" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
NusA
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=NusA Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusA/19150431.nusA.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusA/19150431.NusA.bw BigWig]
|-
|
MG1655
|
ChIP-chip
|
NusG
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=NusG Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusG/19150431.nusG.gff gff]
|-
|
MG1655
|
ChIP-chip
|
Rho
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Rho Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/Rho/19150431.rho.gff gff]
|-
|
MG1655
|
ChIP-chip
|
RNAP
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=RNAp Gbrowse]
|-
|
MG1655
|
ChIP-chip
|
RpoD (Sigma70)
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Sigma70 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/Sigma70/19150431.rpoD.gff gff]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183193.Z51a42a9f1c63c&page=183193&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==
* Information about [http://openwetware.org/wiki/ChIP-Chip_E._coli ChIP-chip for E. coli] at OpenWetWare
* Wikipedia article about [http://en.wikipedia.org/wiki/ChIP-on-chip ChIP-chip]

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]
[[Category:High-Throughput Papers]]
[[Category:RNA_polymerase_tracks]]

PMID:19150431

2013-06-12T17:44:54Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="R51a429996fc2e" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Mooney, RA, Davis, SE, Peters, JM, Rowland, JL, Ansari, AZ and Landick, R''' (2009) Regulator trafficking on bacterial transcription units in vivo. ''Mol. Cell'' '''33''':97-108
|-
!align=left |Abstract
||
The trafficking patterns of the bacterial regulators of transcript elongation sigma(70), rho, NusA, and NusG on genes in vivo and the explanation for promoter-proximal peaks of RNA polymerase (RNAP) are unknown. Genome-wide, E. coli ChIP-chip revealed distinct association patterns of regulators as RNAP transcribes away from promoters (rho first, then NusA, then NusG). However, the interactions of elongating complexes with these regulators did not differ significantly among most transcription units. A modest variation of NusG signal among genes reflected increased NusG interaction as transcription progresses, rather than functional specialization of elongating complexes. Promoter-proximal RNAP peaks were offset from sigma(70) peaks in the direction of transcription and co-occurred with NusA and rho peaks, suggesting that the RNAP peaks reflected elongating, rather than initiating, complexes. However, inhibition of rho did not increase RNAP levels within genes downstream from the RNAP peaks, suggesting the peaks are caused by a mechanism other than rho-dependent attenuation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19150431 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747249 PMC2747249]
Online version:[http://dx.doi.org/10.1016/j.molcel.2008.12.021 10.1016/j.molcel.2008.12.021]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183193.R51a429996fc2e&page=183193&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Brief Description==
This paper uses ChIP-chip methods to investigate the occupancy of 5 proteins along the ''E. coli'' chromosome:
* the RNA Polymerase (RNAP)
* [[nusA|NusA]]
* [[nusG|NusG]]
* [[:Category:Complex:RNA_polymerase_sigma70|σ70]]
* [[rho|ρ]]

== Main Points ==
* There is not a one-to-one relationship between the (observed) occupancy of [[:Category:Complex:RNA_polymerase_sigma70|σ70]] and [[RNA Polymerase|RNAP]].
* Evidence sustaining the idea that [[nusA|NusA]] displaces σ70 during transcript elongation. (Previously reported in <ref name='PMID:6263495'/>)
* Elongating RNAPs do not exhibit transcription-unit specific variations in affinities for σ70, NusA, NusG or ρ. This suggests these proteins are ''general'' elongation regulators and not ''specific'' regulators (as in the case of [[rfaH]].)
* σ70 binds almost exclusively to the promoter regions.
* NusG is associated with elongation complexes more slowly than NusA (on most transcription units.)
* ρ binding is most evident between the σ70 and RNAP signals near the promoter. This suggests ρ may associate with the nascent transcripts soon after transcription initiation.

==Methods and Calculations==

; High Quality TUs
: 109 "high-quality" transciption units were identified in which overlap from adjacent transcription units did not obscure the patterns. (Fig 1D & Table S1)

; RNA Polymerase Control
: 170 regions of the genome (greater than 1kb in length) were identified as similar in transcript level to the cryptic gene ''[[bglB]]''. This gave a non-specific background - see Fig 1B & 1C.

; Apparent Occupancy
: The Occapp was defined by linearly scaling the signals for each protein between 0 (basal level of RNAP) and 1 (the average of the 10 3-probe clusters with highest average value).

* IP samples were compared to control samples of input DNA (recovered from cell extract immediately prior to IP.)
* The microarray contains two copies of 187,204 Tm-matched ≥45bp oligos.
** This tiled the chromosome with an average of 24.5bp separation.

===EcoliWiki data manipulation===
In order to show the results of this paper across the entire genome, we first downloaded the data-sets ([http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13938 GSE13938]) from the [[Gene Expression Omnibus (GEO)]].

Tracks for the PortEco GBrowse were added for
*
*
*
*
[Category:GBrowse]

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="Y4b8d6b9bd9a1a" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.171538.Y4b8d6b9bd9a1a&page=171538&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z51a42a9f1c63c" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
NusA
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=NusA Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusA/19150431.nusA.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusA/19150431.nusA.bw BigWig]
|-
|
MG1655
|
ChIP-chip
|
NusG
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=NusG Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusG/19150431.nusG.gff gff]
|-
|
MG1655
|
ChIP-chip
|
Rho
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Rho Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/Rho/19150431.rho.gff gff]
|-
|
MG1655
|
ChIP-chip
|
RNAP
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=RNAp Gbrowse]
|-
|
MG1655
|
ChIP-chip
|
RpoD (Sigma70)
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Sigma70 Gbrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/Sigma70/19150431.rpoD.gff gff]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183193.Z51a42a9f1c63c&page=183193&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==
* Information about [http://openwetware.org/wiki/ChIP-Chip_E._coli ChIP-chip for E. coli] at OpenWetWare
* Wikipedia article about [http://en.wikipedia.org/wiki/ChIP-on-chip ChIP-chip]

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]
[[Category:High-Throughput Papers]]
[[Category:RNA_polymerase_tracks]]

PMID:16963779

2013-06-12T16:44:46Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="B512d848714402" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Grainger, DC , Hurd, D , Goldberg, MD and Busby, SJ ''' (2006) Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. ''Nucleic Acids Res.'' '''34''':4642-52
|-
!align=left |Abstract
||
The Escherichia coli chromosome is condensed into an ill-defined structure known as the nucleoid. Nucleoid-associated DNA-binding proteins are involved in maintaining this structure and in mediating chromosome compaction. We have exploited chromatin immunoprecipitation and high-density microarrays to study the binding of three such proteins, FIS, H-NS and IHF, across the E.coli genome in vivo. Our results show that the distribution of these proteins is biased to intergenic parts of the genome, and that the binding profiles overlap. Hence some targets are associated with combinations of bound FIS, H-NS and IHF. In addition, many regions associated with FIS and H-NS are also associated with RNA polymerase.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16963779 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636352 PMC1636352]
Online version:[http://dx.doi.org/10.1093/nar/gkl542 10.1093/nar/gkl542]
;Data tracks
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/FIS.gff3 FIS.gff3 12K]
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/H-NS/HNS.gff3 H-NS.gff3 8K]
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/IHF/IHF.gff3 IHF.gff3 8K]
|-
!align=left |Keywords
||
Bacterial Proteins/metabolism; Binding Sites; Chromatin Immunoprecipitation; Chromosomes, Bacterial; DNA, Bacterial/metabolism; DNA, Intergenic/metabolism; DNA-Binding Proteins/isolation & purification; DNA-Binding Proteins/metabolism; DNA-Directed RNA Polymerases/metabolism; Escherichia coli/genetics; Escherichia coli Proteins/isolation & purification; Escherichia coli Proteins/metabolism; Factor For Inversion Stimulation Protein; Genome, Bacterial; Integration Host Factors/metabolism; Oligonucleotide Array Sequence Analysis; Transcription Factors/metabolism; Transcription, Genetic

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.B512d848714402&page=182924&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="J512d848771fec" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.J512d848771fec&page=182924&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect></protect>

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="T519d0fd60cf30" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
FIS
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_FIS_density&t=Nucleoid_Protein_FIS_xy GBrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/16963779.FIS.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/16963779.FIS.bw BigWig]

|-
|
MG1655
|
ChIP-chip
|
H-NS
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_HNS_density&t=Nucleoid_Protein_HNS_xy GBrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/H-NS/16963779.HNS.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/H-NS/16963779.HNS.bw BigWig]
|-
|
MG1655
|
ChIP-chip
|
IHF
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_IHF_density&t=Nucleoid_Protein_IHF_xy GBrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/IHF/16963779.IHF.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/IHF/16963779.IHF.bw BigWig]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.T519d0fd60cf30&page=182924&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[Category:Papers_with_tracks_in_Gbrowse]]

PMID:16963779

2013-06-12T16:31:49Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="B512d848714402" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Grainger, DC , Hurd, D , Goldberg, MD and Busby, SJ ''' (2006) Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. ''Nucleic Acids Res.'' '''34''':4642-52
|-
!align=left |Abstract
||
The Escherichia coli chromosome is condensed into an ill-defined structure known as the nucleoid. Nucleoid-associated DNA-binding proteins are involved in maintaining this structure and in mediating chromosome compaction. We have exploited chromatin immunoprecipitation and high-density microarrays to study the binding of three such proteins, FIS, H-NS and IHF, across the E.coli genome in vivo. Our results show that the distribution of these proteins is biased to intergenic parts of the genome, and that the binding profiles overlap. Hence some targets are associated with combinations of bound FIS, H-NS and IHF. In addition, many regions associated with FIS and H-NS are also associated with RNA polymerase.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16963779 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636352 PMC1636352]
Online version:[http://dx.doi.org/10.1093/nar/gkl542 10.1093/nar/gkl542]
;Data tracks
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/FIS.gff3 FIS.gff3 12K]
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/H-NS/HNS.gff3 H-NS.gff3 8K]
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/IHF/IHF.gff3 IHF.gff3 8K]
|-
!align=left |Keywords
||
Bacterial Proteins/metabolism; Binding Sites; Chromatin Immunoprecipitation; Chromosomes, Bacterial; DNA, Bacterial/metabolism; DNA, Intergenic/metabolism; DNA-Binding Proteins/isolation & purification; DNA-Binding Proteins/metabolism; DNA-Directed RNA Polymerases/metabolism; Escherichia coli/genetics; Escherichia coli Proteins/isolation & purification; Escherichia coli Proteins/metabolism; Factor For Inversion Stimulation Protein; Genome, Bacterial; Integration Host Factors/metabolism; Oligonucleotide Array Sequence Analysis; Transcription Factors/metabolism; Transcription, Genetic

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.B512d848714402&page=182924&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="J512d848771fec" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.J512d848771fec&page=182924&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect></protect>

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="T519d0fd60cf30" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
FIS
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_FIS_density&t=Nucleoid_Protein_FIS_xy GBrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/16963779.FIS.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/16963779.FIS.bw BigWig]

|-
|
MG1655
|
ChIP-chip
|
H-NS
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_HNS_density&t=Nucleoid_Protein_HNS_xy GBrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/H-NS/16963779.HNS.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/H-NS/16963779.HNS.bw BigWig]
|-
|
MG1655
|
ChIP-chip
|
IHF
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_IHF_density&t=Nucleoid_Protein_IHF_xy GBrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/IHF/16963779.IHF.gff gff]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.T519d0fd60cf30&page=182924&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[Category:Papers_with_tracks_in_Gbrowse]]

PMID:16963779

2013-06-12T16:28:33Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="B512d848714402" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Grainger, DC , Hurd, D , Goldberg, MD and Busby, SJ ''' (2006) Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. ''Nucleic Acids Res.'' '''34''':4642-52
|-
!align=left |Abstract
||
The Escherichia coli chromosome is condensed into an ill-defined structure known as the nucleoid. Nucleoid-associated DNA-binding proteins are involved in maintaining this structure and in mediating chromosome compaction. We have exploited chromatin immunoprecipitation and high-density microarrays to study the binding of three such proteins, FIS, H-NS and IHF, across the E.coli genome in vivo. Our results show that the distribution of these proteins is biased to intergenic parts of the genome, and that the binding profiles overlap. Hence some targets are associated with combinations of bound FIS, H-NS and IHF. In addition, many regions associated with FIS and H-NS are also associated with RNA polymerase.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16963779 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636352 PMC1636352]
Online version:[http://dx.doi.org/10.1093/nar/gkl542 10.1093/nar/gkl542]
;Data tracks
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/FIS.gff3 FIS.gff3 12K]
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/H-NS/HNS.gff3 H-NS.gff3 8K]
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/IHF/IHF.gff3 IHF.gff3 8K]
|-
!align=left |Keywords
||
Bacterial Proteins/metabolism; Binding Sites; Chromatin Immunoprecipitation; Chromosomes, Bacterial; DNA, Bacterial/metabolism; DNA, Intergenic/metabolism; DNA-Binding Proteins/isolation & purification; DNA-Binding Proteins/metabolism; DNA-Directed RNA Polymerases/metabolism; Escherichia coli/genetics; Escherichia coli Proteins/isolation & purification; Escherichia coli Proteins/metabolism; Factor For Inversion Stimulation Protein; Genome, Bacterial; Integration Host Factors/metabolism; Oligonucleotide Array Sequence Analysis; Transcription Factors/metabolism; Transcription, Genetic

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.B512d848714402&page=182924&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="J512d848771fec" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.J512d848771fec&page=182924&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect></protect>

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="T519d0fd60cf30" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
FIS
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_FIS_density&t=Nucleoid_Protein_FIS_xy GBrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/16963779.FIS.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/16963779.FIS.bw BigWig]

|-
|
MG1655
|
ChIP-chip
|
H-NS
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_HNS_density&t=Nucleoid_Protein_HNS_xy GBrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/HNS/16963779.HNS.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/HNS/16963779.HNS.bw BigWig]
|-
|
MG1655
|
ChIP-chip
|
IHF
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_IHF_density&t=Nucleoid_Protein_IHF_xy GBrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/IHF/16963779.IHF.gff gff]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.T519d0fd60cf30&page=182924&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[Category:Papers_with_tracks_in_Gbrowse]]

PMID:16963779

2013-06-12T16:23:13Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="B512d848714402" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Grainger, DC , Hurd, D , Goldberg, MD and Busby, SJ ''' (2006) Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. ''Nucleic Acids Res.'' '''34''':4642-52
|-
!align=left |Abstract
||
The Escherichia coli chromosome is condensed into an ill-defined structure known as the nucleoid. Nucleoid-associated DNA-binding proteins are involved in maintaining this structure and in mediating chromosome compaction. We have exploited chromatin immunoprecipitation and high-density microarrays to study the binding of three such proteins, FIS, H-NS and IHF, across the E.coli genome in vivo. Our results show that the distribution of these proteins is biased to intergenic parts of the genome, and that the binding profiles overlap. Hence some targets are associated with combinations of bound FIS, H-NS and IHF. In addition, many regions associated with FIS and H-NS are also associated with RNA polymerase.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16963779 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636352 PMC1636352]
Online version:[http://dx.doi.org/10.1093/nar/gkl542 10.1093/nar/gkl542]
;Data tracks
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/FIS.gff3 FIS.gff3 12K]
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/H-NS/HNS.gff3 H-NS.gff3 8K]
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/IHF/IHF.gff3 IHF.gff3 8K]
|-
!align=left |Keywords
||
Bacterial Proteins/metabolism; Binding Sites; Chromatin Immunoprecipitation; Chromosomes, Bacterial; DNA, Bacterial/metabolism; DNA, Intergenic/metabolism; DNA-Binding Proteins/isolation & purification; DNA-Binding Proteins/metabolism; DNA-Directed RNA Polymerases/metabolism; Escherichia coli/genetics; Escherichia coli Proteins/isolation & purification; Escherichia coli Proteins/metabolism; Factor For Inversion Stimulation Protein; Genome, Bacterial; Integration Host Factors/metabolism; Oligonucleotide Array Sequence Analysis; Transcription Factors/metabolism; Transcription, Genetic

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.B512d848714402&page=182924&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="J512d848771fec" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.J512d848771fec&page=182924&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect></protect>

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="T519d0fd60cf30" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
FIS
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_FIS_density&t=Nucleoid_Protein_FIS_xy GBrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/16963779.FIS.gff gff]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/16963779.FIS.bw BigWig]

|-
|
MG1655
|
ChIP-chip
|
H-NS
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_HNS_density&t=Nucleoid_Protein_HNS_xy GBrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/HNS/16963779.HNS.gff gff]
|-
|
MG1655
|
ChIP-chip
|
IHF
|

|

|
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_IHF_density&t=Nucleoid_Protein_IHF_xy GBrowse]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/IHF/16963779.IHF.gff gff]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.T519d0fd60cf30&page=182924&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[Category:Papers_with_tracks_in_Gbrowse]]

PMID:19706412

2013-05-30T21:34:24Z

Johnlew:

{{RightTOC}}


{| id="M50ad199107b8a" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Peters, JM, Mooney, RA, Kuan, PF, Rowland, JL, Keles, S and Landick, R''' (2009) Rho directs widespread termination of intragenic and stable RNA transcription.''Proc. Natl. Acad. Sci. U.S.A.'' '''106''':15406-11
|-
!align=left |Abstract
||
The transcription termination factor Rho is a global regulator of RNA polymerase (RNAP). Although individual Rho-dependent terminators have been studied extensively, less is known about the sites of RNAP regulation by Rho on a genome-wide scale. Using chromatin immunoprecipitation and microarrays (ChIP-chip), we examined changes in the distribution of Escherichia coli RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM). We found approximately 200 Rho-terminated loci that were divided evenly into 2 classes: intergenic (at the ends of genes) and intragenic (within genes). The intergenic class contained noncoding RNAs such as small RNAs (sRNAs) and transfer RNAs (tRNAs), establishing a previously unappreciated role of Rho in termination of stable RNA synthesis. The intragenic class of terminators included a previously uncharacterized set of short antisense transcripts, as judged by a shift in the distribution of RNAP in BCM-treated cells that was opposite to the direction of the corresponding gene. These Rho-terminated antisense transcripts point to a role of noncoding transcription in E. coli gene regulation that may resemble the ubiquitous noncoding transcription recently found to play myriad roles in eukaryotic gene regulation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19706412 PubMed]
Online version:[http://dx.doi.org/10.1073/pnas.0903846106 10.1073/pnas.0903846106]
 [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B)_+BCM(3428302)_normalized.gff RNAP(B)_+BCM(3428302)_normalized.gff3 20M]
 [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B)_untreated(3427302)_normalized.gff RNAP(B)_untreated(3427302)_normalized.gff3 20M]

|-
!align=left |Keywords
||
Bicyclo Compounds, Heterocyclic; Chromatin Immunoprecipitation; DNA-Directed RNA Polymerases; Escherichia coli; Genes, Bacterial; Microarray Analysis; RNA; Transcription, Genetic; rho GTP-Binding Proteins

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.M50ad199107b8a&page=182751&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="O50ad19913835a" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.O50ad19913835a&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z519f8d526b29b" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
RNAP

|
RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)
|
Replicates with and w/o BCM are shown as subtracks.
|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=3428302&t=3427302 GBrowse Track]
:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B)_+BCM(3428302)_normalized.gff RNAP(B)_+BCM(3428302)_normalized.gff3 20M]

:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B)_untreated(3427302)_normalized.gff RNAP(B)_untreated(3427302)_normalized.gff3 20M]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.Z519f8d526b29b&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]

PMID:19706412

2013-05-30T21:33:01Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="M50ad199107b8a" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Peters, JM, Mooney, RA, Kuan, PF, Rowland, JL, Keles, S and Landick, R''' (2009) Rho directs widespread termination of intragenic and stable RNA transcription.''Proc. Natl. Acad. Sci. U.S.A.'' '''106''':15406-11
|-
!align=left |Abstract
||
The transcription termination factor Rho is a global regulator of RNA polymerase (RNAP). Although individual Rho-dependent terminators have been studied extensively, less is known about the sites of RNAP regulation by Rho on a genome-wide scale. Using chromatin immunoprecipitation and microarrays (ChIP-chip), we examined changes in the distribution of Escherichia coli RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM). We found approximately 200 Rho-terminated loci that were divided evenly into 2 classes: intergenic (at the ends of genes) and intragenic (within genes). The intergenic class contained noncoding RNAs such as small RNAs (sRNAs) and transfer RNAs (tRNAs), establishing a previously unappreciated role of Rho in termination of stable RNA synthesis. The intragenic class of terminators included a previously uncharacterized set of short antisense transcripts, as judged by a shift in the distribution of RNAP in BCM-treated cells that was opposite to the direction of the corresponding gene. These Rho-terminated antisense transcripts point to a role of noncoding transcription in E. coli gene regulation that may resemble the ubiquitous noncoding transcription recently found to play myriad roles in eukaryotic gene regulation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19706412 PubMed]
Online version:[http://dx.doi.org/10.1073/pnas.0903846106 10.1073/pnas.0903846106]
 [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B)_+BCM(3428302)_normalized.gff RNAP(B)_+BCM(3428302)_normalized.gff3 20M]
 [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B')_+BCM(94828)_normalized.gff RNAP(B')_+BCM(94828)_normalized.gff3 19M]
 [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B')_untreated(100040)_normalized.gff RNAP(B')_untreated(100040)_normalized.gff3 19M]
 [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B)_untreated(3427302)_normalized.gff RNAP(B)_untreated(3427302)_normalized.gff3 20M]

|-
!align=left |Keywords
||
Bicyclo Compounds, Heterocyclic; Chromatin Immunoprecipitation; DNA-Directed RNA Polymerases; Escherichia coli; Genes, Bacterial; Microarray Analysis; RNA; Transcription, Genetic; rho GTP-Binding Proteins

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.M50ad199107b8a&page=182751&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="O50ad19913835a" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.O50ad19913835a&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z519f8d526b29b" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
RNAP

|
RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)
|
Replicates with and w/o BCM are shown as subtracks.
|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=3428302&t=3427302 GBrowse Track]
:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B)_+BCM(3428302)_normalized.gff RNAP(B)_+BCM(3428302)_normalized.gff3 20M]

:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B)_untreated(3427302)_normalized.gff RNAP(B)_untreated(3427302)_normalized.gff3 20M]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.Z519f8d526b29b&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]

PMID:21321206

2013-05-29T20:19:07Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="U51a4ec9fc71f9" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Cho, H, McManus, HR, Dove, SL and Bernhardt, TG''' (2011) Nucleoid occlusion factor SlmA is a DNA-activated FtsZ polymerization antagonist. ''Proc. Natl. Acad. Sci. U.S.A.'' '''108''':3773-8
|-
!align=left |Abstract
||
The tubulin-like FtsZ protein initiates assembly of the bacterial cytokinetic machinery by polymerizing into a ring structure, the Z ring, at the prospective site of division. To block Z-ring formation over the nucleoid and help coordinate cell division with chromosome segregation, Escherichia coli employs the nucleoid-associated division inhibitor, SlmA. Here, we investigate the mechanism by which SlmA regulates FtsZ assembly. We show that SlmA disassembles FtsZ polymers in vitro. In addition, using chromatin immunoprecipitation (ChIP), we identified 24 SlmA-binding sequences (SBSs) on the chromosome. Remarkably, SlmA binding to SBSs dramatically enhanced its ability to interfere with FtsZ polymerization, and ChIP studies indicate that SlmA regulates FtsZ assembly at these sites in vivo. Because of the dynamic and highly organized nature of the chromosome, coupling SlmA activation to specific DNA binding provides a mechanism for the precise spatiotemporal control of its anti-FtsZ activity within the cell.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21321206 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048121 PMC3048121]
Online version:[http://dx.doi.org/10.1073/pnas.1018674108 10.1073/pnas.1018674108]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183199.U51a4ec9fc71f9&page=183199&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="B51a4eca008efb" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183199.B51a4eca008efb&page=183199&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="X51a4edafde310" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
SlmA
|

|

|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SlmA&t=SlmA_density SlmA GBrowse Track]

:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/21321206/SlmA/SlmA.gff3 SlmA.gff3]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183199.X51a4edafde310&page=183199&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[Category:Papers_with_tracks_in_Gbrowse]]

PMID:16963779

2013-05-29T20:08:17Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="B512d848714402" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Grainger, DC , Hurd, D , Goldberg, MD and Busby, SJ ''' (2006) Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. ''Nucleic Acids Res.'' '''34''':4642-52
|-
!align=left |Abstract
||
The Escherichia coli chromosome is condensed into an ill-defined structure known as the nucleoid. Nucleoid-associated DNA-binding proteins are involved in maintaining this structure and in mediating chromosome compaction. We have exploited chromatin immunoprecipitation and high-density microarrays to study the binding of three such proteins, FIS, H-NS and IHF, across the E.coli genome in vivo. Our results show that the distribution of these proteins is biased to intergenic parts of the genome, and that the binding profiles overlap. Hence some targets are associated with combinations of bound FIS, H-NS and IHF. In addition, many regions associated with FIS and H-NS are also associated with RNA polymerase.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16963779 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636352 PMC1636352]
Online version:[http://dx.doi.org/10.1093/nar/gkl542 10.1093/nar/gkl542]
;Data tracks
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/FIS.gff3 FIS.gff3 12K]
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/H-NS/HNS.gff3 H-NS.gff3 8K]
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/IHF/IHF.gff3 IHF.gff3 8K]
|-
!align=left |Keywords
||
Bacterial Proteins/metabolism; Binding Sites; Chromatin Immunoprecipitation; Chromosomes, Bacterial; DNA, Bacterial/metabolism; DNA, Intergenic/metabolism; DNA-Binding Proteins/isolation & purification; DNA-Binding Proteins/metabolism; DNA-Directed RNA Polymerases/metabolism; Escherichia coli/genetics; Escherichia coli Proteins/isolation & purification; Escherichia coli Proteins/metabolism; Factor For Inversion Stimulation Protein; Genome, Bacterial; Integration Host Factors/metabolism; Oligonucleotide Array Sequence Analysis; Transcription Factors/metabolism; Transcription, Genetic

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.B512d848714402&page=182924&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="J512d848771fec" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.J512d848771fec&page=182924&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect></protect>

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="T519d0fd60cf30" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
FIS
|

|

|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_FIS_density&t=Nucleoid_Protein_FIS_xy FIS GBrowse Track]
:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/FIS.gff3 FIS.gff3]
|-
|
MG1655
|
ChIP-chip
|
H-NS
|

|

|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_HNS_density&t=Nucleoid_Protein_HNS_xy HNS GBrowse Track]

:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/HNS/HNS.gff3 HNS.gff3]
|-
|
MG1655
|
ChIP-chip
|
IHF
|

|

|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_IHF_density&t=Nucleoid_Protein_IHF_xy IHF GBrowse Track]

:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/IHF/IHF.gff3 IHF.gff3]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.T519d0fd60cf30&page=182924&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[Category:Papers_with_tracks_in_Gbrowse]]

PMID:20689753

2013-05-29T18:46:02Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="O5110505532e46" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Sánchez-Romero, MA , Busby, SJ , Dyer, NP , Ott, S , Millard, AD and Grainger, DC ''' (2010) Dynamic distribution of seqa protein across the chromosome of escherichia coli K-12. ''MBio'' '''1'''
|-
!align=left |Abstract
||
The bacterial SeqA protein binds to hemi-methylated GATC sequences that arise in newly synthesized DNA upon passage of the replication machinery. In Escherichia coli K-12, the single replication origin oriC is a well-characterized target for SeqA, which binds to multiple hemi-methylated GATC sequences immediately after replication has initiated. This sequesters oriC, thereby preventing reinitiation of replication. However, the genome-wide DNA binding properties of SeqA are unknown, and hence, here, we describe a study of the binding of SeqA across the entire Escherichia coli K-12 chromosome, using chromatin immunoprecipitation in combination with DNA microarrays. Our data show that SeqA binding correlates with the frequency and spacing of GATC sequences across the entire genome. Less SeqA is found in highly transcribed regions, as well as in the ter macrodomain. Using synchronized cultures, we show that SeqA distribution differs with the cell cycle. SeqA remains bound to some targets after replication has ceased, and these targets locate to genes encoding factors involved in nucleotide metabolism, chromosome replication, and methyl transfer.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20689753 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912659 PMC2912659]
Online version:[http://dx.doi.org/10.1128/mBio.00012-10 10.1128/mBio.00012-10]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.O5110505532e46&page=182904&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="O5110505579ecb" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.O5110505579ecb&page=182904&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="N519f9885e1384" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
SeqA
|

|

|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SeqA_Bigwig_density&t=SeqA_Bigwig SeqA Gbrowse Track]
:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/SeqA/SeqAtimeA.gff3 SeqAtimeA.gff3]
:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/SeqA/SeqAtimeB.gff3 SeqAtimeB.gff3]
:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/SeqA/SeqAtimeC.gff3 SeqAtimeC.gff3]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.N519f9885e1384&page=182904&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[Category:Papers with tracks in Gbrowse]]
[[Category:High-Throughput Papers]]

PMID:19150431

2013-05-29T17:30:39Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="R51a429996fc2e" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Mooney, RA, Davis, SE, Peters, JM, Rowland, JL, Ansari, AZ and Landick, R''' (2009) Regulator trafficking on bacterial transcription units in vivo. ''Mol. Cell'' '''33''':97-108
|-
!align=left |Abstract
||
The trafficking patterns of the bacterial regulators of transcript elongation sigma(70), rho, NusA, and NusG on genes in vivo and the explanation for promoter-proximal peaks of RNA polymerase (RNAP) are unknown. Genome-wide, E. coli ChIP-chip revealed distinct association patterns of regulators as RNAP transcribes away from promoters (rho first, then NusA, then NusG). However, the interactions of elongating complexes with these regulators did not differ significantly among most transcription units. A modest variation of NusG signal among genes reflected increased NusG interaction as transcription progresses, rather than functional specialization of elongating complexes. Promoter-proximal RNAP peaks were offset from sigma(70) peaks in the direction of transcription and co-occurred with NusA and rho peaks, suggesting that the RNAP peaks reflected elongating, rather than initiating, complexes. However, inhibition of rho did not increase RNAP levels within genes downstream from the RNAP peaks, suggesting the peaks are caused by a mechanism other than rho-dependent attenuation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19150431 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747249 PMC2747249]
Online version:[http://dx.doi.org/10.1016/j.molcel.2008.12.021 10.1016/j.molcel.2008.12.021]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183193.R51a429996fc2e&page=183193&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Brief Description==
This paper uses ChIP-chip methods to investigate the occupancy of 5 proteins along the ''E. coli'' chromosome:
* the RNA Polymerase (RNAP)
* [[nusA|NusA]]
* [[nusG|NusG]]
* [[:Category:Complex:RNA_polymerase_sigma70|σ70]]
* [[rho|ρ]]

== Main Points ==
* There is not a one-to-one relationship between the (observed) occupancy of [[:Category:Complex:RNA_polymerase_sigma70|σ70]] and [[RNA Polymerase|RNAP]].
* Evidence sustaining the idea that [[nusA|NusA]] displaces σ70 during transcript elongation. (Previously reported in <ref name='PMID:6263495'/>)
* Elongating RNAPs do not exhibit transcription-unit specific variations in affinities for σ70, NusA, NusG or ρ. This suggests these proteins are ''general'' elongation regulators and not ''specific'' regulators (as in the case of [[rfaH]].)
* σ70 binds almost exclusively to the promoter regions.
* NusG is associated with elongation complexes more slowly than NusA (on most transcription units.)
* ρ binding is most evident between the σ70 and RNAP signals near the promoter. This suggests ρ may associate with the nascent transcripts soon after transcription initiation.

==Methods and Calculations==

; High Quality TUs
: 109 "high-quality" transciption units were identified in which overlap from adjacent transcription units did not obscure the patterns. (Fig 1D & Table S1)

; RNA Polymerase Control
: 170 regions of the genome (greater than 1kb in length) were identified as similar in transcript level to the cryptic gene ''[[bglB]]''. This gave a non-specific background - see Fig 1B & 1C.

; Apparent Occupancy
: The Occapp was defined by linearly scaling the signals for each protein between 0 (basal level of RNAP) and 1 (the average of the 10 3-probe clusters with highest average value).

* IP samples were compared to control samples of input DNA (recovered from cell extract immediately prior to IP.)
* The microarray contains two copies of 187,204 Tm-matched ≥45bp oligos.
** This tiled the chromosome with an average of 24.5bp separation.

===EcoliWiki data manipulation===
In order to show the results of this paper across the entire genome, we first downloaded the data-sets ([http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13938 GSE13938]) from the [[Gene Expression Omnibus (GEO)]].

Tracks for the PortEco GBrowse were added for
*
*
*
*
[Category:GBrowse]

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="Y4b8d6b9bd9a1a" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.171538.Y4b8d6b9bd9a1a&page=171538&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z51a42a9f1c63c" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
NusA
|

|

|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=NusA NusA Gbrowse Track]

:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusA/NusA.gff3 NusA.gff3]
|-
|
MG1655
|
ChIP-chip
|
NusG
|

|

|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=NusG NusG Gbrowse Track]

:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusG/NusG.gff3 NusG.gff3]
|-
|
MG1655
|
ChIP-chip
|
Rho
|

|

|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Rho Rho Gbrowse Track]

:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/Rho/Rho.gff3 Rho.gff3]
|-
|
MG1655
|
ChIP-chip
|
RNAp
|

|

|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=RNAp RNAp Gbrowse Track]
|-
|
MG1655
|
ChIP-chip
|
Sigma70
|

|

|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Sigma70 Sigma70 GBrowse Track]

:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/Sigma70/Sigma70.gff3 Sigma70.gff3]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183193.Z51a42a9f1c63c&page=183193&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==
* Information about [http://openwetware.org/wiki/ChIP-Chip_E._coli ChIP-chip for E. coli] at OpenWetWare
* Wikipedia article about [http://en.wikipedia.org/wiki/ChIP-on-chip ChIP-chip]

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]
[[Category:High-Throughput Papers]]
[[Category:RNA_polymerase_tracks]]

PMID:19150431

2013-05-29T17:16:45Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="R51a429996fc2e" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Mooney, RA, Davis, SE, Peters, JM, Rowland, JL, Ansari, AZ and Landick, R''' (2009) Regulator trafficking on bacterial transcription units in vivo. ''Mol. Cell'' '''33''':97-108
|-
!align=left |Abstract
||
The trafficking patterns of the bacterial regulators of transcript elongation sigma(70), rho, NusA, and NusG on genes in vivo and the explanation for promoter-proximal peaks of RNA polymerase (RNAP) are unknown. Genome-wide, E. coli ChIP-chip revealed distinct association patterns of regulators as RNAP transcribes away from promoters (rho first, then NusA, then NusG). However, the interactions of elongating complexes with these regulators did not differ significantly among most transcription units. A modest variation of NusG signal among genes reflected increased NusG interaction as transcription progresses, rather than functional specialization of elongating complexes. Promoter-proximal RNAP peaks were offset from sigma(70) peaks in the direction of transcription and co-occurred with NusA and rho peaks, suggesting that the RNAP peaks reflected elongating, rather than initiating, complexes. However, inhibition of rho did not increase RNAP levels within genes downstream from the RNAP peaks, suggesting the peaks are caused by a mechanism other than rho-dependent attenuation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19150431 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747249 PMC2747249]
Online version:[http://dx.doi.org/10.1016/j.molcel.2008.12.021 10.1016/j.molcel.2008.12.021]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183193.R51a429996fc2e&page=183193&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Brief Description==
This paper uses ChIP-chip methods to investigate the occupancy of 5 proteins along the ''E. coli'' chromosome:
* the RNA Polymerase (RNAP)
* [[nusA|NusA]]
* [[nusG|NusG]]
* [[:Category:Complex:RNA_polymerase_sigma70|σ70]]
* [[rho|ρ]]

== Main Points ==
* There is not a one-to-one relationship between the (observed) occupancy of [[:Category:Complex:RNA_polymerase_sigma70|σ70]] and [[RNA Polymerase|RNAP]].
* Evidence sustaining the idea that [[nusA|NusA]] displaces σ70 during transcript elongation. (Previously reported in <ref name='PMID:6263495'/>)
* Elongating RNAPs do not exhibit transcription-unit specific variations in affinities for σ70, NusA, NusG or ρ. This suggests these proteins are ''general'' elongation regulators and not ''specific'' regulators (as in the case of [[rfaH]].)
* σ70 binds almost exclusively to the promoter regions.
* NusG is associated with elongation complexes more slowly than NusA (on most transcription units.)
* ρ binding is most evident between the σ70 and RNAP signals near the promoter. This suggests ρ may associate with the nascent transcripts soon after transcription initiation.

==Methods and Calculations==

; High Quality TUs
: 109 "high-quality" transciption units were identified in which overlap from adjacent transcription units did not obscure the patterns. (Fig 1D & Table S1)

; RNA Polymerase Control
: 170 regions of the genome (greater than 1kb in length) were identified as similar in transcript level to the cryptic gene ''[[bglB]]''. This gave a non-specific background - see Fig 1B & 1C.

; Apparent Occupancy
: The Occapp was defined by linearly scaling the signals for each protein between 0 (basal level of RNAP) and 1 (the average of the 10 3-probe clusters with highest average value).

* IP samples were compared to control samples of input DNA (recovered from cell extract immediately prior to IP.)
* The microarray contains two copies of 187,204 Tm-matched ≥45bp oligos.
** This tiled the chromosome with an average of 24.5bp separation.

===EcoliWiki data manipulation===
In order to show the results of this paper across the entire genome, we first downloaded the data-sets ([http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13938 GSE13938]) from the [[Gene Expression Omnibus (GEO)]].

Tracks for the PortEco GBrowse were added for
*
*
*
*
[Category:GBrowse]

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="Y4b8d6b9bd9a1a" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.171538.Y4b8d6b9bd9a1a&page=171538&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z51a42a9f1c63c" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
NusA
|

|

|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=NusA NusA Gbrowse Track]

:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusA/NusA.gff3 NusA.gff3]
|-
|
MG1655
|
ChIP-chip
|
NusG
|

|

|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=NusG NusG Gbrowse Track]

:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusG/NusG.gff3 NusG.gff3]
|-
|
MG1655
|
ChIP-chip
|
Rho
|

|

|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Rho Rho Gbrowse Track]

:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/Rho/Rho.gff3 Rho.gff3]
|-
|
MG1655
|
ChIP-chip
|
RNAp
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=RNAp
|-
|
MG1655
|
ChIP-chip
|
Sigma70
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Sigma70

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183193.Z51a42a9f1c63c&page=183193&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==
* Information about [http://openwetware.org/wiki/ChIP-Chip_E._coli ChIP-chip for E. coli] at OpenWetWare
* Wikipedia article about [http://en.wikipedia.org/wiki/ChIP-on-chip ChIP-chip]

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]
[[Category:High-Throughput Papers]]
[[Category:RNA_polymerase_tracks]]

PMID:19150431

2013-05-29T17:11:39Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="R51a429996fc2e" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Mooney, RA, Davis, SE, Peters, JM, Rowland, JL, Ansari, AZ and Landick, R''' (2009) Regulator trafficking on bacterial transcription units in vivo. ''Mol. Cell'' '''33''':97-108
|-
!align=left |Abstract
||
The trafficking patterns of the bacterial regulators of transcript elongation sigma(70), rho, NusA, and NusG on genes in vivo and the explanation for promoter-proximal peaks of RNA polymerase (RNAP) are unknown. Genome-wide, E. coli ChIP-chip revealed distinct association patterns of regulators as RNAP transcribes away from promoters (rho first, then NusA, then NusG). However, the interactions of elongating complexes with these regulators did not differ significantly among most transcription units. A modest variation of NusG signal among genes reflected increased NusG interaction as transcription progresses, rather than functional specialization of elongating complexes. Promoter-proximal RNAP peaks were offset from sigma(70) peaks in the direction of transcription and co-occurred with NusA and rho peaks, suggesting that the RNAP peaks reflected elongating, rather than initiating, complexes. However, inhibition of rho did not increase RNAP levels within genes downstream from the RNAP peaks, suggesting the peaks are caused by a mechanism other than rho-dependent attenuation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19150431 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747249 PMC2747249]
Online version:[http://dx.doi.org/10.1016/j.molcel.2008.12.021 10.1016/j.molcel.2008.12.021]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183193.R51a429996fc2e&page=183193&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Brief Description==
This paper uses ChIP-chip methods to investigate the occupancy of 5 proteins along the ''E. coli'' chromosome:
* the RNA Polymerase (RNAP)
* [[nusA|NusA]]
* [[nusG|NusG]]
* [[:Category:Complex:RNA_polymerase_sigma70|σ70]]
* [[rho|ρ]]

== Main Points ==
* There is not a one-to-one relationship between the (observed) occupancy of [[:Category:Complex:RNA_polymerase_sigma70|σ70]] and [[RNA Polymerase|RNAP]].
* Evidence sustaining the idea that [[nusA|NusA]] displaces σ70 during transcript elongation. (Previously reported in <ref name='PMID:6263495'/>)
* Elongating RNAPs do not exhibit transcription-unit specific variations in affinities for σ70, NusA, NusG or ρ. This suggests these proteins are ''general'' elongation regulators and not ''specific'' regulators (as in the case of [[rfaH]].)
* σ70 binds almost exclusively to the promoter regions.
* NusG is associated with elongation complexes more slowly than NusA (on most transcription units.)
* ρ binding is most evident between the σ70 and RNAP signals near the promoter. This suggests ρ may associate with the nascent transcripts soon after transcription initiation.

==Methods and Calculations==

; High Quality TUs
: 109 "high-quality" transciption units were identified in which overlap from adjacent transcription units did not obscure the patterns. (Fig 1D & Table S1)

; RNA Polymerase Control
: 170 regions of the genome (greater than 1kb in length) were identified as similar in transcript level to the cryptic gene ''[[bglB]]''. This gave a non-specific background - see Fig 1B & 1C.

; Apparent Occupancy
: The Occapp was defined by linearly scaling the signals for each protein between 0 (basal level of RNAP) and 1 (the average of the 10 3-probe clusters with highest average value).

* IP samples were compared to control samples of input DNA (recovered from cell extract immediately prior to IP.)
* The microarray contains two copies of 187,204 Tm-matched ≥45bp oligos.
** This tiled the chromosome with an average of 24.5bp separation.

===EcoliWiki data manipulation===
In order to show the results of this paper across the entire genome, we first downloaded the data-sets ([http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13938 GSE13938]) from the [[Gene Expression Omnibus (GEO)]].

Tracks for the PortEco GBrowse were added for
*
*
*
*
[Category:GBrowse]

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="Y4b8d6b9bd9a1a" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.171538.Y4b8d6b9bd9a1a&page=171538&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z51a42a9f1c63c" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
NusA
|

|

|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=NusA NusA Gbrowse Track]

:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusA/NusA.gff3 NusA.gff3]
|-
|
MG1655
|
ChIP-chip
|
NusG
|

|

|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=NusG NusG Gbrowse Track]

:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusG/NusG.gff3 NusG.gff3]
|-
|
MG1655
|
ChIP-chip
|
Rho
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Rho
|-
|
MG1655
|
ChIP-chip
|
RNAp
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=RNAp
|-
|
MG1655
|
ChIP-chip
|
Sigma70
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Sigma70

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183193.Z51a42a9f1c63c&page=183193&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==
* Information about [http://openwetware.org/wiki/ChIP-Chip_E._coli ChIP-chip for E. coli] at OpenWetWare
* Wikipedia article about [http://en.wikipedia.org/wiki/ChIP-on-chip ChIP-chip]

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]
[[Category:High-Throughput Papers]]
[[Category:RNA_polymerase_tracks]]

PMID:19150431

2013-05-29T16:30:32Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="R51a429996fc2e" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Mooney, RA, Davis, SE, Peters, JM, Rowland, JL, Ansari, AZ and Landick, R''' (2009) Regulator trafficking on bacterial transcription units in vivo. ''Mol. Cell'' '''33''':97-108
|-
!align=left |Abstract
||
The trafficking patterns of the bacterial regulators of transcript elongation sigma(70), rho, NusA, and NusG on genes in vivo and the explanation for promoter-proximal peaks of RNA polymerase (RNAP) are unknown. Genome-wide, E. coli ChIP-chip revealed distinct association patterns of regulators as RNAP transcribes away from promoters (rho first, then NusA, then NusG). However, the interactions of elongating complexes with these regulators did not differ significantly among most transcription units. A modest variation of NusG signal among genes reflected increased NusG interaction as transcription progresses, rather than functional specialization of elongating complexes. Promoter-proximal RNAP peaks were offset from sigma(70) peaks in the direction of transcription and co-occurred with NusA and rho peaks, suggesting that the RNAP peaks reflected elongating, rather than initiating, complexes. However, inhibition of rho did not increase RNAP levels within genes downstream from the RNAP peaks, suggesting the peaks are caused by a mechanism other than rho-dependent attenuation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19150431 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747249 PMC2747249]
Online version:[http://dx.doi.org/10.1016/j.molcel.2008.12.021 10.1016/j.molcel.2008.12.021]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183193.R51a429996fc2e&page=183193&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Brief Description==
This paper uses ChIP-chip methods to investigate the occupancy of 5 proteins along the ''E. coli'' chromosome:
* the RNA Polymerase (RNAP)
* [[nusA|NusA]]
* [[nusG|NusG]]
* [[:Category:Complex:RNA_polymerase_sigma70|σ70]]
* [[rho|ρ]]

== Main Points ==
* There is not a one-to-one relationship between the (observed) occupancy of [[:Category:Complex:RNA_polymerase_sigma70|σ70]] and [[RNA Polymerase|RNAP]].
* Evidence sustaining the idea that [[nusA|NusA]] displaces σ70 during transcript elongation. (Previously reported in <ref name='PMID:6263495'/>)
* Elongating RNAPs do not exhibit transcription-unit specific variations in affinities for σ70, NusA, NusG or ρ. This suggests these proteins are ''general'' elongation regulators and not ''specific'' regulators (as in the case of [[rfaH]].)
* σ70 binds almost exclusively to the promoter regions.
* NusG is associated with elongation complexes more slowly than NusA (on most transcription units.)
* ρ binding is most evident between the σ70 and RNAP signals near the promoter. This suggests ρ may associate with the nascent transcripts soon after transcription initiation.

==Methods and Calculations==

; High Quality TUs
: 109 "high-quality" transciption units were identified in which overlap from adjacent transcription units did not obscure the patterns. (Fig 1D & Table S1)

; RNA Polymerase Control
: 170 regions of the genome (greater than 1kb in length) were identified as similar in transcript level to the cryptic gene ''[[bglB]]''. This gave a non-specific background - see Fig 1B & 1C.

; Apparent Occupancy
: The Occapp was defined by linearly scaling the signals for each protein between 0 (basal level of RNAP) and 1 (the average of the 10 3-probe clusters with highest average value).

* IP samples were compared to control samples of input DNA (recovered from cell extract immediately prior to IP.)
* The microarray contains two copies of 187,204 Tm-matched ≥45bp oligos.
** This tiled the chromosome with an average of 24.5bp separation.

===EcoliWiki data manipulation===
In order to show the results of this paper across the entire genome, we first downloaded the data-sets ([http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13938 GSE13938]) from the [[Gene Expression Omnibus (GEO)]].

Tracks for the PortEco GBrowse were added for
*
*
*
*
[Category:GBrowse]

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="Y4b8d6b9bd9a1a" class=" tableEdit GO_table_reference"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.171538.Y4b8d6b9bd9a1a&page=171538&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z51a42a9f1c63c" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
NusA
|

|

|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=NusA NusA Gbrowse Track]

:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19150431/NusA/NusA.gff3 NusA.gff3]
|-
|
MG1655
|
ChIP-chip
|
NusG
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=NusG
|-
|
MG1655
|
ChIP-chip
|
Rho
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Rho
|-
|
MG1655
|
ChIP-chip
|
RNAp
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=RNAp
|-
|
MG1655
|
ChIP-chip
|
Sigma70
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Sigma70

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.183193.Z51a42a9f1c63c&page=183193&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==
* Information about [http://openwetware.org/wiki/ChIP-Chip_E._coli ChIP-chip for E. coli] at OpenWetWare
* Wikipedia article about [http://en.wikipedia.org/wiki/ChIP-on-chip ChIP-chip]

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]
[[Category:High-Throughput Papers]]
[[Category:RNA_polymerase_tracks]]

PMID:19706412

2013-05-29T15:47:07Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="M50ad199107b8a" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Peters, JM, Mooney, RA, Kuan, PF, Rowland, JL, Keles, S and Landick, R''' (2009) Rho directs widespread termination of intragenic and stable RNA transcription.''Proc. Natl. Acad. Sci. U.S.A.'' '''106''':15406-11
|-
!align=left |Abstract
||
The transcription termination factor Rho is a global regulator of RNA polymerase (RNAP). Although individual Rho-dependent terminators have been studied extensively, less is known about the sites of RNAP regulation by Rho on a genome-wide scale. Using chromatin immunoprecipitation and microarrays (ChIP-chip), we examined changes in the distribution of Escherichia coli RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM). We found approximately 200 Rho-terminated loci that were divided evenly into 2 classes: intergenic (at the ends of genes) and intragenic (within genes). The intergenic class contained noncoding RNAs such as small RNAs (sRNAs) and transfer RNAs (tRNAs), establishing a previously unappreciated role of Rho in termination of stable RNA synthesis. The intragenic class of terminators included a previously uncharacterized set of short antisense transcripts, as judged by a shift in the distribution of RNAP in BCM-treated cells that was opposite to the direction of the corresponding gene. These Rho-terminated antisense transcripts point to a role of noncoding transcription in E. coli gene regulation that may resemble the ubiquitous noncoding transcription recently found to play myriad roles in eukaryotic gene regulation.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19706412 PubMed]
Online version:[http://dx.doi.org/10.1073/pnas.0903846106 10.1073/pnas.0903846106]
 [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B)_+BCM(3428302)_normalized.gff RNAP(B)_+BCM(3428302)_normalized.gff3 20M]
 [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B')_+BCM(94828)_normalized.gff RNAP(B')_+BCM(94828)_normalized.gff3 19M]
 [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B')_untreated(100040)_normalized.gff RNAP(B')_untreated(100040)_normalized.gff3 19M]
 [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B)_untreated(3427302)_normalized.gff RNAP(B)_untreated(3427302)_normalized.gff3 20M]

|-
!align=left |Keywords
||
Bicyclo Compounds, Heterocyclic; Chromatin Immunoprecipitation; DNA-Directed RNA Polymerases; Escherichia coli; Genes, Bacterial; Microarray Analysis; RNA; Transcription, Genetic; rho GTP-Binding Proteins

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.M50ad199107b8a&page=182751&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="O50ad19913835a" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.O50ad19913835a&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z519f8d526b29b" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
RNAP

|
RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)
|
Replicates with and w/o BCM are shown as subtracks.
|
:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=19706412 GBrowse Track]
:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B)_+BCM(3428302)_normalized.gff RNAP(B)_+BCM(3428302)_normalized.gff3 20M]
:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B')_+BCM(94828)_normalized.gff RNAP(B')_+BCM(94828)_normalized.gff3 19M]
:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B')_untreated(100040)_normalized.gff RNAP(B')_untreated(100040)_normalized.gff3 19M]
:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/19706412/RNAP(B)_untreated(3427302)_normalized.gff RNAP(B)_untreated(3427302)_normalized.gff3 20M]

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182751.Z519f8d526b29b&page=182751&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]

PMID:22153074

2013-05-28T20:56:52Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="W4f8607bbb0ead" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Oh, E, Becker, AH, Sandikci, A, Huber, D, Chaba, R, Gloge, F, Nichols, RJ, Typas, A, Gross, CA, Kramer, G, Weissman, JS and Bukau, B''' (2011) Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo.''Cell'' '''147''':1295-308
|-
!align=left |Abstract
||
As nascent polypeptides exit ribosomes, they are engaged by a series of processing, targeting, and folding factors. Here, we present a selective ribosome profiling strategy that enables global monitoring of when these factors engage polypeptides in the complex cellular environment. Studies of the Escherichia coli chaperone trigger factor (TF) reveal that, though TF can interact with many polypeptides, β-barrel outer-membrane proteins are the most prominent substrates. Loss of TF leads to broad outer-membrane defects and premature, cotranslational protein translocation. Whereas in vitro studies suggested that TF is prebound to ribosomes waiting for polypeptides to emerge from the exit channel, we find that in vivo TF engages ribosomes only after ~100 amino acids are translated. Moreover, excess TF interferes with cotranslational removal of the N-terminal formyl methionine. Our studies support a triaging model in which proper protein biogenesis relies on the fine-tuned, sequential engagement of processing, targeting, and folding factors.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22153074 PubMed]
Online version:[http://dx.doi.org/10.1016/j.cell.2011.10.044 10.1016/j.cell.2011.10.044]
 Raw Data from Authors: [http://heptamer.tamu.edu/gbrowse2/Public/BW2952/22153074/Ribosomal_Profiling_non-normalized_Wiggle.zip Ribosome Profiling non-normalized Wiggles]
|-
!align=left |Keywords
||
Cytoplasm; Escherichia coli; Escherichia coli Proteins; Membrane Proteins; Molecular Chaperones; Molecular Sequence Data; Peptidylprolyl Isomerase; Protein Biosynthesis; Protein Transport; Ribosomes

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181070.W4f8607bbb0ead&page=181070&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

:* Extended Ribosome Profiling to prokaryotes to enable the analysis of both translation and co-translational processes (such as Trigger Factor) that promote maturation of nascent polypeptides.

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

:* Four distinct steps (1) generation of cell extracts, in which ribosomes have been halted along the mRNA that they are translating; (2) treatment of polysomes with nuclease to remove regions of the message not protected by the ribosomes; (3) conversion of these RNA fragments into double stranded DNA copies and (4) analysis of these fragments by high throughput sequencing.

===EcoliWiki data manipulation===

:* Non-normalized wiggle files were sent from Eugene Oh; three replicates of dithiobis succinimidyl propionate (DSP) affinity purified (AP) for the forward strand, three replicates of DSP AP reverse strand, three replicates of the total ribosome profile for the forward strand, three replicates for the total profile of the reverse strand, one replicate each of 1-ethyl-3-[3-dimethylaminopropyl]carbodiimide (EDC) AP forward and reverse strand, and one replicate each of EDC total ribosome profile forward and reverse strand. Replicates data sets were normalized by dividing all read values by the highest read value within each data set. After normalization, replicates were then averaged together. EDC replicates were normalized in the same manner, but not averaged due to only one replicate.

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="P4f8607bbc5687" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181070.P4f8607bbc5687&page=181070&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="O51a5135900c75" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
BW2952
|
Ribosome Profiling
|

|
dithiobis succinimidyl propionate (DSP) affinity purified (AP),
1-ethyl 3-[3-dimethylaminopropyl]carbodiimide (EDC) AP
|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/BW2952/?t=22153074_1&t=22153074_2&t=22153074_3&t=22153074_4&t=22153074_5&t=22153074_6&t=22153074_7&t=22153074_8

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181070.O51a5135900c75&page=181070&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==
* [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33671 GEO GSE33671]

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]

PMID:22153074

2013-05-28T20:49:18Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}}


{| id="W4f8607bbb0ead" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Oh, E, Becker, AH, Sandikci, A, Huber, D, Chaba, R, Gloge, F, Nichols, RJ, Typas, A, Gross, CA, Kramer, G, Weissman, JS and Bukau, B''' (2011) Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo.''Cell'' '''147''':1295-308
|-
!align=left |Abstract
||
As nascent polypeptides exit ribosomes, they are engaged by a series of processing, targeting, and folding factors. Here, we present a selective ribosome profiling strategy that enables global monitoring of when these factors engage polypeptides in the complex cellular environment. Studies of the Escherichia coli chaperone trigger factor (TF) reveal that, though TF can interact with many polypeptides, β-barrel outer-membrane proteins are the most prominent substrates. Loss of TF leads to broad outer-membrane defects and premature, cotranslational protein translocation. Whereas in vitro studies suggested that TF is prebound to ribosomes waiting for polypeptides to emerge from the exit channel, we find that in vivo TF engages ribosomes only after ~100 amino acids are translated. Moreover, excess TF interferes with cotranslational removal of the N-terminal formyl methionine. Our studies support a triaging model in which proper protein biogenesis relies on the fine-tuned, sequential engagement of processing, targeting, and folding factors.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22153074 PubMed]
Online version:[http://dx.doi.org/10.1016/j.cell.2011.10.044 10.1016/j.cell.2011.10.044]
 Raw Data from Authors: [http://heptamer.tamu.edu/gbrowse2/Public/BW2952/22153074/Ribosomal_Profiling_non-normalized_Wiggle.zip Ribosome Profiling non-normalized Wiggles]
|-
!align=left |Keywords
||
Cytoplasm; Escherichia coli; Escherichia coli Proteins; Membrane Proteins; Molecular Chaperones; Molecular Sequence Data; Peptidylprolyl Isomerase; Protein Biosynthesis; Protein Transport; Ribosomes

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181070.W4f8607bbb0ead&page=181070&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

:* Extended Ribosome Profiling to prokaryotes to enable the analysis of both translation and co-translational processes (such as Trigger Factor) that promote maturation of nascent polypeptides.

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

:* Four distinct steps (1) generation of cell extracts, in which ribosomes have been halted along the mRNA that they are translating; (2) treatment of polysomes with nuclease to remove regions of the message not protected by the ribosomes; (3) conversion of these RNA fragments into double stranded DNA copies and (4) analysis of these fragments by high throughput sequencing.

===EcoliWiki data manipulation===

:* Non-normalized wiggle files were sent from Eugene Oh; three replicates of dithiobis succinimidyl propionate (DSP) affinity purified (AP) for the forward strand, three replicates of DSP AP reverse strand, three replicates of the total ribosome profile for the forward strand, three replicates for the total profile of the reverse strand, one replicate each of 1-ethyl-3-[3-dimethylaminopropyl]carbodiimide (EDC) AP forward and reverse strand, and one replicate each of EDC total ribosome profile forward and reverse strand. Replicates data sets were normalized by dividing all read values by the highest read value within each data set. After normalization, replicates were then averaged together. EDC replicates were normalized in the same manner, but not averaged due to only one replicate.

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="P4f8607bbc5687" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181070.P4f8607bbc5687&page=181070&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="O51a5135900c75" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
BW2952
|
Ribosome Profiling
|

|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/BW2952/?t=22153074_1&t=22153074_2&t=22153074_3&t=22153074_4&t=22153074_5&t=22153074_6&t=22153074_7&t=22153074_8

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181070.O51a5135900c75&page=181070&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==
* [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33671 GEO GSE33671]

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]

Template:Gbrowse table

2013-05-28T20:31:50Z

Johnlew:

<pre>
<headings>
Strain/Organism||strain|select| |MG1655|BW25113|BW2952|W3110|phage lambda
Assay||experiment|select| |ChIP-chip|ChIP-seq|Ribosome Profiling|SELEX
Analyte
Variable Conditions
Notes
Links
<headings>
</pre>
[[Category:Table templates|Gbrowse table]]

PMID:22153074

2013-05-28T20:28:09Z

Johnlew: /* Data */

{{RightTOC}}


{| id="W4f8607bbb0ead" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Oh, E, Becker, AH, Sandikci, A, Huber, D, Chaba, R, Gloge, F, Nichols, RJ, Typas, A, Gross, CA, Kramer, G, Weissman, JS and Bukau, B''' (2011) Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo.''Cell'' '''147''':1295-308
|-
!align=left |Abstract
||
As nascent polypeptides exit ribosomes, they are engaged by a series of processing, targeting, and folding factors. Here, we present a selective ribosome profiling strategy that enables global monitoring of when these factors engage polypeptides in the complex cellular environment. Studies of the Escherichia coli chaperone trigger factor (TF) reveal that, though TF can interact with many polypeptides, β-barrel outer-membrane proteins are the most prominent substrates. Loss of TF leads to broad outer-membrane defects and premature, cotranslational protein translocation. Whereas in vitro studies suggested that TF is prebound to ribosomes waiting for polypeptides to emerge from the exit channel, we find that in vivo TF engages ribosomes only after ~100 amino acids are translated. Moreover, excess TF interferes with cotranslational removal of the N-terminal formyl methionine. Our studies support a triaging model in which proper protein biogenesis relies on the fine-tuned, sequential engagement of processing, targeting, and folding factors.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22153074 PubMed]
Online version:[http://dx.doi.org/10.1016/j.cell.2011.10.044 10.1016/j.cell.2011.10.044]
 Raw Data from Authors: [http://heptamer.tamu.edu/gbrowse2/Public/BW2952/22153074/Ribosomal_Profiling_non-normalized_Wiggle.zip Ribosome Profiling non-normalized Wiggles]
|-
!align=left |Keywords
||
Cytoplasm; Escherichia coli; Escherichia coli Proteins; Membrane Proteins; Molecular Chaperones; Molecular Sequence Data; Peptidylprolyl Isomerase; Protein Biosynthesis; Protein Transport; Ribosomes

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181070.W4f8607bbb0ead&page=181070&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

:* Extended Ribosome Profiling to prokaryotes to enable the analysis of both translation and co-translational processes (such as Trigger Factor) that promote maturation of nascent polypeptides.

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

:* Four distinct steps (1) generation of cell extracts, in which ribosomes have been halted along the mRNA that they are translating; (2) treatment of polysomes with nuclease to remove regions of the message not protected by the ribosomes; (3) conversion of these RNA fragments into double stranded DNA copies and (4) analysis of these fragments by high throughput sequencing.

===EcoliWiki data manipulation===

:* Non-normalized wiggle files were sent from Eugene Oh; three replicates of dithiobis succinimidyl propionate (DSP) affinity purified (AP) for the forward strand, three replicates of DSP AP reverse strand, three replicates of the total ribosome profile for the forward strand, three replicates for the total profile of the reverse strand, one replicate each of 1-ethyl-3-[3-dimethylaminopropyl]carbodiimide (EDC) AP forward and reverse strand, and one replicate each of EDC total ribosome profile forward and reverse strand. Replicates data sets were normalized by dividing all read values by the highest read value within each data set. After normalization, replicates were then averaged together. EDC replicates were normalized in the same manner, but not averaged due to only one replicate.

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="P4f8607bbc5687" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181070.P4f8607bbc5687&page=181070&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="O51a5135900c75" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181070.O51a5135900c75&page=181070&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==
* [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33671 GEO GSE33671]

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]

PMID:22153074

2013-05-28T20:27:38Z

Johnlew: /* Annotations {{HelpIcon|Help:Literature}} */

{{RightTOC}}


{| id="W4f8607bbb0ead" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Oh, E, Becker, AH, Sandikci, A, Huber, D, Chaba, R, Gloge, F, Nichols, RJ, Typas, A, Gross, CA, Kramer, G, Weissman, JS and Bukau, B''' (2011) Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo.''Cell'' '''147''':1295-308
|-
!align=left |Abstract
||
As nascent polypeptides exit ribosomes, they are engaged by a series of processing, targeting, and folding factors. Here, we present a selective ribosome profiling strategy that enables global monitoring of when these factors engage polypeptides in the complex cellular environment. Studies of the Escherichia coli chaperone trigger factor (TF) reveal that, though TF can interact with many polypeptides, β-barrel outer-membrane proteins are the most prominent substrates. Loss of TF leads to broad outer-membrane defects and premature, cotranslational protein translocation. Whereas in vitro studies suggested that TF is prebound to ribosomes waiting for polypeptides to emerge from the exit channel, we find that in vivo TF engages ribosomes only after ~100 amino acids are translated. Moreover, excess TF interferes with cotranslational removal of the N-terminal formyl methionine. Our studies support a triaging model in which proper protein biogenesis relies on the fine-tuned, sequential engagement of processing, targeting, and folding factors.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22153074 PubMed]
Online version:[http://dx.doi.org/10.1016/j.cell.2011.10.044 10.1016/j.cell.2011.10.044]
 Raw Data from Authors: [http://heptamer.tamu.edu/gbrowse2/Public/BW2952/22153074/Ribosomal_Profiling_non-normalized_Wiggle.zip Ribosome Profiling non-normalized Wiggles]
|-
!align=left |Keywords
||
Cytoplasm; Escherichia coli; Escherichia coli Proteins; Membrane Proteins; Molecular Chaperones; Molecular Sequence Data; Peptidylprolyl Isomerase; Protein Biosynthesis; Protein Transport; Ribosomes

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181070.W4f8607bbb0ead&page=181070&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

:* Extended Ribosome Profiling to prokaryotes to enable the analysis of both translation and co-translational processes (such as Trigger Factor) that promote maturation of nascent polypeptides.

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

:* Four distinct steps (1) generation of cell extracts, in which ribosomes have been halted along the mRNA that they are translating; (2) treatment of polysomes with nuclease to remove regions of the message not protected by the ribosomes; (3) conversion of these RNA fragments into double stranded DNA copies and (4) analysis of these fragments by high throughput sequencing.

===EcoliWiki data manipulation===

:* Non-normalized wiggle files were sent from Eugene Oh; three replicates of dithiobis succinimidyl propionate (DSP) affinity purified (AP) for the forward strand, three replicates of DSP AP reverse strand, three replicates of the total ribosome profile for the forward strand, three replicates for the total profile of the reverse strand, one replicate each of 1-ethyl-3-[3-dimethylaminopropyl]carbodiimide (EDC) AP forward and reverse strand, and one replicate each of EDC total ribosome profile forward and reverse strand. Replicates data sets were normalized by dividing all read values by the highest read value within each data set. After normalization, replicates were then averaged together. EDC replicates were normalized in the same manner, but not averaged due to only one replicate.

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="P4f8607bbc5687" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181070.P4f8607bbc5687&page=181070&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==
* [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33671 GEO GSE33671]

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]

PMID:22082910

2013-05-28T20:09:52Z

Johnlew: /* References */

{{RightTOC}}


{| id="G4f8032d44ba77" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Cho, BK, Federowicz, S, Park, YS, Zengler, K and Palsson, BØ''' (2012) Deciphering the transcriptional regulatory logic of amino acid metabolism.''Nat. Chem. Biol.'' '''8''':65-71
|-
!align=left |Abstract
||
Although metabolic networks have been reconstructed on a genome scale, the corresponding reconstruction and integration of governing transcriptional regulatory networks has not been fully achieved. Here we reconstruct such an integrated network for amino acid metabolism in Escherichia coli. Analysis of ChIP-chip and gene expression data for the transcription factors ArgR, Lrp and TrpR showed that 19 out of 20 amino acid biosynthetic pathways are either directly or indirectly controlled by these regulators. Classifying the regulated genes into three functional categories of transport, biosynthesis and metabolism leads to the elucidation of regulatory motifs that constitute the integrated network's basic building blocks. The regulatory logic of these motifs was determined on the basis of relationships between transcription factor binding and changes in the amount of transcript in response to exogenous amino acids. Remarkably, the resulting logic shows how amino acids are differentiated as signaling and nutrient molecules, revealing the overarching regulatory principles of the amino acid stimulon.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22082910 PubMed]
Online version:[http://dx.doi.org/10.1038/nchembio.710 10.1038/nchembio.710]
|-
!align=left |Keywords
||
Amino Acids; Escherichia coli; Gene Expression Regulation; Genome-Wide Association Study; Transcription Factors; Transcription, Genetic

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181016.G4f8032d44ba77&page=181016&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="H4f8032dfcb937" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181016.H4f8032dfcb937&page=181016&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="R51a509670686a" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|

|

|

|

|

|

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181016.R51a509670686a&page=181016&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:22082910

2013-05-28T19:45:59Z

Johnlew: Table edited by Johnlew via TableEdit

PMID:22082910

2013-05-28T19:45:43Z

Johnlew: /* Data */

{{RightTOC}}


{| id="G4f8032d44ba77" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Cho, BK, Federowicz, S, Park, YS, Zengler, K and Palsson, BØ''' (2012) Deciphering the transcriptional regulatory logic of amino acid metabolism.''Nat. Chem. Biol.'' '''8''':65-71
|-
!align=left |Abstract
||
Although metabolic networks have been reconstructed on a genome scale, the corresponding reconstruction and integration of governing transcriptional regulatory networks has not been fully achieved. Here we reconstruct such an integrated network for amino acid metabolism in Escherichia coli. Analysis of ChIP-chip and gene expression data for the transcription factors ArgR, Lrp and TrpR showed that 19 out of 20 amino acid biosynthetic pathways are either directly or indirectly controlled by these regulators. Classifying the regulated genes into three functional categories of transport, biosynthesis and metabolism leads to the elucidation of regulatory motifs that constitute the integrated network's basic building blocks. The regulatory logic of these motifs was determined on the basis of relationships between transcription factor binding and changes in the amount of transcript in response to exogenous amino acids. Remarkably, the resulting logic shows how amino acids are differentiated as signaling and nutrient molecules, revealing the overarching regulatory principles of the amino acid stimulon.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22082910 PubMed]
Online version:[http://dx.doi.org/10.1038/nchembio.710 10.1038/nchembio.710]
|-
!align=left |Keywords
||
Amino Acids; Escherichia coli; Gene Expression Regulation; Genome-Wide Association Study; Transcription Factors; Transcription, Genetic

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181016.G4f8032d44ba77&page=181016&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="H4f8032dfcb937" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181016.H4f8032dfcb937&page=181016&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="R51a509670686a" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181016.R51a509670686a&page=181016&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]

PMID:22082910

2013-05-28T19:45:07Z

Johnlew: /* Annotations {{HelpIcon|Help:Literature}} */

{{RightTOC}}


{| id="G4f8032d44ba77" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Cho, BK, Federowicz, S, Park, YS, Zengler, K and Palsson, BØ''' (2012) Deciphering the transcriptional regulatory logic of amino acid metabolism.''Nat. Chem. Biol.'' '''8''':65-71
|-
!align=left |Abstract
||
Although metabolic networks have been reconstructed on a genome scale, the corresponding reconstruction and integration of governing transcriptional regulatory networks has not been fully achieved. Here we reconstruct such an integrated network for amino acid metabolism in Escherichia coli. Analysis of ChIP-chip and gene expression data for the transcription factors ArgR, Lrp and TrpR showed that 19 out of 20 amino acid biosynthetic pathways are either directly or indirectly controlled by these regulators. Classifying the regulated genes into three functional categories of transport, biosynthesis and metabolism leads to the elucidation of regulatory motifs that constitute the integrated network's basic building blocks. The regulatory logic of these motifs was determined on the basis of relationships between transcription factor binding and changes in the amount of transcript in response to exogenous amino acids. Remarkably, the resulting logic shows how amino acids are differentiated as signaling and nutrient molecules, revealing the overarching regulatory principles of the amino acid stimulon.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22082910 PubMed]
Online version:[http://dx.doi.org/10.1038/nchembio.710 10.1038/nchembio.710]
|-
!align=left |Keywords
||
Amino Acids; Escherichia coli; Gene Expression Regulation; Genome-Wide Association Study; Transcription Factors; Transcription, Genetic

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181016.G4f8032d44ba77&page=181016&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="H4f8032dfcb937" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181016.H4f8032dfcb937&page=181016&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]

PMID:21572102

2013-05-28T19:39:10Z

Johnlew: Table edited by Johnlew via TableEdit

{{RightTOC}} [[Category:Expression data]]


{| id="D4f91a308b1e7c" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Cho, BK, Federowicz, SA, Embree, M, Park, YS, Kim, D and Palsson, BØ''' (2011) The PurR regulon in Escherichia coli K-12 MG1655.''Nucleic Acids Res.'' '''39''':6456-64
|-
!align=left |Abstract
||
The PurR transcription factor plays a critical role in transcriptional regulation of purine metabolism in enterobacteria. Here, we elucidate the role of PurR under exogenous adenine stimulation at the genome-scale using high-resolution chromatin immunoprecipitation (ChIP)-chip and gene expression data obtained under in vivo conditions. Analysis of microarray data revealed that adenine stimulation led to changes in transcript level of about 10% of Escherichia coli genes, including the purine biosynthesis pathway. The E. coli strain lacking the purR gene showed that a total of 56 genes are affected by the deletion. From the ChIP-chip analysis, we determined that over 73% of genes directly regulated by PurR were enriched in the biosynthesis, utilization and transport of purine and pyrimidine nucleotides, and 20% of them were functionally unknown. Compared to the functional diversity of the regulon of the other general transcription factors in E. coli, the functions and size of the PurR regulon are limited.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21572102 PubMed]
Online version:[http://dx.doi.org/10.1093/nar/gkr307 10.1093/nar/gkr307]
|-
!align=left |Keywords
||
Adenine; Binding Sites; Chromatin Immunoprecipitation; Escherichia coli K12; Escherichia coli Proteins; Gene Deletion; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Genome, Bacterial; Hypoxanthine; Metabolic Networks and Pathways; Regulon; Repressor Proteins

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181648.D4f91a308b1e7c&page=181648&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="W4f91a309407cd" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181648.W4f91a309407cd&page=181648&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="X51a50533dcd77" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
PurR
|
Adenine, Glucose
|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=PurR_Cho

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181648.X51a50533dcd77&page=181648&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]

PMID:21572102

2013-05-28T19:27:47Z

Johnlew: /* Data */

{{RightTOC}} [[Category:Expression data]]


{| id="D4f91a308b1e7c" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Cho, BK, Federowicz, SA, Embree, M, Park, YS, Kim, D and Palsson, BØ''' (2011) The PurR regulon in Escherichia coli K-12 MG1655.''Nucleic Acids Res.'' '''39''':6456-64
|-
!align=left |Abstract
||
The PurR transcription factor plays a critical role in transcriptional regulation of purine metabolism in enterobacteria. Here, we elucidate the role of PurR under exogenous adenine stimulation at the genome-scale using high-resolution chromatin immunoprecipitation (ChIP)-chip and gene expression data obtained under in vivo conditions. Analysis of microarray data revealed that adenine stimulation led to changes in transcript level of about 10% of Escherichia coli genes, including the purine biosynthesis pathway. The E. coli strain lacking the purR gene showed that a total of 56 genes are affected by the deletion. From the ChIP-chip analysis, we determined that over 73% of genes directly regulated by PurR were enriched in the biosynthesis, utilization and transport of purine and pyrimidine nucleotides, and 20% of them were functionally unknown. Compared to the functional diversity of the regulon of the other general transcription factors in E. coli, the functions and size of the PurR regulon are limited.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21572102 PubMed]
Online version:[http://dx.doi.org/10.1093/nar/gkr307 10.1093/nar/gkr307]
|-
!align=left |Keywords
||
Adenine; Binding Sites; Chromatin Immunoprecipitation; Escherichia coli K12; Escherichia coli Proteins; Gene Deletion; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Genome, Bacterial; Hypoxanthine; Metabolic Networks and Pathways; Regulon; Repressor Proteins

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181648.D4f91a308b1e7c&page=181648&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="W4f91a309407cd" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181648.W4f91a309407cd&page=181648&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="X51a50533dcd77" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181648.X51a50533dcd77&page=181648&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]

PMID:21572102

2013-05-28T19:27:00Z

Johnlew: /* Annotations {{HelpIcon|Help:Literature}} */

{{RightTOC}} [[Category:Expression data]]


{| id="D4f91a308b1e7c" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Cho, BK, Federowicz, SA, Embree, M, Park, YS, Kim, D and Palsson, BØ''' (2011) The PurR regulon in Escherichia coli K-12 MG1655.''Nucleic Acids Res.'' '''39''':6456-64
|-
!align=left |Abstract
||
The PurR transcription factor plays a critical role in transcriptional regulation of purine metabolism in enterobacteria. Here, we elucidate the role of PurR under exogenous adenine stimulation at the genome-scale using high-resolution chromatin immunoprecipitation (ChIP)-chip and gene expression data obtained under in vivo conditions. Analysis of microarray data revealed that adenine stimulation led to changes in transcript level of about 10% of Escherichia coli genes, including the purine biosynthesis pathway. The E. coli strain lacking the purR gene showed that a total of 56 genes are affected by the deletion. From the ChIP-chip analysis, we determined that over 73% of genes directly regulated by PurR were enriched in the biosynthesis, utilization and transport of purine and pyrimidine nucleotides, and 20% of them were functionally unknown. Compared to the functional diversity of the regulon of the other general transcription factors in E. coli, the functions and size of the PurR regulon are limited.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21572102 PubMed]
Online version:[http://dx.doi.org/10.1093/nar/gkr307 10.1093/nar/gkr307]
|-
!align=left |Keywords
||
Adenine; Binding Sites; Chromatin Immunoprecipitation; Escherichia coli K12; Escherichia coli Proteins; Gene Deletion; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Genome, Bacterial; Hypoxanthine; Metabolic Networks and Pathways; Regulon; Repressor Proteins

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181648.D4f91a308b1e7c&page=181648&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| id="W4f91a309407cd" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.181648.W4f91a309407cd&page=181648&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]

PMID:21097887

2013-05-28T19:25:11Z

Johnlew: /* Data */

{{RightTOC}}


{| id="M5125381f8a945" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Kahramanoglou, C , Seshasayee, AS , Prieto, AI , Ibberson, D , Schmidt, S , Zimmermann, J , Benes, V , Fraser, GM and Luscombe, NM ''' (2011) Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. ''Nucleic Acids Res.'' '''39''':2073-91
|-
!align=left |Abstract
||
Nucleoid-associated proteins (NAPs) are global regulators of gene expression in Escherichia coli, which affect DNA conformation by bending, wrapping and bridging the DNA. Two of these--H-NS and Fis--bind to specific DNA sequences and structures. Because of their importance to global gene expression, the binding of these NAPs to the DNA was previously investigated on a genome-wide scale using ChIP-chip. However, variation in their binding profiles across the growth phase and the genome-scale nature of their impact on gene expression remain poorly understood. Here, we present a genome-scale investigation of H-NS and Fis binding to the E. coli chromosome using chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-seq). By performing our experiments under multiple time-points during growth in rich media, we show that the binding regions of the two proteins are mutually exclusive under our experimental conditions. H-NS binds to significantly longer tracts of DNA than Fis, consistent with the linear spread of H-NS binding from high- to surrounding lower-affinity sites; the length of binding regions is associated with the degree of transcriptional repression imposed by H-NS. For Fis, a majority of binding events do not lead to differential expression of the proximal gene; however, it has a significant indirect effect on gene expression partly through its effects on the expression of other transcription factors. We propose that direct transcriptional regulation by Fis is associated with the interaction of tandem arrays of Fis molecules to the DNA and possible DNA bending, particularly at operon-upstream regions. Our study serves as a proof-of-principle for the use of ChIP-seq for global DNA-binding proteins in bacteria, which should become significantly more economical and feasible with the development of multiplexing techniques.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21097887 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064808 PMC3064808]
Online version:[http://dx.doi.org/10.1093/nar/gkq934 10.1093/nar/gkq934]
|-
!align=left |Keywords
||
Binding Sites; Chromosomes, Bacterial/metabolism; DNA, Bacterial/chemistry; DNA, Bacterial/metabolism; Escherichia coli/genetics; Escherichia coli/growth & development; Escherichia coli/metabolism; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Factor For Inversion Stimulation Protein/genetics; Factor For Inversion Stimulation Protein/metabolism; Fimbriae Proteins/genetics; Fimbriae Proteins/metabolism; Gene Deletion; Gene Expression Regulation, Bacterial; Transcription, Genetic

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182919.M5125381f8a945&page=182919&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="O5125382002614" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182919.O5125382002614&page=182919&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="C519fb333edb69" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-seq
|
Fis
|
early and mid exponential phase.
|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Fis21097887
|-
|
MG1655
|
ChIP-seq
|
Hns
|
Early exponential, mid exponential, stationary, transition-to-stationary
|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Hns21097887
|-
|
MG1655
|
ChIP-seq
|
RNAP
|
Deletion Fis mid-exponential phase, deletion Hns mid-exponential phase, wildtype mid-exponential phase.
|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Rpo21097887

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182919.C519fb333edb69&page=182919&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]

[[Category:RNA_polymerase_tracks]]

PMID:21097887

2013-05-28T19:24:57Z

Johnlew: /* EcoliWiki Links {{HelpIcon|Help:Literature}} */

{{RightTOC}}


{| id="M5125381f8a945" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Kahramanoglou, C , Seshasayee, AS , Prieto, AI , Ibberson, D , Schmidt, S , Zimmermann, J , Benes, V , Fraser, GM and Luscombe, NM ''' (2011) Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. ''Nucleic Acids Res.'' '''39''':2073-91
|-
!align=left |Abstract
||
Nucleoid-associated proteins (NAPs) are global regulators of gene expression in Escherichia coli, which affect DNA conformation by bending, wrapping and bridging the DNA. Two of these--H-NS and Fis--bind to specific DNA sequences and structures. Because of their importance to global gene expression, the binding of these NAPs to the DNA was previously investigated on a genome-wide scale using ChIP-chip. However, variation in their binding profiles across the growth phase and the genome-scale nature of their impact on gene expression remain poorly understood. Here, we present a genome-scale investigation of H-NS and Fis binding to the E. coli chromosome using chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-seq). By performing our experiments under multiple time-points during growth in rich media, we show that the binding regions of the two proteins are mutually exclusive under our experimental conditions. H-NS binds to significantly longer tracts of DNA than Fis, consistent with the linear spread of H-NS binding from high- to surrounding lower-affinity sites; the length of binding regions is associated with the degree of transcriptional repression imposed by H-NS. For Fis, a majority of binding events do not lead to differential expression of the proximal gene; however, it has a significant indirect effect on gene expression partly through its effects on the expression of other transcription factors. We propose that direct transcriptional regulation by Fis is associated with the interaction of tandem arrays of Fis molecules to the DNA and possible DNA bending, particularly at operon-upstream regions. Our study serves as a proof-of-principle for the use of ChIP-seq for global DNA-binding proteins in bacteria, which should become significantly more economical and feasible with the development of multiplexing techniques.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21097887 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064808 PMC3064808]
Online version:[http://dx.doi.org/10.1093/nar/gkq934 10.1093/nar/gkq934]
|-
!align=left |Keywords
||
Binding Sites; Chromosomes, Bacterial/metabolism; DNA, Bacterial/chemistry; DNA, Bacterial/metabolism; Escherichia coli/genetics; Escherichia coli/growth & development; Escherichia coli/metabolism; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Factor For Inversion Stimulation Protein/genetics; Factor For Inversion Stimulation Protein/metabolism; Fimbriae Proteins/genetics; Fimbriae Proteins/metabolism; Gene Deletion; Gene Expression Regulation, Bacterial; Transcription, Genetic

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182919.M5125381f8a945&page=182919&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="O5125382002614" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182919.O5125382002614&page=182919&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="C519fb333edb69" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-seq
|
Fis
|
early and mid exponential phase.
|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Fis21097887
|-
|
MG1655
|
ChIP-seq
|
Hns
|
Early exponential, mid exponential, stationary, transition-to-stationary
|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Hns21097887
|-
|
MG1655
|
ChIP-seq
|
RNAP
|
Deletion Fis mid-exponential phase, deletion Hns mid-exponential phase, wildtype mid-exponential phase.
|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Rpo21097887

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182919.C519fb333edb69&page=182919&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>
==See also==

==References==
{{RefHelp}}
<references/>

[[Category:Papers with tracks in Gbrowse]]

[[Category:RNA_polymerase_tracks]]

PMID:20689753

2013-05-28T19:23:09Z

Johnlew: /* EcoliWiki Links {{HelpIcon|Help:Literature}} */

{{RightTOC}}


{| id="O5110505532e46" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Sánchez-Romero, MA , Busby, SJ , Dyer, NP , Ott, S , Millard, AD and Grainger, DC ''' (2010) Dynamic distribution of seqa protein across the chromosome of escherichia coli K-12. ''MBio'' '''1'''
|-
!align=left |Abstract
||
The bacterial SeqA protein binds to hemi-methylated GATC sequences that arise in newly synthesized DNA upon passage of the replication machinery. In Escherichia coli K-12, the single replication origin oriC is a well-characterized target for SeqA, which binds to multiple hemi-methylated GATC sequences immediately after replication has initiated. This sequesters oriC, thereby preventing reinitiation of replication. However, the genome-wide DNA binding properties of SeqA are unknown, and hence, here, we describe a study of the binding of SeqA across the entire Escherichia coli K-12 chromosome, using chromatin immunoprecipitation in combination with DNA microarrays. Our data show that SeqA binding correlates with the frequency and spacing of GATC sequences across the entire genome. Less SeqA is found in highly transcribed regions, as well as in the ter macrodomain. Using synchronized cultures, we show that SeqA distribution differs with the cell cycle. SeqA remains bound to some targets after replication has ceased, and these targets locate to genes encoding factors involved in nucleotide metabolism, chromosome replication, and methyl transfer.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20689753 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912659 PMC2912659]
Online version:[http://dx.doi.org/10.1128/mBio.00012-10 10.1128/mBio.00012-10]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.O5110505532e46&page=182904&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="O5110505579ecb" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.O5110505579ecb&page=182904&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="N519f9885e1384" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
SeqA
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SeqA_Bigwig_density&t=SeqA_Bigwig

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.N519f9885e1384&page=182904&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[Category:Papers with tracks in Gbrowse]]
[[Category:High-Throughput Papers]]

PMID:20689753

2013-05-28T19:23:02Z

Johnlew: /* See also */

{{RightTOC}}


{| id="O5110505532e46" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Sánchez-Romero, MA , Busby, SJ , Dyer, NP , Ott, S , Millard, AD and Grainger, DC ''' (2010) Dynamic distribution of seqa protein across the chromosome of escherichia coli K-12. ''MBio'' '''1'''
|-
!align=left |Abstract
||
The bacterial SeqA protein binds to hemi-methylated GATC sequences that arise in newly synthesized DNA upon passage of the replication machinery. In Escherichia coli K-12, the single replication origin oriC is a well-characterized target for SeqA, which binds to multiple hemi-methylated GATC sequences immediately after replication has initiated. This sequesters oriC, thereby preventing reinitiation of replication. However, the genome-wide DNA binding properties of SeqA are unknown, and hence, here, we describe a study of the binding of SeqA across the entire Escherichia coli K-12 chromosome, using chromatin immunoprecipitation in combination with DNA microarrays. Our data show that SeqA binding correlates with the frequency and spacing of GATC sequences across the entire genome. Less SeqA is found in highly transcribed regions, as well as in the ter macrodomain. Using synchronized cultures, we show that SeqA distribution differs with the cell cycle. SeqA remains bound to some targets after replication has ceased, and these targets locate to genes encoding factors involved in nucleotide metabolism, chromosome replication, and methyl transfer.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20689753 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912659 PMC2912659]
Online version:[http://dx.doi.org/10.1128/mBio.00012-10 10.1128/mBio.00012-10]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.O5110505532e46&page=182904&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="O5110505579ecb" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.O5110505579ecb&page=182904&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="N519f9885e1384" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
SeqA
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SeqA_Bigwig_density&t=SeqA_Bigwig

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.N519f9885e1384&page=182904&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[Category:Papers with tracks in Gbrowse]]
[[Category:High-Throughput Papers]]

PMID:20689753

2013-05-28T19:22:55Z

Johnlew: /* EcoliWiki Links {{HelpIcon|Help:Literature}} */

{{RightTOC}}


{| id="O5110505532e46" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Sánchez-Romero, MA , Busby, SJ , Dyer, NP , Ott, S , Millard, AD and Grainger, DC ''' (2010) Dynamic distribution of seqa protein across the chromosome of escherichia coli K-12. ''MBio'' '''1'''
|-
!align=left |Abstract
||
The bacterial SeqA protein binds to hemi-methylated GATC sequences that arise in newly synthesized DNA upon passage of the replication machinery. In Escherichia coli K-12, the single replication origin oriC is a well-characterized target for SeqA, which binds to multiple hemi-methylated GATC sequences immediately after replication has initiated. This sequesters oriC, thereby preventing reinitiation of replication. However, the genome-wide DNA binding properties of SeqA are unknown, and hence, here, we describe a study of the binding of SeqA across the entire Escherichia coli K-12 chromosome, using chromatin immunoprecipitation in combination with DNA microarrays. Our data show that SeqA binding correlates with the frequency and spacing of GATC sequences across the entire genome. Less SeqA is found in highly transcribed regions, as well as in the ter macrodomain. Using synchronized cultures, we show that SeqA distribution differs with the cell cycle. SeqA remains bound to some targets after replication has ceased, and these targets locate to genes encoding factors involved in nucleotide metabolism, chromosome replication, and methyl transfer.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20689753 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912659 PMC2912659]
Online version:[http://dx.doi.org/10.1128/mBio.00012-10 10.1128/mBio.00012-10]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.O5110505532e46&page=182904&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="O5110505579ecb" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.O5110505579ecb&page=182904&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="N519f9885e1384" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
SeqA
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SeqA_Bigwig_density&t=SeqA_Bigwig

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.N519f9885e1384&page=182904&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[Category:Papers with tracks in Gbrowse]]
[[Category:High-Throughput Papers]]

PMID:20689753

2013-05-28T19:22:35Z

Johnlew: /* Data */

{{RightTOC}}


{| id="O5110505532e46" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Sánchez-Romero, MA , Busby, SJ , Dyer, NP , Ott, S , Millard, AD and Grainger, DC ''' (2010) Dynamic distribution of seqa protein across the chromosome of escherichia coli K-12. ''MBio'' '''1'''
|-
!align=left |Abstract
||
The bacterial SeqA protein binds to hemi-methylated GATC sequences that arise in newly synthesized DNA upon passage of the replication machinery. In Escherichia coli K-12, the single replication origin oriC is a well-characterized target for SeqA, which binds to multiple hemi-methylated GATC sequences immediately after replication has initiated. This sequesters oriC, thereby preventing reinitiation of replication. However, the genome-wide DNA binding properties of SeqA are unknown, and hence, here, we describe a study of the binding of SeqA across the entire Escherichia coli K-12 chromosome, using chromatin immunoprecipitation in combination with DNA microarrays. Our data show that SeqA binding correlates with the frequency and spacing of GATC sequences across the entire genome. Less SeqA is found in highly transcribed regions, as well as in the ter macrodomain. Using synchronized cultures, we show that SeqA distribution differs with the cell cycle. SeqA remains bound to some targets after replication has ceased, and these targets locate to genes encoding factors involved in nucleotide metabolism, chromosome replication, and methyl transfer.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20689753 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912659 PMC2912659]
Online version:[http://dx.doi.org/10.1128/mBio.00012-10 10.1128/mBio.00012-10]
|-
!align=left |Keywords
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.O5110505532e46&page=182904&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="O5110505579ecb" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.O5110505579ecb&page=182904&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==Data==

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="N519f9885e1384" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
SeqA
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SeqA_Bigwig_density&t=SeqA_Bigwig

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182904.N519f9885e1384&page=182904&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==References==
{{RefHelp}}
<references/>
[[Category:Papers with tracks in Gbrowse]]
[[Category:High-Throughput Papers]]

PMID:16963779

2013-05-28T19:16:21Z

Johnlew: /* See also */

{{RightTOC}}


{| id="B512d848714402" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Grainger, DC , Hurd, D , Goldberg, MD and Busby, SJ ''' (2006) Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. ''Nucleic Acids Res.'' '''34''':4642-52
|-
!align=left |Abstract
||
The Escherichia coli chromosome is condensed into an ill-defined structure known as the nucleoid. Nucleoid-associated DNA-binding proteins are involved in maintaining this structure and in mediating chromosome compaction. We have exploited chromatin immunoprecipitation and high-density microarrays to study the binding of three such proteins, FIS, H-NS and IHF, across the E.coli genome in vivo. Our results show that the distribution of these proteins is biased to intergenic parts of the genome, and that the binding profiles overlap. Hence some targets are associated with combinations of bound FIS, H-NS and IHF. In addition, many regions associated with FIS and H-NS are also associated with RNA polymerase.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16963779 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636352 PMC1636352]
Online version:[http://dx.doi.org/10.1093/nar/gkl542 10.1093/nar/gkl542]
;Data tracks
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/FIS.gff3 FIS.gff3 12K]
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/H-NS/HNS.gff3 H-NS.gff3 8K]
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/IHF/IHF.gff3 IHF.gff3 8K]
|-
!align=left |Keywords
||
Bacterial Proteins/metabolism; Binding Sites; Chromatin Immunoprecipitation; Chromosomes, Bacterial; DNA, Bacterial/metabolism; DNA, Intergenic/metabolism; DNA-Binding Proteins/isolation & purification; DNA-Binding Proteins/metabolism; DNA-Directed RNA Polymerases/metabolism; Escherichia coli/genetics; Escherichia coli Proteins/isolation & purification; Escherichia coli Proteins/metabolism; Factor For Inversion Stimulation Protein; Genome, Bacterial; Integration Host Factors/metabolism; Oligonucleotide Array Sequence Analysis; Transcription Factors/metabolism; Transcription, Genetic

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.B512d848714402&page=182924&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="J512d848771fec" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.J512d848771fec&page=182924&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==Data==

<protect></protect>

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="T519d0fd60cf30" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
FIS
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_FIS_density&t=Nucleoid_Protein_FIS_xy
|-
|
MG1655
|
ChIP-chip
|
H-NS
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_HNS_density&t=Nucleoid_Protein_HNS_xy
|-
|
MG1655
|
ChIP-chip
|
IHF
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_IHF_density&t=Nucleoid_Protein_IHF_xy

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.T519d0fd60cf30&page=182924&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[Category:Papers_with_tracks_in_Gbrowse]]

PMID:16963779

2013-05-28T19:16:13Z

Johnlew: /* EcoliWiki Links {{HelpIcon|Help:Literature}} */

{{RightTOC}}


{| id="B512d848714402" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Grainger, DC , Hurd, D , Goldberg, MD and Busby, SJ ''' (2006) Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. ''Nucleic Acids Res.'' '''34''':4642-52
|-
!align=left |Abstract
||
The Escherichia coli chromosome is condensed into an ill-defined structure known as the nucleoid. Nucleoid-associated DNA-binding proteins are involved in maintaining this structure and in mediating chromosome compaction. We have exploited chromatin immunoprecipitation and high-density microarrays to study the binding of three such proteins, FIS, H-NS and IHF, across the E.coli genome in vivo. Our results show that the distribution of these proteins is biased to intergenic parts of the genome, and that the binding profiles overlap. Hence some targets are associated with combinations of bound FIS, H-NS and IHF. In addition, many regions associated with FIS and H-NS are also associated with RNA polymerase.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16963779 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636352 PMC1636352]
Online version:[http://dx.doi.org/10.1093/nar/gkl542 10.1093/nar/gkl542]
;Data tracks
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/FIS.gff3 FIS.gff3 12K]
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/H-NS/HNS.gff3 H-NS.gff3 8K]
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/IHF/IHF.gff3 IHF.gff3 8K]
|-
!align=left |Keywords
||
Bacterial Proteins/metabolism; Binding Sites; Chromatin Immunoprecipitation; Chromosomes, Bacterial; DNA, Bacterial/metabolism; DNA, Intergenic/metabolism; DNA-Binding Proteins/isolation & purification; DNA-Binding Proteins/metabolism; DNA-Directed RNA Polymerases/metabolism; Escherichia coli/genetics; Escherichia coli Proteins/isolation & purification; Escherichia coli Proteins/metabolism; Factor For Inversion Stimulation Protein; Genome, Bacterial; Integration Host Factors/metabolism; Oligonucleotide Array Sequence Analysis; Transcription Factors/metabolism; Transcription, Genetic

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.B512d848714402&page=182924&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="J512d848771fec" class=" tableEdit GO_table_reference dataTable"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.J512d848771fec&page=182924&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==See also==

==Data==

<protect></protect>

<protect>

{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="T519d0fd60cf30" class=" tableEdit Gbrowse_table"
|-
!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
|-
|
MG1655
|
ChIP-chip
|
FIS
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_FIS_density&t=Nucleoid_Protein_FIS_xy
|-
|
MG1655
|
ChIP-chip
|
H-NS
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_HNS_density&t=Nucleoid_Protein_HNS_xy
|-
|
MG1655
|
ChIP-chip
|
IHF
|

|

|
http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_IHF_density&t=Nucleoid_Protein_IHF_xy

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182924.T519d0fd60cf30&page=182924&pagename={{FULLPAGENAMEE}}&type=0&template=Gbrowse_table edit table] || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[Category:Papers_with_tracks_in_Gbrowse]]

PMID:16963779

2013-05-28T19:16:04Z

Johnlew: /* References */

{{RightTOC}}


{| id="B512d848714402" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Grainger, DC , Hurd, D , Goldberg, MD and Busby, SJ ''' (2006) Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. ''Nucleic Acids Res.'' '''34''':4642-52
|-
!align=left |Abstract
||
The Escherichia coli chromosome is condensed into an ill-defined structure known as the nucleoid. Nucleoid-associated DNA-binding proteins are involved in maintaining this structure and in mediating chromosome compaction. We have exploited chromatin immunoprecipitation and high-density microarrays to study the binding of three such proteins, FIS, H-NS and IHF, across the E.coli genome in vivo. Our results show that the distribution of these proteins is biased to intergenic parts of the genome, and that the binding profiles overlap. Hence some targets are associated with combinations of bound FIS, H-NS and IHF. In addition, many regions associated with FIS and H-NS are also associated with RNA polymerase.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16963779 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636352 PMC1636352]
Online version:[http://dx.doi.org/10.1093/nar/gkl542 10.1093/nar/gkl542]
;Data tracks
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/FIS/FIS.gff3 FIS.gff3 12K]
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/H-NS/HNS.gff3 H-NS.gff3 8K]
* [http://heptamer.tamu.edu/gbrowse2/Public/MG1655/16963779/IHF/IHF.gff3 IHF.gff3 8K]
|-
!align=left |Keywords
||
Bacterial Proteins/metabolism; Binding Sites; Chromatin Immunoprecipitation; Chromosomes, Bacterial; DNA, Bacterial/metabolism; DNA, Intergenic/metabolism; DNA-Binding Proteins/isolation & purification; DNA-Binding Proteins/metabolism; DNA-Directed RNA Polymerases/metabolism; Escherichia coli/genetics; Escherichia coli Proteins/isolation & purification; Escherichia coli Proteins/metabolism; Factor For Inversion Stimulation Protein; Genome, Bacterial; Integration Host Factors/metabolism; Oligonucleotide Array Sequence Analysis; Transcription Factors/metabolism; Transcription, Genetic

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==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
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!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

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==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==Data==

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<protect>

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!|Strain/Organism!!Assay!!Analyte!!Variable Conditions!!Notes!!Links
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MG1655
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ChIP-chip
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FIS
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http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_FIS_density&t=Nucleoid_Protein_FIS_xy
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MG1655
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ChIP-chip
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H-NS
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http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_HNS_density&t=Nucleoid_Protein_HNS_xy
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MG1655
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ChIP-chip
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IHF
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http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_IHF_density&t=Nucleoid_Protein_IHF_xy

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==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>
[[Category:Papers_with_tracks_in_Gbrowse]]