PMID:16963779: Difference between revisions

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'''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
'''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
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!align=left  |Abstract
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[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]
[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]
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]
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==Significance {{HelpIcon|Help:Literature}} ==
==Significance {{HelpIcon|Help:Literature}} ==
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==Annotations {{HelpIcon|Help:Literature}}==
==Annotations {{HelpIcon|Help:Literature}}==
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==See also==
 
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==Data==
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http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_FIS_density&t=Nucleoid_Protein_FIS_xy  
*[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]
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http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_HNS_density&t=Nucleoid_Protein_HNS_xy  
*[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]
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http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Nucleoid_Protein_IHF_density&t=Nucleoid_Protein_IHF_xy  
*[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]


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[[Category:Papers_with_tracks_in_Gbrowse]]
[[Category:Papers_with_tracks_in_Gbrowse]]
[[Category:ChIP-chip experiments]]

Latest revision as of 04:30, 15 September 2013

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

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.

Links

PubMed PMC1636352 Online version:10.1093/nar/gkl542

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

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Useful Materials and Methods

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Annotations

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Data


Strain/Organism Assay Analyte Variable Conditions Notes Links

MG1655

ChIP-chip

FIS

MG1655

ChIP-chip

H-NS

MG1655

ChIP-chip

IHF

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References

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