PMID:20689753: Difference between revisions

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!align=left  |Citation
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'''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'''
'''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'''
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!align=left  |Abstract
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==Significance {{HelpIcon|Help:Literature}} ==
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}
{{LitSignificance}}
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==Annotations {{HelpIcon|Help:Literature}}==
==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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==Data==
==Data==
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SeqA
SeqA
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dnaC(ts) at 30°ree;C
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*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SeqA_Bigwig_density&t=SeqA_Bigwig Gbrowse]
*[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]
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MG1655
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ChIP-chip
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SeqA
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dnaC(ts) at 42°ree;C for 1 hour; replication ceased
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*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SeqA_Bigwig_density&t=SeqA_Bigwig Gbrowse]
*[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]
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MG1655
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ChIP-chip
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SeqA
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dnaC(ts) at 42°ree;C for 1 hour; shifted back to 30°ree;C for 6 min; synchronized initiation of replication
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:*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SeqA_Bigwig_density&t=SeqA_Bigwig SeqA Gbrowse Track]
*[http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=SeqA_Bigwig_density&t=SeqA_Bigwig Gbrowse]
:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/SeqA/SeqAtimeA.gff3 SeqAtimeA.gff3]
*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/SeqA/20689753.seqA.tC.gff timeC gff]  
:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/SeqA/SeqAtimeB.gff3 SeqAtimeB.gff3]
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:*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/SeqA/SeqAtimeC.gff3 SeqAtimeC.gff3]  
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MG1655
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ChIP-chip
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RNAP
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dnaC(ts) at 30°C for 1 hour; shifted back to 30°C for 6 min; synchronized initiation of replication
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*[http://heptamer.tamu.edu/gbrowse2/Public/MG1655/20689753/RNAp/20689753.rnap.tC.gff timeC gff]  


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==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
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[[Category:Papers with tracks in Gbrowse]]
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[[Category:High-Throughput Papers]]
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[[Category:ChIP-chip experiments]]

Latest revision as of 22:29, 31 October 2013

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

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.

Links

PubMed PMC2912659 Online version:10.1128/mBio.00012-10

Keywords


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Significance

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Annotations

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Data

Strain/Organism Assay Analyte Variable Conditions Notes Links

MG1655

ChIP-chip

SeqA

dnaC(ts) at 30°ree;C

MG1655

ChIP-chip

SeqA

dnaC(ts) at 42°ree;C for 1 hour; replication ceased

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

MG1655

ChIP-chip

RNAP

dnaC(ts) at 30°C for 1 hour; shifted back to 30°C for 6 min; synchronized initiation of replication

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