SeqA Chip-chip analysis of E. coli MG1655 and derivatives
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ABSTRACT:
PROVIDER: PRJNA139379 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Chromosomes are composed of enormously long DNA molecules which must be distributed correctly as the cells grow and divide. In Escherichia coli the new DNA behind the replication forks is specifically bound by the SeqA protein. SeqA binds to GATC sequences which are methylated on the A of the old strand but not on the new strand. Binding lasts for a period of time until Dam methyltransferase methylates the new strand. It is therefore believed that a region of hemi-methylated DNA covered by SeqA follows the replication fork. We show that this is indeed the case by using global ChIP on Chip analysis and a newly developed method for methylation analysis. A comparison of rapid and slow growth conditions showed that in cells with multiple replication forks per chromosome, the old forks bind little SeqA. Analysis of strains with strong SeqA binding sites at different chromosomal loci supported this finding. The results indicate that a re-organization of the chromosome occurs at a timepoint when new forks have travelled about 20% and old forks about 75% of the way to the terminus. This timepoint coincides with the end of origin sequestration. It is so far not known what brings about the end of origin sequestration. Here we suggest that a reorganization event occurs resulting in both origin desequestration and loss of old replication forks from the SeqA structures. SeqA ChIP-Chip analysis of unsynchronized E. coli MG1655 and in cells synchronized regarding initiation of DNA replication; SeqA ChIP-Chip of Dam overproducing strain and SeqA4 mutant; SeqA ChIP-Chip of strains with chromosomal insertions of strong SeqA binding site. Methylation analysis of synchronized E. coli MG1655dnaC2 cells 0 and 15 min after initiation.
2012-02-22 | E-GEOD-28280 | biostudies-arrayexpress
Project description:Mapping the occupancy of ArcA throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anaerobic and aerobic growth conditions. As a control, we also performed ChIP-chip onArcA in a ∆arcA mutant strain of Escherchia coli MG1655 K-12. Described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli
2013-10-17 | GSE46413 | GEO
Project description:Mapping the occupancy of FNR, HNS, and IHF throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anerobic growth conditions. We also mapped the binding of the ß subunit of RNA Polymerase under both aerobic and anaerobic growth conditions. As a control, we also performed ChIP-chip on FNR in a ∆fnr mutant strain of Escherchia coli MG1655 K-12. We also examined FNR immunoprecipitation at various FNR concentrations using IPTG and Ptac::fnr (PK8263). The ∆hns/∆stpA strains were also used. Descirbed in the manuscript Genome-scale Analysis of E. coli FNR Reveals the Complexity of Bacterial Regulon Structure
2013-06-20 | GSE41186 | GEO
Project description:We mapped the genome-wide binding of the flagellar regulators FlhD, FlhC, and FliA in FLAG-tagged derivatives of E. coli K-12 MG1655 using ChIP coupled with deep sequencing (ChIP-seq). We identify new binding sites for each factor.
2014-04-10 | E-MTAB-2457 | biostudies-arrayexpress
Project description:Expression profiling of wild type and purR deletion strains of E. coli K-12 MG1655 under both M9 minimal media and addition of adenine.
2011-06-14 | GSE26588 | GEO
Project description:Chromosomes are composed of enormously long DNA molecules which must be distributed correctly as the cells grow and divide. In Escherichia coli the new DNA behind the replication forks is specifically bound by the SeqA protein. SeqA binds to GATC sequences which are methylated on the A of the old strand but not on the new strand. Binding lasts for a period of time until Dam methyltransferase methylates the new strand. It is therefore believed that a region of hemi-methylated DNA covered by SeqA follows the replication fork. We show that this is indeed the case by using global ChIP on Chip analysis and a newly developed method for methylation analysis. A comparison of rapid and slow growth conditions showed that in cells with multiple replication forks per chromosome, the old forks bind little SeqA. Analysis of strains with strong SeqA binding sites at different chromosomal loci supported this finding. The results indicate that a re-organization of the chromosome occurs at a timepoint when new forks have travelled about 20% and old forks about 75% of the way to the terminus. This timepoint coincides with the end of origin sequestration. It is so far not known what brings about the end of origin sequestration. Here we suggest that a reorganization event occurs resulting in both origin desequestration and loss of old replication forks from the SeqA structures.
2012-02-22 | GSE28280 | GEO
Project description:We integrated RNAP binding regions (RBRs) and mRNA transcript abundance to determine segments of contiguous transcription originating from promoter regions. To measure RBRs at a genome scale, we employed a ChIP-chip method to E. coli K-12 MG1655 grown in the presence or absence of rifampicin under multiple growth conditions using antibody against E. coli RNAP beta subunit.
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Project description:Mapping the occupancy of FNR, HNS, and IHF throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anerobic growth conditions. We also mapped the binding of the M-CM-^_ subunit of RNA Polymerase under both aerobic and anaerobic growth conditions. As a control, we also performed ChIP-chip on FNR in a M-bM-^HM-^Ffnr mutant strain of Escherchia coli MG1655 K-12. We also examined FNR immunoprecipitation at various FNR concentrations using IPTG and Ptac::fnr (PK8263). The M-bM-^HM-^Fhns/M-bM-^HM-^FstpA strains were also used. Descirbed in the manuscript Genome-scale Analysis of E. coli FNR Reveals the Complexity of Bacterial Regulon Structure Mapping of occupancy of FNR, NNS, IHF and M-CM-^_ of RNAP in the genome of Escherchia coli MG1655 K-12 under aerobic or anaerobic growth conditions. Immunoprecipitated DNA compared to INPUT for each sample.
2013-06-20 | E-GEOD-41186 | biostudies-arrayexpress
Project description:Mapping the occupancy of ArcA throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anaerobic and aerobic growth conditions. As a control, we also performed ChIP-chip onArcA in a M-bM-^HM-^FarcA mutant strain of Escherchia coli MG1655 K-12. Described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli Mapping of occupancy of ArcA in the genome of Escherchia coli MG1655 K-12 during anaerobic fermentation and aerobic respiration. Immunoprecipitated DNA compared to INPUT for each sample.
2013-10-17 | E-GEOD-46413 | biostudies-arrayexpress
Project description:Expression profiling of wild type and purR deletion strains of E. coli K-12 MG1655 under both M9 minimal media and addition of adenine. An eight chip study with two different strains under two separate culture conditions.
2011-06-14 | E-GEOD-26588 | biostudies-arrayexpress