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Chip-chip from E. coli MG1655 cells with different methods to detect SeqA and σ32 binding and causes of high background

ABSTRACT: Reinvestigation of the chromatin immunoprecipitation procedure led us to discover four causes of high background: non-unique sequences, incomplete reversion of crosslinks, washing with spin-columns and insufficient RNase treatment. We used a publishd method giving a high background signal and a modified chromatin immunoprecipitation method which could greatly reduce the false positive rate and apply it to analyze genome wide binding of SeqA and σ32 binding in E. coli.

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

PROVIDER: GSE19053 | GEO | 2010/07/12

SECONDARY ACCESSION(S): PRJNA120553

REPOSITORIES: GEO

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Chip-chip from E. coli MG1655 cells with different methods to detect SeqA and σ32 binding and causes of high background

Project description:Reinvestigation of the chromatin immunoprecipitation procedure led us to discover four causes of high background: non-unique sequences, incomplete reversion of crosslinks, washing with spin-columns and insufficient RNase treatment. We used a publishd method giving a high background signal and a modified chromatin immunoprecipitation method which could greatly reduce the false positive rate and apply it to analyze genome wide binding of SeqA and σ32 binding in E. coli. RNA polymerase binding in wt E. coli MG1655 with old method (two biological relpicates); comparison of SeqA-binding to wt with old and modified method (two biological replicates each); comparison of SeqA-binding with old and modified method to E. coli ΔseqA (one array each); comparison of crosslinked/reversed to non crosslinked E. coli chrom. DNA; σ32 binding at 30°C and 43°C (two biological replicates each); σ32 binding at 30°C and 43°C with shortened RNase digestion during ChIP (one array each).

2010-07-12 | E-GEOD-19053 | biostudies-arrayexpress

Escherichia coli str. K-12 substr. MG1655

Project description:Chip-chip from E. coli MG1655 cells with different methods to detect SeqA and σ32 binding and causes of high background

| PRJNA120553 | ENA

SeqA Chip-chip analysis of E. coli MG1655 and derivatives

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

SeqA Chip-chip analysis of E. coli MG1655 and derivatives

2012-02-22 | E-GEOD-28280 | biostudies-arrayexpress

SPIN reveals genome-wide landscape of nuclear compartmentalization

Project description:We develop a new computational method called SPIN (Spatial Position Inference of the Nuclear genome) to identify genome-wide chromosome localization patterns relative to multiple nuclear compartments. SPIN states correlations with other features of genome structure and function, such as Hi-C subcompartments, TADs (Dixon et al., 2012; Nora et al., 2012), histone modification, and DNA replication timing.

2020-08-01 | GSE148362 | GEO

SeqA Chip-chip analysis of E. coli MG1655 and derivatives

Project description:SeqA Chip-chip analysis of E. coli MG1655 and derivatives

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Effects of culture conditions on epigenomic profiles of brain tumor cells

Project description:We performed epigenomic analysis of brain tumor cells that were collected from micro-engineered three-dimensional tumor models. We used a low-input epigenomic analysis method known as microfluidic-oscillatory-washing-based chromatin immunoprecipitation with sequencing (MOWChIP-seq) to analyze genome-wide histone modification (H3K4me3). We compared H3K4me3 patterns in standard 2D cultures and 3D cultures based on type I collagen hydrogels, under both normoxic and hypoxic conditions. Our work illustrates a direct connection between cell culture or tissue niche condition and genome-wide alterations in histone modification.

2019-02-01 | GSE113824 | GEO

A chromatin immunoprecipitation database for prokarytic organisms [E. coli K-12 MG1655 mixTF]

Project description:Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. Although rapidly accumulating publicly-available ChIP data are a valuable resource for the study of gene regulation, there are no full datasets of key regulators in E. coli K-12 MG1655. Here, we present the genome-wide binding for major TFs in the E. coli K-12 MG1655.

2021-08-17 | GSE182078 | GEO

A chromatin immunoprecipitation database for prokarytic organisms [E. coli K-12 MG1655 ArcA]

2021-08-17 | GSE182077 | GEO

DNA-Protein Crosslink sequencing (DPC-seq) in RPE-1 cells treated with formaldehyde

Project description:Covalent DNA-protein crosslinks (DPC) are toxic DNA lesions that require repair by global-genome and replication-coupled pathways. How cells respond when RNA polymerases stall at DPCs during transcription is unknown. DPC-seq is new method for the genome-wide mapping of covalent DNA-protein adducts.

2024-02-24 | E-MTAB-12912 | biostudies-arrayexpress

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