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Genome-wide expression profiling in 293T cells upon depletion of H1.2, Cul4A or PAF1

ABSTRACT: Increasing evidence suggests that linker histone H1 can influence distinct cellular processes by acting as a gene-specific regulator. However, the mechanistic basis underlying such H1 specificity and whether H1 acts in concert with other chromatin-altering activities remain unclear. To investigate the cooperative role of H1.2, Cul4A and PAF1 on gene regulation, genome-wide gene expression analysis is carried out in 293T cells expressing control shRNA, H1.2 shRNA, Cul4A shRNA or PAF1 shRNA.

ORGANISM(S): Homo sapiens

PROVIDER: GSE52544 | GEO | 2013/12/20

SECONDARY ACCESSION(S): PRJNA229182

REPOSITORIES: GEO

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Genome-wide expression profiling in 293T cells upon depletion of H1.2, Cul4A or PAF1

Project description:Increasing evidence suggests that linker histone H1 can influence distinct cellular processes by acting as a gene-specific regulator. However, the mechanistic basis underlying such H1 specificity and whether H1 acts in concert with other chromatin-altering activities remain unclear. To investigate the cooperative role of H1.2, Cul4A and PAF1 on gene regulation, genome-wide gene expression analysis is carried out in 293T cells expressing control shRNA, H1.2 shRNA, Cul4A shRNA or PAF1 shRNA. Total RNA was isolated from 293T cells expressing NCsh, H1.2sh, Cul4Ash, or PAF1sh

2013-12-20 | E-GEOD-52544 | biostudies-arrayexpress

Linker histone H1.2 establishes chromatin comapction and gene silencing through recognition of H3K27me3

Project description:Linker histone H1 is a protein component of chromatin and has been linked to chromatin compaction and global gene silencing.It has been sugegsted that H1 plays a significant role, regulating a relatively small number of genes. Here we show that H1.2- a variant of H1 subtype is recruited to chromatin region and is dependent on EZH2-mediated H3K27me3. Therefore a Gene expression array analysis was carried out with H1.2 as well as EZH2 knockout MCF7 cells to confirm the interlationship of H1.2 and EZH2 activity. Total RNA was isolated from MCF7 cells in which EZH2 and H1.2 genes have been depleted along with the wild type cells to study the differential regulation of various genes in each case.

2015-12-21 | E-GEOD-68050 | biostudies-arrayexpress

Linker histone H1.2 establishes chromatin comapction and gene silencing through recognition of H3K27me3

2015-12-21 | GSE68050 | GEO

Interactome of intact chromatosome variants with site-specifically ubiquitylated and acetylated linker histone H1.2

Project description:Post-translational modifications (PTMs) of histones have fundamental effects on chromatin structure and function. While the impact of PTMs on the function of core histones are increasingly well understood, this is much less the case for modifications of linker histone H1, which is at least in part due to a lack of proper tools. In this work, we establish the assembly of intact chromatosomes containing site-specifically ubiquitylated and acetylated linker histone H1.2 variants obtained by a combination of chemical biology approaches. We then use these complexes in a tailored affinity enrichment mass spectrometry workflow to identify and comprehensively characterize chromatosome-specific cellular interactomes and the impact of site-specific linker histone modifications on a proteome-wide scale. We validate and benchmark our approach by western-blotting and by confirming the involvement of chromatin-bound H1.2 in the recruitment of proteins involved in DNA double-strand break repair using an in vitro ligation assay. We relate our data to previous work and in particular compare it to data on modification-specific interaction partners of free H1. Taken together, our data supports the role of chromatin-bound H1 as a regulatory protein with distinct functions beyond DNA compaction and constitutes an important resource for future investigations of histone epigenetic modifications.

2023-11-02 | PXD040236 | Pride

Homo sapiens

Project description:Genome-wide expression profiling in 293T cells upon depletion of H1.2, Cul4A or PAF1

| PRJNA229182 | ENA

ChIP-seq for histone H1.2 in A549

Project description:Our study represents the detailed analysis of whole-genome DNA-binding sites of linker histone variant H1.2 in human lung cancer cell line A549, with biologic replicates, generated by ChIP-seq technology

2023-08-30 | GSE237852 | GEO

The linker histone H1.2 directs the genome-wide chromatin-association and facilitates the biological effects of the retinoblastoma tumour suppressor protein

Project description:ChIPseq of Retinoblastoma protein in MCF7 cells in which linker histone H1.2 has been knocked down.

2017-06-13 | GSE98728 | GEO

Mapping of somatic linker histone H1 variants in T47D-MTVL and HeLa cells

Project description:At least six histone H1 variants exist in mammalian somatic cells that bind to the linker DNA and stabilize the nucleosome particle contributing to higher order chromatin compaction. In addition, H1 seems to be involved in the active regulation of gene expression. It is not well known whether the different variants have specific roles, are distributed differentially along the genome, or regulate specific promoters. By taking advantage of specific antibodies to H1 variants and HA-tagged recombinant H1 variants expressed in a breast cancer-derived cell line, we have investigated the distribution of the different somatic H1 variants (H1.2 to H1.5, H1.0 and H1X) in particular promoters and genome-wide. Analysis of H1 (H1.0, H1.2, H1.3, H1.4, H1.5 and H1X) and H3 abundance in promoter regions

2014-02-04 | E-GEOD-49333 | biostudies-arrayexpress

Mapping of somatic linker histone H1 variants in T47D-MTVL cells

Project description:At least six histone H1 variants exist in mammalian somatic cells that bind to the linker DNA and stabilize the nucleosome particle contributing to higher order chromatin compaction. In addition, H1 seems to be involved in the active regulation of gene expression. It is not well known whether the different variants have specific roles, are distributed differentially along the genome, or regulate specific promoters. By taking advantage of specific antibodies to H1 variants and HA-tagged recombinant H1 variants expressed in a breast cancer-derived cell line, we have investigated the distribution of the different somatic H1 variants (H1.2 to H1.5, H1.0 and H1X) in particular promoters and genome-wide. Genome-wide analysis of H1.0, H1.2, H1.4, H1X and H3

2014-02-04 | E-GEOD-49334 | biostudies-arrayexpress

The genomic landscape of the somatic linker histone subtypes H1.1 to H1.5 in human cells

Project description:We employed the DamID technique to systematically map the genomic distribution of all canonical somatic H1 subtypes (H1.1-H1.5) in human IMR90 cells. Human cells contain up to eleven histone H1 proteins, with different spatial and temporal expression patterns. These include five canonical, replication-dependent somatic H1 subtypes (H1.1, H1.2, H1.3, H1.4 and H1.5). Despite being a key chromatin component, the genomic distribution of the somatic canonical H1 subtypes is still unknown and their role in chromatin related processes has so far remained elusive. Here we employed a DamID approach to map for the first time the genomic localization of all somatic canonical H1 subtypes in human cells. Our integrative analysis reveals novel insights into H1 subtype distribution and uncovers functional chromatin features potentially regulating the H1 genomic landscape. In general H1.2 to H1.5 are depleted from GC-rich regions and regulatory regions associated with active transcription. H1.1 shows a binding profile distinct from the other subtypes, suggesting a unique function for H1.1 in chromatin-regulated processes. Interestingly, our data indicate a novel role for somatic H1 subtypes in the three-dimensional organization of the genome by marking repressive regions within topological domains such as LADs. Our work integrates the five somatic linker histone H1 subtypes into the epigenome maps of human cells and provides a resource to refine our understanding of the significance of H1 and its heterogeneity in the control of genome function. DamID profiling of somatic linker histone variants H1.1, H1.2, H1.3, H1.4 and H1.5 in human fibroblasts. Two biological replicate samples of all H1 variants were hybridized on NimbleGen Human ChIP-chip 2.1M Economy Whole-Genome Tiling - Array GPL16055 covering small human chromosomes.

2013-06-15 | E-GEOD-40886 | biostudies-arrayexpress

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