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Analysis of the DNA accessibility upon multiple histone H1 variants by ATAC-seq

ABSTRACT: Combined depletion of H1.2 and H1.4 has a strong deleterious effect in the cancer cells examined, and induces a strong interferon (IFN) response with up-regulation of many IFN-stimulated genes (ISGs), which is not seen in individual H1 knock-downs. Although H1 participates to repress ISG promoters, its activation upon H1 KD is mainly generated by the activation of the IFN response through cytosolic nucleic acids receptors, IFN synthesis and JAK-STAT pathway activation. The IFN response may be triggered by the expression of noncoding dsRNAs generated from heterochromatic repeats or endogenous retroviruses upon H1 KD. H1 KD promotes the appearance of accessibility sites genome wide and, particularly, at satellites and other repeats.

ORGANISM(S): Homo sapiens

PROVIDER: GSE99384 | GEO | 2018/05/26

REPOSITORIES: GEO

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Analysis of the DNA accessibility upon multiple histone H1 variants by ATAC-seq (6 samples)

Project description:Combined depletion of H1.2 and H1.4 has a strong deleterious effect in the cancer cells examined, and induces a strong interferon (IFN) response with up-regulation of many IFN-stimulated genes (ISGs), which is not seen in individual H1 knock-downs. Although H1 participates to repress ISG promoters, its activation upon H1 KD is mainly generated by the activation of the IFN response through cytosolic nucleic acids receptors, IFN synthesis and JAK-STAT pathway activation. The IFN response may be triggered by the expression of noncoding dsRNAs generated from heterochromatic repeats or endogenous retroviruses upon H1 KD. H1 KD promotes the appearance of accessibility sites genome wide and, particularly, at satellites and other repeats.

2017-08-14 | GSE100762 | GEO

Genome-wide profiling of histone H1 variants and H3K9me3 in T47D-MTVL cells upon multiple H1 depletion

Project description:Human somatic cells may contain up to seven members of the histone H1 family contributing to chromatin compaction and regulation of nuclear processes, apparently with certain subtype specificities. In breast cancer cells, the combined depletion of H1.2 and H1.4 has a strong deleterious effect, deregulates many genes, promotes the appearance of accessibility sites genome-wide, and triggers an interferon response via activation of heterochromatic repeats. We have further analyzed the consequences of multiple H1 variants depletion by profiling the occupancy of five somatic histone H1 variants and H3K9me3 post-translational modification in T47D-MTVL cancer cells. Specifically, stable breast cancer-derived cell lines expressing an shRNA against multiple histone H1 isoforms in response to doxycycline (Dox) were grown for six days in the presence or absence of Dox. ChIP-Seq experiments were subsequently performed to analyze the genome-wide localization of histone H1 variants and H3K9me3.

2021-08-16 | GSE156036 | GEO

Analysis of the DNA topology upon multiple histone H1 variants depletion by Hi-C experiments

Project description:The combined depletion of histones H1.2 and H1.4 in T47D-MTVL human breast cancer cells has a strong deleterious effect, deregulates gene expression, promotes the appearance of genome-wide accessibility sites, and triggers the interferon response. We have further analyzed the consequences of multiple H1 variants depletion at the topological level by performing Hi-C experiments on T47D-MTVL cancer cells expressing a Dox-inducible shRNA against multiple H1 variants.

2022-03-23 | GSE172618 | GEO

Genome-wide profiling of histone H1 variants in T47D-MTVL cells

Project description:Human somatic cells may contain up to seven members of the histone H1 family contributing to chromatin compaction and regulation of nuclear processes, apparently with certain subtype specificities. Previous studies in T47D breast cancer cells determined that H1 variants are distributed in a variant-specific manner throughout the genome, although only H1.2 and H1X endogenous variants were mapped. Now, we performed ChIP-seq of five endogenous H1 variants (H1.0, H1.2, H1.4, H1.5, H1X) in T47D cells.

2021-08-16 | GSE166645 | 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

Genome-wide profiling of linker histone variant H1.3 in T47D-MTVL cancer cell line

Project description:Human somatic cells may contain up to seven members of the histone H1 family contributing to chromatin compaction and regulation of nuclear processes, apparently with certain subtype specificities. Our previous studies of H1.0, H1.2, H1.4, H1.5, and H1X genome-wide distribution determined that H1 variants are distributed in a variant-specific manner throughout the genome. We have been able to extend our study of the genomic distribution of the H1 family from five to six proteins thanks to the acquisition and validation of a new ChIP-grade endogenous antibody against histone H1.3.

2024-01-09 | GSE236878 | GEO

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

2013-06-15 | GSE40886 | GEO

RNA-seq of human neutrophil-like cell line PLB-985 at various stages of differentiation with CRISPR knock-outs of H1 linker histones

Project description:Finding that PLB-985 knockouts of H1.2 or H1.4 were deficient in their differentiation to neutrophil-like cells, we decided to perform RNA-seq on 2 single-cell clones of knockouts of each of the linker histones H1.1-H1.5.

2020-05-11 | E-MTAB-8459 | biostudies-arrayexpress

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