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

ABSTRACT: 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

ORGANISM(S): Homo sapiens

SUBMITTER: Albert Jordan

PROVIDER: E-GEOD-49334 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Mapping of six somatic linker histone H1 variants in human breast cancer cells uncovers specific features of H1.2.

Millán-Ariño Lluís L Islam Abul B M M K AB Izquierdo-Bouldstridge Andrea A Mayor Regina R Terme Jean-Michel JM Luque Neus N Sancho Mónica M López-Bigas Núria N Jordan Albert A

Nucleic acids research 20140129 7

Seven linker histone H1 variants are present in human somatic cells with distinct prevalence across cell types. Despite being key structural components of chromatin, it is not known whether the different variants have specific roles in the regulation of nuclear processes or are differentially distributed throughout the genome. Using variant-specific antibodies to H1 and hemagglutinin (HA)-tagged recombinant H1 variants expressed in breast cancer cells, we have investigated the distribution of si ...[more]

PMID: 24476918

Similar Datasets

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

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

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

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

2014-02-04 | GSE49333 | GEO

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

2014-02-04 | GSE49334 | 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

Histone H1 distribution and epitope exposure within chromatin high-order structure

Project description:Within the cell nucleus, histone H1 is the most mobile histone. Yet, it is regarded as key to the establishment and stability of chromatin higher-order structure. The implication is that chromatin higher-order structure is dynamic, in part due to the mobility of H1. Defining the positions of H1 on chromatin in situ, therefore, represents a challenge. Immunoprecipitation of formaldehyde-fixed and sonicated chromatin, followed by DNA sequencing (xChIP-seq) is traditionally the method for mapping histones onto DNA elements. But since sonication fragmentation precedes ChIP, there is a consequent loss of information about chromatin higher-order structure. A second formaldehyde fixation after antibody binding to intact in situ chromatin, but before sonication (xxChIP-seq), preserves this information and reveals which histone epitopes are inaccessible in situ. In this study, the distribution of two histone H1 variants H1.2 and H1.5 is defined and compared by both xChIP-seq and xxChIP-seq in undifferentiated HL-60/S4 cells, illustrating the influences of preserved chromatin higher-order structure. We have found that xChIP and xxChIP signals are anticorrelated. H1.2 versus H1.5-enrichments were particularly distinct near bound Pol II, SMC3 proteins, as well as domains marked by H3K4me1, H3K9ac, H3K27ac and H3K36me3. H1.5-enriched regions have an average nucleosome repeat length NRL=184 bp, as opposed to 190 bp for H1.2-enriched regions. We have also studied the distribution of H1 variants with respect to DNA methylation. Most changes of DNA methylation during differentiation appear within ~60bp from the nucleosome entry/exit and are preferably associated with H1.2-bound nucleosomes, whereas H1.5 histones are depleted from CpGs. Our results suggest that different physical packing of nucleosomes may exist in H1.2- versus H1.5-enriched areas, characterized by differential H1 epitope exposure as assessed by xChIP and xxChIP.

2020-06-14 | GSE136264 | GEO

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

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

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