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Dynamic placement of the linker histone H1 regulates nucleosome arrangement and coordinates gene transcription in early Drosophila embryos

ABSTRACT: Dynamic placement of the linker histone H1 regulates nucleosome arrangement and coordinates gene transcription in early Drosophila embryos

PROVIDER: PRJNA394008 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5820981.fastq.gz	Fastqsanger.gz
	SRR5820982.fastq.gz	Fastqsanger.gz
	SRR5820983.fastq.gz	Fastqsanger.gz
	SRR5820984.fastq.gz	Fastqsanger.gz
	SRR5820985.fastq.gz	Fastqsanger.gz

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Dynamic placement of the linker histone H1 regulates nucleosome arrangement and coordinates gene transcription in early Drosophila embryos[ChIP-Seq]

Project description:H1 ChIP-seq profiling and nucleosome MNase-seq profiling were performed in after egg laying (AEL) 3-4 hours (hr) and 14-15hr Drosophila melanogaster embryos (W1118).

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The interactome of site-specifically acetylated linker histone H1

Project description:Linker histone H1 plays a key role in chromatin organization and maintenance, however, our knowledge of the regulation of H1 functions by its posttranslational modifications (PTMs) is very limited. In this study, we report on the generation of homogeneously and site-specifically mono- and di-acetylated H1 (H1 Ac) using genetic code expansion. We used these modified histones to identify and comprehensively characterize the acetylation-dependent cellular interactome for linker histone H1 and show that site-specific acetylation results in overlapping, but distinct groups of interacting partners. Intriguingly, H1 acetylation-specific interactors comprise translational initiation factors and are involved in transcriptional regulation, suggesting that acetylation of H1 may indeed act as a regulator of the linker histone H1 by modulation of protein-protein interactions.

2021-07-09 | PXD025832 | Pride

Dynamic placement of the linker histone H1 regulates nucleosome arrangement and coordinates gene transcription in early Drosophila embryos

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-07-12 | GSE101330 | GEO

Novel nucleosomal particles containing core histones and linker DNA but no histone H1

Project description:Eukaryotic chromosomal DNA is assembled into regularly spaced nucleosomes, which play a central role in gene regulation by determining accessibility of control regions. The nucleosome contains ~147 bp of DNA wrapped ~1.7 times around a central core histone octamer. The linker histone, H1, binds both to the nucleosome, sealing the DNA coils, and to the linker DNA between nucleosomes, directing chromatin folding. Micrococcal nuclease (MNase) digests the linker to yield the chromatosome, containing H1 and ~160 bp, and then converts it to a core particle, containing ~147 bp and no H1. Sequencing of nucleosomal DNA obtained after MNase digestion (MNase-seq) generates genome-wide nucleosome maps that are important for understanding gene regulation. We present an improved MNase-seq method involving simultaneous digestion with exonuclease III, which removes linker DNA. Remarkably, we discovered two novel intermediate particles containing 154 or 161 bp, corresponding to 7 bp protruding from one or both sides of the nucleosome core. These particles are detected in yeast lacking H1 and in H1-depleted mouse chromatin. They can be reconstituted in vitro using purified core histones and DNA. We propose that these "proto-chromatosomes" are fundamental chromatin subunits, which include the H1 binding site and influence nucleosome spacing independently of H1.

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MNase analysis of linker histone H1 mutant

Project description:MNase analysis of linker histone H1 mutant

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Transcriptiomic analysis of linker histone H1 mutant

Project description:Transcriptiomic analysis of linker histone H1 mutant

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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

Dynamic placement of the linker histone H1 regulates nucleosome arrangement and coordinates gene transcription in early Drosophila embryos[RNA-Seq]

Project description:Expression profiles of in after egg laying (AEL) 3-4 hours (hr) and 14-15hr Drosophila melanogaster embryos (W1118)

2018-07-12 | GSE101328 | GEO

High Resolution Mapping of H1 Linker Histone Variants in Embryonic Stem Cells

Project description:H1 linker histones facilitate higher order chromatin folding and are essential for mammalian development. To achieve high resolution mapping of H1 variants H1d and H1c in embryonic stem cells (ESCs), we have established a knock-in system and shown that the N-terminally tagged H1 proteins are functionally interchangeable to their endogenous counterparts in vivo. H1d and H1c are depleted from GC- and gene-rich regions and active promoters, inversely correlated with H3K4me3, but positively correlated with H3K9me3 and associated with characteristic sequence features. Surprisingly, both H1d and H1c are significantly enriched at major satellites, which display increased nucleosome spacing compared with bulk chromatin. While also depleted at active promoters and enriched at major satellites, overexpressed H10 displays differential binding patterns in specific repetitive sequences compared with H1d and H1c. Depletion of H1c, H1d and H1e causes pericentric chromocenter clustering and de-repression of major satellites. These results integrate the localization of an understudied type of chromatin proteins, namely the H1 variants, into the epigenome map of mouse ESCs, and we identify significant changes at pericentric heterochromatin upon depletion of this epigenetic mark. Mapping linker histone H1 variants H1d, H1c and H10 as well as 3 core histone modifications in mouse ESC genome.

2013-04-29 | E-GEOD-46134 | biostudies-arrayexpress

The functional interactome of site-specifically ubiquitylated linker histone H1

Project description:Decoding the role of histone posttranslational modifications (PTMs) is key to understand the fundamental process of epigenetic regulation. While this process is well studied for core histones and many of their PTMs, this is not the case for linker histone H1 in general and its ubiquitylation in particular due to a lack of proper tools. Here, we report on the generation of site-specifically mono-ubiquitylated H1.2 via click chemistry and identify its ubiquitin-dependent interactome on a proteome-wide scale. We show that the H1 interactome is generally modulated by ubiquitylation and that site-specific ubiquitylation results in overlapping, but distinct interactomes. We further demonstrate that site-specific ubiquitylation of H1 affects the interaction with enzymes relevant for deubiquitylation and deacetylation. We finally show that site-specific ubiquitylation at position K64 impacts H1-dependent chromatosome assembly as well as H1-induced phase separation. In summary, we demonstrate that site-specific ubiquitylation is a general functional regulator for linker histone H1.

2021-07-20 | PXD020686 | Pride

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