Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ACCESS DATA

Json Xml

Dataset's files

Source:

			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

Items per page:

1 - 5 of 7

Similar Datasets

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).

2018-07-12 | GSE101327 | GEO

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

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.

2015-09-23 | GSE65889 | GEO

MNase analysis of linker histone H1 mutant

Project description:MNase analysis of linker histone H1 mutant

| PRJNA451507 | ENA

Transcriptiomic analysis of linker histone H1 mutant

Project description:Transcriptiomic analysis of linker histone H1 mutant

| PRJNA451508 | ENA

The nucleoskeleton protein NuMA maintains local chromatin architecture partially through promoting linker histone H1’ binding to chromatin and nucleosome stacking [ATAC-Seq]

Project description:Nucleoskeleton is generally considered to be the grid structure involved in regulation of genome expression and maintenance in the eukaryotic nucleus. However, its actual biological functions and mechanisms remain controversial. Here, we show the nuclear mitotic apparatus protein (NuMA), an essential regulator of the spindle, serve as one of the components of nucleoskeleton to regulates genome high-order architecture. In the interphase, fast depletion of NuMA leads to changes in chromatin organization, including increased accessibility of the genome, remodeling of nucleosome fibers and changes of transcription levels in certain heterochromatin regions. These effects are probably due to NuMA and linker histone H1’s interplay. We prove that NuMA interacts with linker histone H1 and linker DNA through its C-terminal domain. Such interaction facilitates H1’s binding to DNA and promotes nucleosome stacking, and might be part of the reason that NuMA maintains the local condensed state of heterochromatin. Collectively, our results reveal new biological functions of NuMA in the interphase, and also associates nucleoskeleton with genome organization at the mono-nucleosome level for the first time. This in-depth study on the mechanism of NuMA’s regulation on H1 and nucleosomes shed new light on how nucleoskeleton regulates genome architecture and gene expression.

2024-03-01 | GSE227940 | GEO

The nucleoskeleton protein NuMA maintains local chromatin architecture partially through promoting linker histone H1’ binding to chromatin and nucleosome stacking [RNA-Seq]

2024-03-01 | GSE227707 | GEO

The nucleoskeleton protein NuMA maintains local chromatin architecture partially through promoting linker histone H1’ binding to chromatin and nucleosome stacking [Hi-C]

2024-03-01 | GSE227705 | GEO

The nucleoskeleton protein NuMA maintains local chromatin architecture partially through promoting linker histone H1’ binding to chromatin and nucleosome stacking [Cut & Tag]

2024-03-01 | GSE227704 | GEO

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data