Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multiple Overlapping Mammalian Chromatin Remodeling Systems Collaborate Genome-wide at Dynamic Chromatin Transitions (ChIP-Seq)

ABSTRACT: ATP-dependent chromatin remodeling is an essential process required for the dynamic organization of chromatin structure. Here we describe the genome-wide location and activity of three remodeler proteins with diverse physiological functions in the mouse genome: Brg1, Chd4, and Snf2h. The localization patterns of all three proteins significantly overlap with one another and with regions of accessible chromatin. Furthermore, using inducible mutant variants, we demonstrate that the catalytic activity of these proteins contributes to the remodeling of chromatin genome-wide, and that each of these remodelers can independently regulate chromatin reorganization at distinct sites. Most regions require the activity of more than one remodeler to regulate accessibility. These findings provide a dynamic view of chromatin organization, and highlight the differential contributions of remodelers to chromatin maintenance in higher eukaryotes.

ORGANISM(S): Mus musculus

PROVIDER: GSE53583 | GEO | 2013/12/24

SECONDARY ACCESSION(S): PRJNA232448

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Multiple Overlapping Mammalian Chromatin Remodeling Systems Collaborate Genome-wide at Dynamic Chromatin Transitions (ChIP-Seq)

Project description:ATP-dependent chromatin remodeling is an essential process required for the dynamic organization of chromatin structure. Here we describe the genome-wide location and activity of three remodeler proteins with diverse physiological functions in the mouse genome: Brg1, Chd4, and Snf2h. The localization patterns of all three proteins significantly overlap with one another and with regions of accessible chromatin. Furthermore, using inducible mutant variants, we demonstrate that the catalytic activity of these proteins contributes to the remodeling of chromatin genome-wide, and that each of these remodelers can independently regulate chromatin reorganization at distinct sites. Most regions require the activity of more than one remodeler to regulate accessibility. These findings provide a dynamic view of chromatin organization, and highlight the differential contributions of remodelers to chromatin maintenance in higher eukaryotes. We examine the genome-wide location and activity of three remodeler proteins (Brg1, CHD4 and Snf2h)

2013-12-24 | E-GEOD-53583 | biostudies-arrayexpress

Multiple Overlapping Mammalian Chromatin Remodeling Systems Collaborate Genome-wide at Dynamic Chromatin Transitions (Dnase-Seq)

2013-12-24 | E-GEOD-53584 | biostudies-arrayexpress

Multiple Overlapping Mammalian Chromatin Remodeling Systems Collaborate Genome-wide at Dynamic Chromatin Transitions [Affymetrix]

Project description:Expression data from 3134 mouse mammary epithelial cell line -/+ Tet-inducible chromatin remodeler mutant variants ATP-dependent chromatin remodeling is an essential process required for the dynamic organization of chromatin structure. Here we describe the genome-wide location and activity of three remodeler proteins with diverse physiological functions in the mouse genome: Brg1, Chd4 and Snf2h. The localization patterns of all three proteins substantially overlap with one another and with regions of accessible chromatin. Furthermore, using inducible mutant variants, we demonstrate that the catalytic activity of these proteins contributes to the remodeling of chromatin genome wide and that each of these remodelers can independently regulate chromatin reorganization at distinct sites. Many regions require the activity of more than one remodeler to regulate accessibility. We also examined effects of mutant remodeler variants on selective gene expression by global analysis of RNA expression patterns and found more than 800 genes are deregulated by these variants. These findings provide a dynamic view of chromatin organization and highlight the differential contributions of remodelers to chromatin maintenance in higher eukaryotes. Flag tagged dominant negative variants of the chromatin remodelers Brg1, Chd4, and Snf2h were each stably integrated into a cell line containg the tetracycline transactivator regulatory system (3134Tet (7110)). The 3134Tet control cells and each of the dominant-negative remodeler cell lines were grown in media with or without tetracycline for 48 hrs to induce expression of the tetracycline transactivator alone (3134Tet cells) or tetracycline transactivator and dominant negative remodeler variant. Following treatment, cells were harvested for RNA extraction and hybridization to Affymetrix Mouse Gene 1.0 ST arrays.

2015-03-05 | E-GEOD-66544 | biostudies-arrayexpress

Multiple Overlapping Mammalian Chromatin Remodeling Systems Collaborate Genome-wide at Dynamic Chromatin Transitions (Dnase-Seq)

2013-12-24 | GSE53584 | GEO

Multiple Overlapping Mammalian Chromatin Remodeling Systems Collaborate Genome-wide at Dynamic Chromatin Transitions [Affymetrix]

2015-03-05 | GSE66544 | GEO

Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner

Project description:We assessed the interplay between DNA sequences and ATP-dependent chromatin remodelers in defining the nucleosomal organization of the eukaryotic genome. We compared the genome-wide distribution and impact on chromatin of NURD, (P)BAP, INO80 and ISWI representing four major families of Drosophila remodelers. Each remodeler has a unique set of genomic targets, and generates distinct chromatin signatures. Remodeler loci have characteristic DNA sequence features, predicted to influence nucleosome formation. Strikingly, remodelers counteract DNA sequence-driven nucleosome distribution in two ways: NURD, (P)BAP and INO80 increase histone density at their target sequences, which disfavor positioned nucleosome formation. In contrast, ISWI promotes open chromatin at sites that are propitious for precise nucleosome placement. Thus, both selective targeting and distinct mechanisms of remodeling underlie the functional differentiation of remodelers. We conclude that chromatin organization involves a class-specific antagonism between remodeler activity and DNA sequence-driven nucleosome placement. The supplementary bed files (P)BAP_sites.bed, NURD_sites.bed, INO80_sites.bed, ISWI_sites.bed contain high quality binding sites for each remodeler obtained by intersecting the sets of significant ChIP-chip peaks for each antibody.

2011-12-12 | GSE32404 | GEO

Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for proper CTCF function

Project description:Catalytic activity of the ISWI family of remodelers is critical for nucleosomal organization and transcription factor binding, including the insulator protein CTCF. To define which subcomplex mediates these diverse functions we phenotyped a panel of isogenic mouse stem cell lines each lacking one of six ISWI accessory subunits. Individual deletions of either CERF, RSF1, ACF, WICH or NoRC subcomplexes only moderately affect the chromatin landscape, while removal of the NURF-specific subunit BPTF leads to drastic reduction in chromatin accessibility and Snf2h ATPase localization around CTCF sites. While this reduces distances to the adjacent nucleosomes it only modestly impacts CTCF binding itself. In absence of accessibility, the insulator function of CTCF is nevertheless impaired resulting in lower occupancy of cohesin and cohesin-loading factors, and reduced insulation at these sites, highlighting the need of NURF-mediated remodeling for open chromatin and proper CTCF function. Our comprehensive analysis reveals a specific role for NURF in mediating Snf2h localization and chromatin opening at bound CTCF sites showing that local accessibility is critical for cohesin binding and insulator function.

2024-03-13 | PXD042945 | Pride

In vivo Analysis Reveals that ATP-hydrolysis Couples Remodeling to SWI/SNF Release from Chromatin.

Project description:ATP-dependent chromatin remodelers control the accessibility of genomic DNA through nucleosome mobilization. However, the dynamics of genome exploration by remodelers, and the role of ATP hydrolysis in this process remain unclear. We used live-cell imaging of Drosophila polytene nuclei to monitor Brahma (BRM) remodeler interactions with its chromosomal targets. In parallel, we measured local chromatin condensation and its effect on BRM association. Surprisingly, only a small portion of BRM is bound to chromatin at any given time. BRM binds decondensed chromatin but is excluded from condensed chromatin, limiting its genomic search space. BRM-chromatin interactions are highly dynamic, whereas histone-exchange is limited and much slower. Intriguingly, loss of ATP hydrolysis enhanced chromatin retention and clustering of BRM, which was associated with reduced histone turnover. Thus, ATP hydrolysis couples nucleosome remodeling to remodeler release, driving a continuous transient probing of the genome.

2022-01-20 | PXD025474 | Pride

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (RNA-seq data sets)

Project description:Remodelers define nucleosome composition, presence and position. Mammalian imitation-switch-type (ISWI) comprise one class, mostly relying on the ATPase Snf2h for activity. We show that embryonic stem cells are viable without Snf2h, enabling to study its function and contrast it to Brg1, the ATPase of SWI/SNF. Loss of Snf2h specifically affects nucleosomal positioning and increases linker lengths genome-wide providing in vivo evidence for ISWI function in ruling nucleosomal spacing. Systematic analysis of transcription factor binding reveals selective requirement on either remodeling activity. One group, containing the transcriptional repressor REST depend on BRG1, while a non-overlapping set including the insulator protein CTCF, relies on Snf2h. Importantly localized reduction in CTCF binding decreases long-range interactions. Collectively, this links mammalian ISWI to nuclear organization, demonstrates its cellular role for nucleosomal periodicity and reveals that transcription factors rely on specific remodeling pathways for proper genomic binding.

2019-04-18 | GSE112135 | GEO

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (MNase-seq data sets)

2019-04-18 | GSE112134 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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