Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Localization of the pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression [ChIP-Seq]

ABSTRACT: The eukaryotic genome is organized to enable the precise regulation of gene expression required for development. This organization is established during early development when the embryo transitions from a fertilized germ cell to the totipotent zygote. To understand the factors and processes that drive genomic organization, we focused on the pioneer factor GAGA factor (GAF) that is required for early embryonic development in Drosophila. GAF transcriptionally activates the zygotic genome and is localized to subnuclear foci. We show that this non-uniform distribution is driven by binding to the highly abundant GA-satellite repeats. At GA-repeats, GAF is necessary to form heterochromatin and silence transcription. Thus, GAF is required to establish both active and silent regions. We propose that the foci formation enables GAF to have opposing transcriptional roles within a single nucleus. Our data support a model in which modulation of the subnuclear concentration of transcription factors acts to organize the nucleus into functionally distinct domains that are essential for the robust regulation of gene expression.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE218019 | GEO | 2023/06/27

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Expression of human C9ORF72 hexanucleotide expansion reproduces RNA foci and dipeptide repeat proteins but not neurodegeneration in BAC transgenic mice

Project description:Nuclear RNA foci are often associated with mis-regulation of RNA processing in repeat expansion diseases. Here we report transcriptomic analysis of mice expressing expanded G4C2 repeats, the most common genetic cause of FTD/ALS. We show that the presence of numerous nuclear G4C2 repeat RNA foci does not cause extensive changes in RNA processing in this model organism.

2015-11-14 | GSE74973 | GEO

Differential Toxicity of Nuclear RNA Foci Versus Dipeptide Repeat Proteins in a Drosophila Model of C9ORF72 FTD/ALS

Project description:Nuclear RNA foci are often associated with mis-regulation of RNA processing in repeat expansion diseases. Here we report transcriptomic analysis of flies carrying expanded G4C2 repeats, the most common genetic cause of FTD/ALS. By obtaining an average of 32 million reads per library, we show that the presence of numerous nuclear G4C2 repeat RNA foci does not cause extensive changes in RNA processing in this model organism.

2015-09-11 | GSE72771 | GEO

Differential Toxicity of Nuclear RNA Foci Versus Dipeptide Repeat Proteins in a Drosophila Model of C9ORF72 FTD/ALS

Project description:Nuclear RNA foci are often associated with mis-regulation of RNA processing in repeat expansion diseases. Here we report transcriptomic analysis of flies carrying expanded G4C2 repeats, the most common genetic cause of FTD/ALS. By obtaining an average of 32 million reads per library, we show that the presence of numerous nuclear G4C2 repeat RNA foci does not cause extensive changes in RNA processing in this model organism. Comparision of the transcriptomic profile of flies expressing 5R or 160R from two different chromosomes

2015-09-11 | E-GEOD-72771 | biostudies-arrayexpress

An RNA-dependent and phase-separated active subnuclear compartment safeguards repressive chromatin domains

Project description:The nucleus is composed of functionally distinct membrane-less compartments which undergo phase separation (PS). However, whether different subnuclear compartments are connected remain elusive. We identified a type of nuclear bodies with PS features composed of BAZ2A that associates with active chromatin. BAZ2A-bodies depend on RNA transcription and BAZ2A non-disordered RNA-binding TAM domain. Although BAZ2A and H3K27me3 occupancies anticorrelate in the linear genome, in the nuclear space BAZ2A-bodies contact H3K27me3-bodies. BAZ2A-bodies disruption promotes BAZ2A invasion into H3K27me3-domains, causing H3K27me3-bodies loss and gene upregulation. Weak BAZ2A-RNA interactions, such as with nascent transcripts, promote BAZ2A-bodies whereas the strong binder lncRNA Malat1 impairs them while mediating BAZ2A association to chromatin at nuclear speckles. In addition to unravelling a direct connection between nuclear active and repressive compartments through PS mechanisms, the results also showed that the strength of RNA-protein interactions regulates this process contributing to nuclear organization and the regulation of chromatin and gene expression.

2024-04-09 | GSE225898 | GEO

A phase separated active subnuclear compartment safeguards repressive chromatin domains [iCLIP]

Project description:The nucleus is composed of membrane-less subnuclear compartments, containing intrinsically disordered proteins and RNAs that phase separate (PS) and contribute to specific nuclear reactions. However, whether and how different subnuclear compartments can intercommunicate remains elusive. Here we identified nuclear bodies with PS features composed of BAZ2A, a factor associating with active chromatin. BAZ2A-bodies depend on active transcription, RNAs, and the non-disordered BAZ2A RNA-binding TAM domain. Although BAZ2A and H3K27me3 occupancies anticorrelate in the linear genome, in the nuclear space BAZ2A-bodies contact H3K27me3-bodies. Disruption of BAZ2A-bodies promotes BAZ2A invasion into H3K27me3-domains, causing H3K27me3-bodies loss, H3K27me3 decrease, and gene upregulation. BAZ2A-bodies formation is negatively regulated by the nuclear-speckles associated lncRNA Malat1 that interacts with BAZ2A and mediates BAZ2A association to chromatin at nuclear speckles, which do not contact BAZ2A-bodies. The results unravel how active compartments protect repressive compartments using PS mechanisms that are promoted or impaired according to the type of RNA interactions with RNA-binding proteins.

2024-04-09 | GSE225896 | GEO

A phase separated active subnuclear compartment safeguards repressive chromatin domains [TSA-seq]

2024-04-09 | GSE225897 | GEO

A phase separated active subnuclear compartment safeguards repressive chromatin domains [ChIP-seq]

2024-04-09 | GSE225895 | GEO

A phase separated active subnuclear compartment safeguards repressive chromatin domains [RNA-seq]

2024-04-09 | GSE225894 | GEO

SAM domain polymerization links subnuclear clustering of PRC1 to silencing

Project description:Polycomb group (PcG) proteins mediate heritable but reversible silencing of developmental regulator genes by modifying their chromatin configuration. Accumulating evidence documents a role for PcG proteins in regulating higher order chromatin structures likely by their clustering, however, underlying mechanisms and its impact on transcriptional regulation remain obscure. In this study, we found that subnuclear clustering of PRC1 at canonical PcG target genes depended on head-to-tail polymerization property of SAM domain of Phc2 and likely Phc1. We show that Phc2-SAM polymerization limits the dynamic nature of PRC1, thereby promotes stable association of PRC1 with PcG target genes and contributes to their robust silencing. Our findings suggest a novel model by which SAM polymerization of Phc2 modulates the structural organization of PcG complexes to enable robust yet reversible PcG-mediated repression during development. Examination of H3K27me3 in wild type and the Phc2 mutant cells

2013-06-01 | E-GEOD-37530 | biostudies-arrayexpress

SAM domain polymerization links subnuclear clustering of PRC1 to silencing (Affymetrix)

Project description:Polycomb group (PcG) proteins mediate heritable but reversible silencing of developmental regulator genes by modifying their chromatin configuration. Accumulating evidence documents a role for PcG proteins in regulating higher order chromatin structures likely by their clustering, however, underlying mechanisms and its impact on transcriptional regulation remain obscure. In this study, we found that subnuclear clustering of PRC1 at canonical PcG target genes depended on head-to-tail polymerization property of SAM domain of Phc2 and likely Phc1. We show that Phc2-SAM polymerization limits the dynamic nature of PRC1, thereby promotes stable association of PRC1 with PcG target genes and contributes to their robust silencing. Our findings suggest a novel model by which SAM polymerization of Phc2 modulates the structural organization of PcG complexes to enable robust yet reversible PcG-mediated repression during development. Wild type and Phc2L307R/L307R MEFs were used for RNA extraction and hybridization on Affymetrix microarrays.

2013-06-01 | E-GEOD-37346 | biostudies-arrayexpress

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