Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Calcium Signaling Prompts NIPBL Recruitment at Active Enhancers and Promoters via Distinct Mechanisms to Reconstruct Genome Compartmentalization

ABSTRACT: Calcium Signaling Prompts NIPBL Recruitment at Active Enhancers and Promoters via Distinct Mechanisms to Reconstruct Genome Compartmentalization

PROVIDER: PRJNA644932 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12179300_1.fastq.gz	Fastqsanger.gz
	SRR12179300_2.fastq.gz	Fastqsanger.gz
	SRR12179400.fastq.gz	Fastqsanger.gz
	SRR12179301_1.fastq.gz	Fastqsanger.gz
	SRR12179301_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 266

Similar Datasets

Calcium Signaling Prompts NIPBL Recruitment at Active Enhancers and Promoters via Distinct Mechanisms to Reconstruct Genome Compartmentalization

Project description:During developmental progression the genomes of immune cells undergo large-scale changes in chromatin folding. However, insights into the signals and epigenetics that induce alterations in nuclear architecture remain rudimentary. Here, we found that calcium influx rapidly recruited the cohesin-loading factor NIPBL to thousands of binding sites to dictate widespread changes in compartment segregation. The induction of NIPBL-binding was coordinate with increased P300, BRG1 and RNA Polymerase II co-occupancy, via different kinetics at active enhancers and promoters. Through acute degradation system, we found that enhancers, rather than promoters, are dependent on BAF complexes to induce NIPBL recruitment. Finally, we found that calcium signaling acts universally to orchestrate rapid redistribution of NIPBL in both primary innate and adaptive immune cells. Collectively, these data reveal how calcium signaling regulates NIPBL occupancy to orchestrate nuclear architecture.

2020-10-10 | GSE154051 | GEO

Calcium signaling instructs NIPBL recruitment at active enhancers and promoters via distinct mechanisms to reconstruct genome compartmentalization.

Project description:During developmental progression the genomes of immune cells undergo large-scale changes in chromatin folding. However, insights into signaling pathways and epigenetic control of nuclear architecture remain rudimentary. Here, we found that in activated neutrophils calcium influx rapidly recruited the cohesin-loading factor NIPBL to thousands of active enhancers and promoters to dictate widespread changes in compartment segregation. NIPBL recruitment to enhancers and promoters occurred with distinct kinetics. The induction of NIPBL-binding was coordinate with increased P300, BRG1 and RNA polymerase II occupancy. NIPBL-bound enhancers were associated with NFAT, PU.1, and CEBP cis elements, whereas NIPBL-bound promoters were enriched for GC-rich DNA sequences. Using an acute degradation system, we found that the histone acetyltransferases P300 and CBP maintained H3K27ac abundance and facilitated NIPBL occupancy at enhancers and that active transcriptional elongation is essential to maintain H3K27ac abundance. Chromatin remodelers, containing either of the mutually exclusive BRG1 and BRM ATPases, promoted NIPBL recruitment at active enhancers. Conversely, at active promoters, depletion of BRG1 and BRM showed minimal effect on NIPBL occupancy. Finally, we found that calcium signaling in both primary innate and adaptive immune cells swiftly induced NIPBL occupancy. Collectively, these data reveal how transcriptional regulators, histone acetyltransferases, chromatin remodelers, and transcription elongation promote NIPBL occupancy at active enhancers while the induction of NIPLB occupancy at promoters is primarily associated with GC-rich DNA sequences.

| S-EPMC7778268 | biostudies-literature

Transcription factors form a ternary complex with NIPBL/MAU2 to localize cohesin at enhancers

Project description:While the cohesin complex is a key player in genome architecture, how it localizes to specific chromatin sites is not well understood. Recently, we and others have proposed that direct interactions with transcription factors (TFs) lead to the localization of the cohesin-loader complex (NIPBL/MAU2) within enhancers. Here, we identify two clusters of protein-protein interaction (PPI) motifs within the NIPBL sequence that regulate NIPBL dynamics, interactome, and NIPBL-dependent transcriptional programs. These PPIMs directly interact with chromatin-associated proteins, including TFs and one of them is necessary for the maintenance of the NIPBL-MAU2 heterodimer. Finally, using the glucocorticoid receptor (GR) as a model, we investigate its interaction surfaces with NIPBL and MAU2 using AlphaFold2 and surface plasmon resonance to uncover a TF-NIPBL-MAU2 ternary complex and present its importance in GR-dependent gene regulation.

2025-04-17 | PXD058574 | Pride

Nipbl

Project description:Rattus norvegicus Nipbl, NIPBL, cohesin loading factor [Source:RGD Symbol;Acc:1306393], is differentially expressed in 22 experiment(s);

| ENSRNOG00000056907 | ExpressionAtlas

NIPBL

Project description:Monodelphis domestica NIPBL, NIPBL cohesin loading factor [Source:NCBI gene;Acc:100014459], is expressed in 2 baseline experiment(s);

| ENSMODG00000020351 | ExpressionAtlas

Nipbl

Project description:Rattus norvegicus Nipbl, NIPBL, cohesin loading factor [Source:RGD Symbol;Acc:1306393], is expressed in 4 baseline experiment(s);

| ENSRNOG00000056907 | ExpressionAtlas

Nipbl

Project description:Mus musculus Nipbl, NIPBL cohesin loading factor [Source:MGI Symbol;Acc:MGI:1913976], is differentially expressed in 102 experiment(s);

| ENSMUSG00000022141 | ExpressionAtlas

NIPBL

Project description:Oryctolagus cuniculus NIPBL, NIPBL cohesin loading factor [Source:HGNC Symbol;Acc:HGNC:28862], is expressed in 1 baseline experiment(s);

| ENSOCUG00000005888 | ExpressionAtlas

NIPBL

Project description:Equus caballus NIPBL, NIPBL cohesin loading factor [Source:VGNC Symbol;Acc:VGNC:20741], is expressed in 1 baseline experiment(s);

| ENSECAG00000018233 | ExpressionAtlas

NIPBL

Project description:Homo sapiens NIPBL, NIPBL cohesin loading factor [Source:HGNC Symbol;Acc:HGNC:28862], is expressed in 58 baseline experiment(s);

| ENSG00000164190 | ExpressionAtlas

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