Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nucleosome-mediated competition of pioneer transcription factors

ABSTRACT: Nucleosome-mediated competition of pioneer transcription factors

PROVIDER: PRJNA891341 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR30751710.fastq.gz	Fastqsanger.gz
	SRR30751710_1.fastq.gz	Fastqsanger.gz
	SRR30751710_2.fastq.gz	Fastqsanger.gz
	SRR30751711.fastq.gz	Fastqsanger.gz
	SRR30751711_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 75

Similar Datasets

Nucleosome-mediated competition of pioneer transcription factors

Project description:Pioneer transcription factors Nanog, Pou5f3 and Sox19b promote chromatin accessibility on the enhancers of the early zebrafish embryos. It is poorly understood how they act together; it is commonly assumed that they act additively or cooperatively to clear chromatin from the nucleosomes. We investigated this question by comparing chromatin accessibility (Omni ATAC-seq) in seven mutant genotypes: single, double and triple maternal-zygotic mutants by Pou5f3, Sox19b and Nanog, and the wild-type embryos. We found, that at most of the directly bound sites, either Pou or Nanog is required for chromatin accessibility; while at the minority of the sites two factors act additively. Further, on the sites, where Pou5f3 promotes chromatin accessibility, Nanog often suppresses it, and vice versa. To explain this phenomenon, we suggest a model of nucleosome-mediated competition between pioneer transcription factors: Pou5f3 and Nanog compete for the same binding motif on the DNA, but only one of the factors has a pioneer activity on this site. This entry contains only part fo the Omni-ATAC-seq experiments, the other part is in the previously released entry GSE188364.

2023-08-02 | GSE215956 | GEO

Nucleosome binding by the pioneer transcription factor OCT4

Project description:The nucleosome is a fundamental unit of chromatin in eukaryotes, and generally prevents the binding of transcription factors to genomic DNA. Pioneer transcription factors overcome the nucleosome barrier, and bind their target DNA sequences in chromatin. OCT4 is a representative pioneer transcription factor that plays a role in stem cell pluripotency. In the present study, we biochemically analyzed the nucleosome binding by OCT4. Crosslinking mass spectrometry showed that OCT4 binds the nucleosome.

2020-05-13 | PXD019160 | JPOST Repository

Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [MNase-seq]

Project description:Pioneer transcription factors (TF) bind nucleosome-embedded DNA motifs to activate new regulatory elements and promote differentiation. However, the complexity, binding dependencies and temporal effects of their action remain unclear. Here, we dissect how ectopic induction of the pioneer TF GATA6 triggers Primitive Endoderm (PrE) differentiation from pluripotent cells. We show that transient GATA6 binding exploits accessible regions to decommission enhancers and promote pluripotency gene silencing. Simultaneously, GATA6 targets closed chromatin and initiates extensive remodeling culminating in the establishment of fragile nucleosomes flanked by ordered nucleosome arrays and increased accessibility. This is enhanced by rapidly expressed PrE TFs (SOX17) and by pluripotency TFs repurposed for differentiation (OCT4/SOX2). Accordingly, depletion of OCT4 during GATA6 induction decreases Gata6 expression, alters GATA6 and SOX17 binding and impairs differentiation. Therefore, pioneer TFs orchestrate complex regulatory networks involving many if not all available pioneer TFs, including those required to support the original identity of differentiating cells.

2025-11-13 | GSE268717 | GEO

Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [ATAC-seq]

2025-11-13 | GSE268713 | GEO

Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [ChIP-Seq]

2025-11-13 | GSE269897 | GEO

Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [RNA-seq]

2025-11-13 | GSE267441 | GEO

Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation

Project description:Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation

| PRJNA1118310 | ENA

LNCap cell nucleosome footprint elicits novel noncanonical GATA2 pioneer model

Project description:Purpose: The dynamic nucleosome reorganization is the interplay among nucleosome and regulated by pioneer factors, which can access target DNA sequences on nucleosomes.The goals of this study are revealing the dynamic nucleosome footprint and how GATA2 is capable of resetting crowding array to primed, or accessible edge nucleosome states. Methods: LNCaP cells between passage number 30-35 were used for assay. cell nucleus was extracted, digested by MNase to Mono-nucleosome and ChIP/ChIP-exo was performed, the ChIP products were further used to generate library with illumina ChIP-seq kit. Hi-seq 3000 was used for sequencing and the data was analyzed by MACS2 for peaks. Results: GATA2 is associated with condensed nucleosome states and nucleosomes could unwrapped and be more accessible in pioneer factor GATA2 binding sites. Conclusions: Our study represents the first detailed nucleosome footprint of LNCap cells and analysis of the relationship between pioneer factor GATA2 and nucleosome reorganization in whole genomic DNA. These results demonstrated GATA2 play a critical role in an AR-independent manner in prostate cancer.

2021-04-14 | GSE148935 | GEO

Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [ChIP-Seq]

Project description:Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [ChIP-Seq]

| PRJNA1124086 | ENA

Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [RNA-seq]

Project description:Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [RNA-seq]

| PRJNA1111521 | ENA

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