Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [III]

ABSTRACT: Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [III]

PROVIDER: PRJNA576666 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10251900_1.fastq.gz	Fastqsanger.gz
	SRR10251900_2.fastq.gz	Fastqsanger.gz
	SRR10252000_1.fastq.gz	Fastqsanger.gz
	SRR10252000_2.fastq.gz	Fastqsanger.gz
	SRR10287100_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 544

Similar Datasets

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection

Project description:Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection

| PRJNA576665 | ENA

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [II]

Project description:CTCF is a key insulator-binding protein and mammalian genomes contain numerous CTCF-binding sites (CBSs), many of which are organized in tandem arrays. Here we provide direct evidence that CBSs, if located between enhancers and promoters in the clustered Pcdh and b-globin clusters, function as an enhancer-blocking insulator by forming distinct directional chromatin loops, regardless whether enhancers contain CBS or not. Moreover, computational simulation and experimental capture revealed balanced promoter usage in vivo in cell populations and stochastic monoallelic expression in single cells by large arrays of tandem variable CBSs. Finally, gene expression levels are negatively correlated with CBS insulators located between enhancers and promoters on a genome-wide scale. Thus, single CBS insulators ensure proper enhancer insulation and promoter activation while tandem-arrayed CBS insulators determine balanced promoter choice. This finding has interesting implications on the role of topological insulators in 3D genome folding and developmental gene regulation.

2020-03-01 | GSE136328 | GEO

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [III]

2020-03-01 | GSE138645 | GEO

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [V]

2020-03-01 | GSE139679 | GEO

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [I]

2020-03-01 | GSE135394 | GEO

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [IV]

Project description:By CRISPR DNA-fragment editing, in conjunction with chromosome conformation capture, we find that CBSs, if located between enhancers and promoters in the clustered Pcdh and b-globin clusters, function as an enhancer-blocking insulator by forming distinct directional chromatin loops, regardless whether enhancers contain CBS or not. Moreover, computational simulation in silico and genetic deletions in vivo revealed balanced promoter usage in cell populations and stochastic monoallelic expression in single cells by large arrays of tandem variable CBSs. Finally, gene expression levels are negatively correlated with CBS insulators located between enhancers and promoters on a genome-wide scale. Thus, single CBS insulators ensure proper enhancer insulation and promoter activation while tandem-arrayed CBS insulators determine balanced promoter choice. This finding has interesting implications on the role of topological insulators in 3D genome folding and developmental gene regulation.

2020-03-06 | GSE138919 | GEO

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [VIII]

2020-03-01 | GSE140869 | GEO

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [VII]

2020-03-01 | GSE140868 | GEO

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [VI]

2020-03-01 | GSE140570 | GEO

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [II]

Project description:Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [II]

| PRJNA562270 | 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