Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation I

ABSTRACT: Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation I

PROVIDER: PRJNA610603 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

Project description:Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

| PRJNA369741 | ENA

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation IV

Project description:Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation IV

| PRJNA610600 | ENA

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation III

Project description:Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation III

| PRJNA610601 | ENA

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation II

Project description:Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation II

| PRJNA610602 | ENA

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation IV

Project description:The CCCTC-binding factor (CTCF) is widely regarded as a key player in chromosome organization in mammalian cells, yet direct assessment of its role in genome architecture and gene regulation has been difficult. Here, we use auxin-inducible degron techniques to acutely deplete CTCF to determine how loss of CTCF affect chromatin organization and gene expression. In mouse embryonic stem cells, depletion of CTCF results in rapid loss of chromatin loops anchored at CTCF-binding sites without major disruption to chromatin compartments and topological domains. In the absence of CTCF, many lineage-specific genes fail to express properly during differentiation to neural precursor cells, but transcriptional regulation of most genes is unaffected. Genes dependent on CTCF for induction are generally bound by the factor at promoters, which are connected to distal enhancers via CTCF-dependent chromatin loops. By contrast, CTCF-independent genes generally lack CTCF binding at the promoter and are generally closer to enhancers. These results refine our understanding of CTCF function in chromatin organization and gene regulation.

2020-03-06 | GSE146454 | GEO

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation III

2020-03-06 | GSE146451 | GEO

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation II

2020-03-06 | GSE146450 | GEO

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation I

2020-03-06 | GSE146449 | GEO

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation.

Project description: Not available

| S-EPMC7913465 | biostudies-literature

Dynamic-network-guided CRISPRi screen identifies CTCF loop-constrained 1 nonlinear enhancer-gene regulatory activity in cell state transitions

Project description:Enhancers play key roles in gene regulation. However, comprehensive enhancer discovery is challenging because most enhancers, especially those affected in complex diseases, have weak effects on gene expression. Through gene regulatory network modeling, we identified that dynamic cell state transitions, a critical missing component in prevalent enhancer discovery strategies, can be utilized to improve the cells’ sensitivity to enhancer perturbation. Guided by the modeling results, we performed a mid-transition CRISPRi-based enhancer screen utilizing human embryonic stem cell definitive endoderm differentiation as a dynamic transition system. The screen discovered a comprehensive set of enhancers (4 to 9 per locus) for each of the core lineage-specifying transcription factors (TFs), including many enhancers with weak to moderate effects. Integrating the screening results with enhancer activity measurements (ATAC-seq, H3K27ac ChIP-seq) and three-dimensional enhancer-promoter interaction information (CTCF looping, Hi-C), we were able to develop a CTCF loop-constrained Interaction Activity (CIA) model that can better predict functional enhancers compared to models that rely on Hi-C-based enhancer-promoter contact frequency. Together, our dynamic network-guided enhancer screen and the CIA enhancer prediction model provide generalizable strategies for sensitive and more comprehensive enhancer discovery in both normal and pathological cell state transitions.

2023-06-17 | PXD043070 | Pride

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