Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA methylation insulates exons from CTCF loops with nuclear speckles

ABSTRACT: DNA methylation insulates exons from CTCF loops with nuclear speckles

PROVIDER: PRJNA900265 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

DNA methylation insulates exons from CTCF loops with nuclear speckles (HiChIP)

Project description:DNA methylation insulates exons from CTCF loops with nuclear speckles (HiChIP)

| PRJNA900272 | ENA

DNA methylation insulates exons from CTCF loops with nuclear speckles (CUT&TAG)

Project description:DNA methylation insulates exons from CTCF loops with nuclear speckles (CUT&TAG)

| PRJNA900271 | ENA

DNA methylation insulates exons from CTCF loops with nuclear speckles (ChiP-Seq)

Project description:DNA methylation insulates exons from CTCF loops with nuclear speckles (ChiP-Seq)

| PRJNA900264 | ENA

DNA methylation insulates exons from CTCF loops with nuclear speckles (RNA-Seq)

Project description:DNA methylation insulates exons from CTCF loops with nuclear speckles (RNA-Seq)

| PRJNA900270 | ENA

DNA methylation insulates exons from CTCF loops with nuclear speckles (HiChIP)

Project description:CTCF is necessary for the formation and maintenance of many DNA loops and Topologically Associating Domains, but the genomic features that influence CTCF looping are incompletely understood. We characterized the downstream effects of treating cells with a DNMT1 inhibitor and acute depletion of nuclear speckles to study the factors that influence CTCF looping.

2024-11-11 | GSE217754 | GEO

DNA methylation insulates exons from CTCF loops with nuclear speckles (ChiP-Seq)

2024-11-11 | GSE217752 | GEO

DNA methylation insulates exons from CTCF loops with nuclear speckles (RNA-Seq)

2024-11-11 | GSE217759 | GEO

DNA methylation insulates exons from CTCF loops with nuclear speckles (CUT&TAG)

2024-11-11 | GSE217753 | GEO

DNA methylation insulates exons from CTCF loops with nuclear speckles

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-11-11 | GSE217760 | GEO

Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops

Project description:Chromosome loops shift dynamically during development, homeostasis, and disease. CTCF is known to anchor loops and construct 3D genomes, but how anchor sites are selected is not yet understood. Here we unveil Jpx RNA as a determinant of anchor selectivity. Jpx RNA targets thousands of genomic sites, preferentially binding promoters of active genes. Depleting Jpx RNA causes ectopic CTCF binding, massive shifts in chromosome looping, and downregulation of >700 Jpx target genes. Without Jpx, thousands of lost loops are replaced by de novo loops anchored by ectopic CTCF sites. Although Jpx controls CTCF binding on a genome-wide basis, it acts selectively at the subset of developmentally sensitive CTCF sites. Specifically, Jpx targets low-affinity CTCF motifs and displaces CTCF protein through competitive inhibition. We conclude that Jpx acts as a CTCF release factor and shapes the 3D genome by regulating anchor site usage.

2021-12-01 | GSE144056 | GEO

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