Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE198763 | GEO | 2022/07/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Topological screen identifies hundreds of Cp190- and CTCF-dependent <i>Drosophila</i> chromatin insulator elements.

Project description:Drosophila insulators were the first DNA elements found to regulate gene expression by delimiting chromatin contacts. We still do not know how many of them exist and what impact they have on the Drosophila genome folding. Contrary to vertebrates, there is no evidence that fly insulators block cohesin-mediated chromatin loop extrusion. Therefore, their mechanism of action remains uncertain. To bridge these gaps, we mapped chromatin contacts in Drosophila cells lacking the key insulator proteins CTCF and Cp190. With this approach, we found hundreds of insulator elements. Their study indicates that Drosophila insulators play a minor role in the overall genome folding but affect chromatin contacts locally at many loci. Our observations argue that Cp190 promotes cobinding of other insulator proteins and that the model, where Drosophila insulators block chromatin contacts by forming loops, needs revision. Our insulator catalog provides an important resource to study mechanisms of genome folding.

| S-EPMC9897668 | biostudies-literature

Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements [HiC]

Project description:CTCF and Cp190 proteins are implicated at many insulator elements throughout Drosophila genome. Here we compared Hi-C maps, transcriptomes and binding of multiple insulator proteins in cultured Drosophila cells derived from CTCF-KO, Cp190-KO and control embryos.

2022-07-19 | GSE198760 | GEO

Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements [ChIP-seq]

2022-07-19 | GSE198762 | GEO

Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements [RNA-seq]

2022-07-19 | GSE198761 | GEO

Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements

Project description:Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements

| PRJNA816845 | ENA

Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements [HiC]

Project description:Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements [HiC]

| PRJNA816853 | ENA

Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements [RNA-seq]

Project description:Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements [RNA-seq]

| PRJNA816855 | ENA

Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements [ChIP-seq]

Project description:Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements [ChIP-seq]

| PRJNA816854 | ENA

The Drosophila insulator proteins CTCF and CP190 link enhancer blocking to body patterning.

Project description:Insulator sequences guide the function of distantly located enhancer elements to the appropriate target genes by blocking inappropriate interactions. In Drosophila, five different insulator binding proteins have been identified, Zw5, BEAF-32, GAGA factor, Su(Hw) and dCTCF. Only dCTCF has a known conserved counterpart in vertebrates. Here we find that the structurally related factors dCTCF and Su(Hw) have distinct binding targets. In contrast, the Su(Hw) interacting factor CP190 largely overlapped with dCTCF binding sites and interacts with dCTCF. Binding of dCTCF to targets requires CP190 in many cases, whereas others are independent of CP190. Analysis of the bithorax complex revealed that six of the borders between the parasegment specific regulatory domains are bound by dCTCF and by CP190 in vivo. dCTCF null mutations affect expression of Abdominal-B, cause pharate lethality and a homeotic phenotype. A short pulse of dCTCF expression during larval development rescues the dCTCF loss of function phenotype. Overall, we demonstrate the importance of dCTCF in fly development and in the regulation of abdominal segmentation.

| S-EPMC2230845 | biostudies-literature

RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function.

Project description:A major role of the RNAi pathway in Schizosaccharomyces pombe is to nucleate heterochromatin, but it remains unclear whether this mechanism is conserved. To address this question in Drosophila, we performed genome-wide localization of Argonaute2 (AGO2) by chromatin immunoprecipitation (ChIP)-seq in two different embryonic cell lines and found that AGO2 localizes to euchromatin but not heterochromatin. This localization pattern is further supported by immunofluorescence staining of polytene chromosomes and cell lines, and these studies also indicate that a substantial fraction of AGO2 resides in the nucleus. Intriguingly, AGO2 colocalizes extensively with CTCF/CP190 chromatin insulators but not with genomic regions corresponding to endogenous siRNA production. Moreover, AGO2, but not its catalytic activity or Dicer-2, is required for CTCF/CP190-dependent Fab-8 insulator function. AGO2 interacts physically with CTCF and CP190, and depletion of either CTCF or CP190 results in genome-wide loss of AGO2 chromatin association. Finally, mutation of CTCF, CP190, or AGO2 leads to reduction of chromosomal looping interactions, thereby altering gene expression. We propose that RNAi-independent recruitment of AGO2 to chromatin by insulator proteins promotes the definition of transcriptional domains throughout the genome.

| S-EPMC3165934 | biostudies-literature

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