Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ecdysone-induced 3D chromatin reorganization involves active enhancers bound by Pipsqueak and Polycomb

ABSTRACT: Ecdysone-induced 3D chromatin reorganization involves active enhancers bound by Pipsqueak and Polycomb

PROVIDER: PRJNA484189 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7638410_1.fastq.gz	Fastqsanger.gz
	SRR7638410_2.fastq.gz	Fastqsanger.gz
	SRR7638401_1.fastq.gz	Fastqsanger.gz
	SRR7638401_2.fastq.gz	Fastqsanger.gz
	SRR7638411_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 42

Similar Datasets

Ecdysone-induced 3D chromatin reorganization involves active enhancers bound by Pipsqueak and Polycomb

Project description:In Drosophila, Polycomb (Pc) has emerged as a loop-anchored associated protein, but further investigation of its directed chromatin architecture is needed. It is recruited to DNA by GAGA-binding factors GAF and Pipsqueak (Psq). psq encodes distinct isoforms that contain or lack a BTB oligomerization domain, but their contribution to the general epigenetic role of Psq in development and cancer is rarely considered. Here, we use HiChIP in Drosophila cells to characterize the Pc- and Psq-directed genome architecture. We show that PsqS isoforms lacking the BTB domain are consistently found at Pc loop anchors and at active enhancers, including those responsive to ecdysone. PsqS mediates ecdysone-induced enhancer-promoter interactions, coordinating expression of a selective set of genes by chromatin looping. BTB-Psq isoforms, on the other hand, bind at architectural protein binding sites. Our findings support a BTB-directed role of Psq at different types of regulatory elements, mediating selective responses to hormonal cues.

2019-07-16 | GSE118047 | GEO

Ecdysone-Induced 3D Chromatin Reorganization Involves Active Enhancers Bound by Pipsqueak and Polycomb.

Project description:Evidence suggests that Polycomb (Pc) is present at chromatin loop anchors in Drosophila. Pc is recruited to DNA through interactions with the GAGA binding factors GAF and Pipsqueak (Psq). Using HiChIP in Drosophila cells, we find that the psq gene, which has diverse roles in development and tumorigenesis, encodes distinct isoforms with unanticipated roles in genome 3D architecture. The BR-C, ttk, and bab domain (BTB)-containing Psq isoform (PsqL) colocalizes genome-wide with known architectural proteins. Conversely, Psq lacking the BTB domain (PsqS) is consistently found at Pc loop anchors and at active enhancers, including those that respond to the hormone ecdysone. After stimulation by this hormone, chromatin 3D organization is altered to connect promoters and ecdysone-responsive enhancers bound by PsqS. Our findings link Psq variants lacking the BTB domain to Pc-bound active enhancers, thus shedding light into their molecular function in chromatin changes underlying the response to hormone stimulus.

| S-EPMC6754745 | biostudies-literature

Drosophila Ecdysone Receptor Study

Project description:We used the DamID method to systematically identify the binding sites of Ecdysone Receptor and its heterodimeric partner USP across the whole genome in Drosophila Kc cells. We find that the EcR sites are a subset of the USP sites and that only a proportion are ecdysone regulated from an accompanying ecdysone profiling study. The role of EcR/USP in the ecdysone network appears to be coordinated by the recruitment of many transcription factors as well as signaling molecules. Keywords: DamID, chromatin profiling, DNA microarray In this study we mapped the genomic binding sites of steroid hormone nuclear receptor EcR and USP in Kc167 cells using the DamID method. DamID involves the low level expression of a fusion protein consisting of DNA adenine methyltransferase (Dam) and a chromatin protein of interest. This fusion protein is targeted to the native binding sites of the chromatin protein, where Dam methylates adenines in the surrounding DNA. The methylated DNA fragments were isolated and amplified by selective PCR, labeled with a fluorescent dye and hybridized to whole genome tiling microarrays. In this study,experiments were done with samples obtained from independent experiments and include dye swaps.

2008-05-01 | E-GEOD-9156 | biostudies-arrayexpress

Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2

Project description:Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2

| PRJNA769098 | ENA

Drosophila Ecdysone Receptor Study

2008-05-01 | GSE9156 | GEO

Global quantitative proteomics reveals novel factors in the ecdysone signaling pathway in Drosophila melanogaster.

Project description:Global quantitative proteomics reveals novel factors in the ecdysone signaling pathway in Drosophila melanogaster.

2015-01-23 | PXD001455 | Pride

Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2 [Hi-C]

Project description:Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2 [Hi-C]

| PRJNA769206 | ENA

Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2 [ChIP-seq]

Project description:Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2 [ChIP-seq]

| PRJNA769207 | ENA

Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2 [RNA-seq]

Project description:Chromatin reorganization during myoblast differentiation involves the caspase-dependent removal of SATB2 [RNA-seq]

| PRJNA769208 | ENA

Transcription profiling of Drosophila Kc167 cells treaye with ecdysone and gamma irradiation to investigate ecdysone- and stress-induced expression profiles

Project description:Kc167 cells were mock-treated/treated with combinations of steroid hormone ecdysone and gamma-irradiation, and harvested. The expression profiles were determined using Affymetrix Drosophila Genechip 1 arrays. Comparisons between the sample groups allow the identification of genes with ecdysone- and/or radiation-responsive expression patterns. Experiment Overall Design: 1 set of control, ecdysone, gamma-irradiated, ecdysone + irradiated samples was analyzed.

2008-06-12 | E-GEOD-3072 | biostudies-arrayexpress

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