Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [Capture Hi-C]

ABSTRACT: A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [Capture Hi-C]

PROVIDER: PRJNA508609 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8284500_1.fastq.gz	Fastqsanger.gz
	SRR8284500_2.fastq.gz	Fastqsanger.gz
	SRR8284501_1.fastq.gz	Fastqsanger.gz
	SRR8284501_2.fastq.gz	Fastqsanger.gz
	SRR8284502_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 38

Similar Datasets

A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development

Project description:A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development

| PRJNA508608 | ENA

A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [RNA-Seq]

Project description:A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [RNA-Seq]

| PRJNA508610 | ENA

A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [4C-seq]

Project description:A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [4C-seq]

| PRJNA508604 | ENA

A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [ATAC-seq]

Project description:A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [ATAC-seq]

| PRJNA508606 | ENA

A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [ChIP-Seq]

Project description:A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [ChIP-Seq]

| PRJNA508611 | ENA

A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development

Project description:During embryogenesis, enhancer-promoter interactions control gene transcriptional activation. These interactions can be tissue-specific or tissue-invariant and occur mostly within larger insulated regulatory domains called Topologically Associating Domains (TADs). Boundary elements, which delineate the extent of TADs, frequently interact with each other and have been associated with constitutive transcription and CTCF/Cohesin binding. In this work, we set out to investigate the regulatory role of a tissue-invariant, preformed interaction between two boundaries that involve the Shh gene and its unique limb enhancer, the ZRS, located one megabase away. Using CRISPR/Cas9 we specifically perturb CTCF binding sites or constitutive transcription at the ZRS-containing boundary, without altering the enhancer sequence. Using capture-HiC (cHiC) we show that both types of perturbation result in altered preformed chromatin interactions and lead to a reduction of Shh expression in developing limb buds. Finally, we demonstrate that the disruption of the chromatin structure in combination with a hypomorphic ZRS allele results in a dramatic Shh loss- of- function and digit agenesis. We thus propose that preformed chromatin structures can ensure stable enhancer promoter communication during development and robustness of gene transcriptional activation. This SuperSeries is composed of the SubSeries listed below.

2019-05-13 | GSE123388 | GEO

A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [RNA-Seq]

2019-05-13 | GSE123387 | GEO

A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [ChIP-Seq]

2019-05-13 | GSE123386 | GEO

A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [ATAC-seq]

2019-05-13 | GSE123383 | GEO

A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [4C-seq]

Project description:During embryogenesis, enhancer-promoter interactions control gene transcriptional activation. These interactions can be tissue-specific or tissue-invariant and occur mostly within larger insulated regulatory domains called Topologically Associating Domains (TADs). Boundary elements, which delineate the extent of TADs, frequently interact with each other and have been associated with constitutive transcription and CTCF/Cohesin binding. In this work, we set out to investigate the regulatory role of a tissue-invariant, preformed interaction between two boundaries that involve the Shh gene and its unique limb enhancer, the ZRS, located one megabase away. Using CRISPR/Cas9 we specifically perturb CTCF binding sites or constitutive transcription at the ZRS-containing boundary, without altering the enhancer sequence. Using capture-HiC (cHiC) we show that both types of perturbation result in altered preformed chromatin interactions and lead to a reduction of Shh expression in developing limb buds. Finally, we demonstrate that the disruption of the chromatin structure in combination with a hypomorphic ZRS allele results in a dramatic Shh loss of function and digit agenesis. We thus propose that preformed chromatin structures can ensure stable enhancer promoter communication during development and robustness of gene transcriptional activation.

2019-05-13 | GSE123382 | 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