Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A reference map of cardiac transcription factor chromatin occupancy identifies dynamic and conserved transcriptional enhancers

ABSTRACT: A reference map of cardiac transcription factor chromatin occupancy identifies dynamic and conserved transcriptional enhancers

PROVIDER: PRJNA510592 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11798798.fastq.gz	Fastqsanger.gz
	SRR8335330.fastq.gz	Fastqsanger.gz
	SRR8335340.fastq.gz	Fastqsanger.gz
	SRR8335350.fastq.gz	Fastqsanger.gz
	SRR8335331.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 45

Similar Datasets

A reference map of cardiac transcription factor chromatin occupancy identifies dynamic and conserved transcriptional enhancers

Project description:Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering the transcriptional programs that orchestrate organ development and homeostasis. Here we used biotinylated knockin alleles of seven key TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) that regulate heart development and homeostasis to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult heart. Our results show that these TFs have dynamic chromatin occupancy between developmental stages. We observed that multiple TFs often co-occupy the same chromatin region, exhibiting collaborative binding that overall was most consistent with indirect cooperativity. Regions with multiple TF binding were more likely to exhibit features of functional regulatory elements, including evolutionary conservation, chromatin accessibility, and activity in transcriptional enhancer assays. Although histone H3 acetylation on lysine 27 (H3K27ac) has been used to identify active enhancers, many regions occupied by multiple TFs lacked H3K27ac, and TF-bound regions with or without H3K27ac co-occupancy had similar region conservation and enhancer activity. Specific studies of TEAD1 demonstrated that it is a core component of the cardiac transcriptional network: physically interacted with NKX2-5 and MEF2C and co-occupied regulatory loci with other cardiac TFs to regulate cardiomyocyte-specific gene functions. Our study shows that co-occupancy by multiple TFs is a hallmark of a subset of functional transcriptional regulatory elements and provides a rich resource for deciphering the cardiac transcriptional regulatory network.

2019-09-13 | GSE124008 | GEO

A reference map of murine cardiac transcription factor chromatin occupancy identifies dynamic and conserved enhancers.

Project description:Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering developmental transcriptional programs. Here we use biotinylated knockin alleles of seven key cardiac TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult mouse heart. These maps show that TF occupancy is dynamic between developmental stages and that multiple TFs often collaboratively occupy the same chromatin region through indirect cooperativity. Multi-TF regions exhibit features of functional regulatory elements, including evolutionary conservation, chromatin accessibility, and activity in transcriptional enhancer assays. H3K27ac, a feature of many enhancers, incompletely overlaps multi-TF regions, and multi-TF regions lacking H3K27ac retain conservation and enhancer activity. TEAD1 is a core component of the cardiac transcriptional network, co-occupying cardiac regulatory regions and controlling cardiomyocyte-specific gene functions. Our study provides a resource for deciphering the cardiac transcriptional regulatory network and gaining insights into the molecular mechanisms governing heart development.

| S-EPMC6817842 | biostudies-literature

ChIP-seq Identification of Weakly Conserved Heart Enhancers

Project description:Accurate control of tissue-specific gene expression plays a pivotal role in heart development. However, few cardiac transcriptional enhancers have thus far been identified. Extreme non-coding sequence conservation successfully predicts enhancers active in many tissues, but fails to identify substantial numbers of enhancers active in the heart. We used ChIP-seq with the enhancer-associated protein p300 from mouse embryonic heart tissue to identify over three thousand candidate heart enhancers genome-wide. In contrast to other studied tissues at this time-point, most candidate heart enhancers are not deeply conserved in vertebrate evolution. Nevertheless, the testing of 130 candidate regions in a transgenic mouse assay revealed that most of them reproducibly function as enhancers active in the heart, irrespective of their degree of evolutionary constraint. These results provide evidence for tissue-dependent differences in evolutionary constraint of enhancers acting through the transcriptional co-activator p300 at this time-point, and identify a large population of poorly conserved heart enhancers. Examination of p300 binding in embryonic stage 11.5 mouse heart and midbrain

2010-08-22 | E-GEOD-22549 | biostudies-arrayexpress

Genome-wide occupancy map of NFIC in mouse pancreas

Project description:Genome-wide occupancy map of NFIC in mouse pancreas

| PRJNA750709 | ENA

Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome

Project description:Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome

| PRJNA592071 | ENA

Identification of Evolutionarily Conserved VSX2 Enhancers in Retinal Development

Project description:Identification of Evolutionarily Conserved VSX2 Enhancers in Retinal Development

| PRJNA1119636 | ENA

ChIP-seq Identification of Weakly Conserved Heart Enhancers

2010-08-22 | GSE22549 | GEO