Genomics

Dataset Information

303

CapStarr-seq: a high-throughput method for quantitative assessment of enhancer activity in mammals (ChIP-Seq)


ABSTRACT: Here we developed CapStarr-Seq, a novel high-throughput strategy to quantitatively assess enhancer activity in mammals. This approach couples capture of regions of interest to previously developed Starr-seq technique. Extensive assessment of CapStarr-seq demonstrated accurate quantification of enhancer activity. Furthermore, we found that enhancer strength correlates with binding complexity of tissue-specific transcription factors and super-enhancers, while additive enhancer activity isolates key genes involved in cell identity and function. ChIP-seq for the transcription factors HEB and TCF1, the DNaseI and the epigenetic modification H3K9me3 in DP thymocytes.

ORGANISM(S): Mus musculus  

SUBMITTER: Joaquin Zacarias   Laurent Vanhille  Salvatore Spicuglia  Ahmad Maqbool  Jean-Christophe Andrau  Nicolas Fernandez  Aurélien Griffon  Thi Dao  Benoit Ballester 

PROVIDER: E-GEOD-63732 | ArrayExpress | 2015-04-09

SECONDARY ACCESSION(S): GSE63732SRP050373PRJNA268944

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq.

Vanhille Laurent L   Griffon Aurélien A   Maqbool Muhammad Ahmad MA   Zacarias-Cabeza Joaquin J   Dao Lan T M LT   Fernandez Nicolas N   Ballester Benoit B   Andrau Jean Christophe JC   Spicuglia Salvatore S  

Nature communications 20150415


Cell-type specific regulation of gene expression requires the activation of promoters by distal genomic elements defined as enhancers. The identification and the characterization of enhancers are challenging in mammals due to their genome complexity. Here we develop CapStarr-Seq, a novel high-throughput strategy to quantitatively assess enhancer activity in mammals. This approach couples capture of regions of interest to previously developed Starr-seq technique. Extensive assessment of CapStarr-  ...[more]

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