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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: Aurélien Griffon

PROVIDER: E-GEOD-63732 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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]

PMID: 25872643

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