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Nat Commun. 2015 Apr 15;6:6905. doi: 10.1038/ncomms7905.

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

Author information

1
1] Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), F-13009 Marseille, France [2] Aix-Marseille University UMR-S 1090, TAGC, F-13009 Marseille, France.
2
Institute of Molecular Genetics of Montpellier (IGMM), UMR5535 CNRS, 34293 Montpellier, France.
3
Institute of Biomedical Research, University of Birmingham, Birmingham, B15 2TT, UK.
4
1] Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), F-13009 Marseille, France [2] Aix-Marseille University UMR-S 1090, TAGC, F-13009 Marseille, France [3] TGML, IBiSA platform, 13288 Marseille, France.

Abstract

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-seq demonstrates accurate quantification of enhancer activity. Furthermore, we find that enhancer strength is associated with binding complexity of tissue-specific transcription factors and super-enhancers, while additive enhancer activity isolates key genes involved in cell identity and function. The CapStarr-Seq thus provides a fast and cost-effective approach to assess the activity of potential enhancers for a given cell type and will be helpful in decrypting transcription regulation mechanisms.

PMID:
25872643
DOI:
10.1038/ncomms7905
[Indexed for MEDLINE]

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