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.
High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq
Vanhille, L.; Griffon, A.; Maqbool, M. A.; Zacarias-Cabeza, J.; Dao, L. T.; Fernandez, N.; Ballester, B.; Andrau, J. C.; Spicuglia, S.
2015 / vol 6 / pages 6905
2041-1723 (Electronic) 2041-1723 (Linking)
IGMM team(s) involved in this publication
Transcription and Epigenomics in developing T cells
Animals; Mice; Chromatin Immunoprecipitation; Enhancer Elements, Genetic/*genetics; Gene Expression Regulation/*genetics; Gene Expression/*genetics; High-Throughput Nucleotide Sequencing/*methods; Male; NIH 3T3 Cells; Promoter Regions, Genetic/genetics; Sequence Analysis, DNA/methods; Transcription Factors/*genetics