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

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. Overall design: ChIP-seq for the transcription factors HEB and TCF1, the DNaseI and the epigenetic modification H3K9me3 in DP thymocytes.