A tiling1deletion based genetic screen for cis-regulatory element identification in mammalian cells

Millions of cis-regulatory elements are predicted in the human genome, but direct evidence for their biological function is still scarce. Here we report a high-throughput method, Cis-Regulatory Element Scan by Tiling-deletion and sequencing (CREST-seq), for unbiased discovery and functional assessment of cis regulatory sequences in the genome. We use it to interrogate the 2Mbp POU5F1 locus in the human embryonic stem cells and identify 45 cis-regulatory elements of POU5F1. A majority of these elements display active chromatin marks, DNase hypersensitivity and occupancy by multiple transcription factors, confirming the utility of chromatin signatures in cis elements mapping. Notably, 17 of them are previously annotated promoters of functionally unrelated genes, and like typical enhancers, they form extensive spatial contacts with the POU5F1 promoter. Taken together, these results support the utility of CREST-seq for large-scale cis regulatory element discovery and point to commonality of enhancer-like promoters in the human genome.