A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells.

Published

Journal Article

Millions of cis-regulatory elements are predicted to be present in the human genome, but direct evidence for their biological function is scarce. Here we report a high-throughput method, cis-regulatory element scan by tiling-deletion and sequencing (CREST-seq), for the unbiased discovery and functional assessment of cis-regulatory sequences in the genome. We used it to interrogate the 2-Mb POU5F1 locus in human embryonic stem cells, and identified 45 cis-regulatory elements. A majority of these elements have active chromatin marks, DNase hypersensitivity, and occupancy by multiple transcription factors, which confirms the utility of chromatin signatures in cis-element 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. These results point to the commonality of enhancer-like promoters in the human genome.

Full Text

Duke Authors

Cited Authors

  • Diao, Y; Fang, R; Li, B; Meng, Z; Yu, J; Qiu, Y; Lin, KC; Huang, H; Liu, T; Marina, RJ; Jung, I; Shen, Y; Guan, K-L; Ren, B

Published Date

  • June 2017

Published In

Volume / Issue

  • 14 / 6

Start / End Page

  • 629 - 635

PubMed ID

  • 28417999

Pubmed Central ID

  • 28417999

Electronic International Standard Serial Number (EISSN)

  • 1548-7105

International Standard Serial Number (ISSN)

  • 1548-7091

Digital Object Identifier (DOI)

  • 10.1038/nmeth.4264

Language

  • eng