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Nat Methods. 2017 Jun;14(6):629-635. doi: 10.1038/nmeth.4264. Epub 2017 Apr 17.

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

Diao Y1, Fang R1,2, Li B1, Meng Z3,4, Yu J1,5, Qiu Y1,2, Lin KC3,4, Huang H1,6, Liu T1, Marina RJ6, Jung I7, Shen Y8, Guan KL3,4, Ren B1,4,9.

Author information

1
Ludwig Institute for Cancer Research, La Jolla, California, USA.
2
Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, USA.
3
Department of Pharmacology, University of California, San Diego, La Jolla, California, USA.
4
Moores Cancer Center, University of California, San Diego, La Jolla, California, USA.
5
School of Life Sciences, University of Science and Technology of China, Hefei, China.
6
Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California, USA.
7
Biological Science, KAIST, Daejeon, South Korea.
8
Institute for Human Genetics and Department of Neurology, University of California, San Francisco, San Francisco, California, USA.
9
Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, California, USA.

Abstract

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.

PMID:
28417999
PMCID:
PMC5490986
DOI:
10.1038/nmeth.4264
[Indexed for MEDLINE]
Free PMC Article

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