Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

• Published in: Nature biotechnology Vol. 34; no. 2; pp. 192 - 198
• Main Authors: Korkmaz, Gozde, Lopes, Rui, Ugalde, Alejandro P, Nevedomskaya, Ekaterina, Han, Ruiqi, Myacheva, Ksenia, Zwart, Wilbert, Elkon, Ran, Agami, Reuven
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.02.2016; Nature Publishing Group
• Subjects: 13/1; 13/31; 45; 45/15; 45/23; 631/208/191; 631/208/200; 631/80/509; Agriculture; Animals; Bioinformatics; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Cell Line; CRISPR-Cas Systems - genetics; Enhancer Elements, Genetic - genetics; Gene Knockout Techniques; Genetic Engineering - methods; Genetic research; Genetic screening; Genetics; Genome, Human - genetics; Genomes; Genomics - methods; Human genome; Humans; letter; Life Sciences; MCF-7 Cells; Methods; Mice; Studies
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/nbt.3450

CRISPR-Cas9 is used for both enrichment and dropout screens of functional enhancers in human cells. Systematic identification of noncoding regulatory elements has, to date, mainly relied on large-scale reporter assays that do not reproduce endogenous conditions. We present two distinct CRISPR-Cas9 genetic screens to identify and characterize functional enhancers in their native context. Our strategy is to target Cas9 to transcription factor binding sites in enhancer regions. We identified several functional enhancer elements and characterized the role of two of them in mediating p53 ( TP53 ) and ERα ( ESR1 ) gene regulation. Moreover, we show that a genomic CRISPR-Cas9 tiling screen can precisely map functional domains within enhancer elements. Our approach expands the utility of CRISPR-Cas9 to elucidate the functions of the noncoding genome