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Nat Biotechnol. 2016 Feb;34(2):192-8. doi: 10.1038/nbt.3450. Epub 2016 Jan 11.

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

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Division of Biological Stress Response, the Netherlands Cancer Institute, Amsterdam, the Netherlands.
Division of Molecular Pathology, the Netherlands Cancer Institute, Amsterdam, the Netherlands.
Erasmus MC, Rotterdam University, Rotterdam, the Netherlands.


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 ERĪ± (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.

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