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

Gozde Korkmaz; Rui Lopes; Alejandro P. Ugalde; Ekaterina Nevedomskaya; Ruiqi Han; Ksenia Myacheva; Wilbert Zwart; Ran Elkon; Reuven Agami

doi:10.1038/nbt.3450

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

Gozde Korkmaz, Rui Lopes, Alejandro P. Ugalde, Ekaterina Nevedomskaya, Ruiqi Han, Ksenia Myacheva, Wilbert Zwart, Ran Elkon, Reuven Agami^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

310 Scopus citations

Abstract

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.

Original language	English
Pages (from-to)	192-198
Number of pages	7
Journal	Nature Biotechnology
Volume	34
Issue number	2
DOIs	https://doi.org/10.1038/nbt.3450
State	Published - 1 Feb 2016
Externally published	Yes

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abstract = "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.",

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AU - Korkmaz, Gozde

AU - Lopes, Rui

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AU - Han, Ruiqi

AU - Myacheva, Ksenia

AU - Zwart, Wilbert

AU - Elkon, Ran

AU - Agami, Reuven

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

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