Defining Essential Enhancers for Pluripotent Stem Cells Using a Features-Oriented CRISPR-Cas9 Screen

Hao Fei Wang; Tushar Warrier; Chadi A. Farran; Zi Hao Zheng; Qiao Rui Xing; Melissa J. Fullwood; Li Feng Zhang; Hu Li; Jian Xu; Tit Meng Lim; Yuin Han Loh

doi:10.1016/j.celrep.2020.108309

Defining Essential Enhancers for Pluripotent Stem Cells Using a Features-Oriented CRISPR-Cas9 Screen

Hao Fei Wang, Tushar Warrier, Chadi A. Farran, Zi Hao Zheng, Qiao Rui Xing, Melissa J. Fullwood, Li Feng Zhang, Hu Li, Jian Xu, Tit Meng Lim, Yuin Han Loh

Pharmacology

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

Abstract

cis-regulatory elements (CREs) regulate the expression of genes in their genomic neighborhoods and influence cellular processes such as cell-fate maintenance and differentiation. To date, there remain major gaps in the functional characterization of CREs and the identification of their target genes in the cellular native environment. In this study, we perform a features-oriented CRISPR-utilized systematic (FOCUS) screen of OCT4-bound CREs using CRISPR-Cas9 to identify functional enhancers important for pluripotency maintenance in mESCs. From the initial 235 candidates tested, 16 CREs are identified to be essential stem cell enhancers. Using RNA-seq and genomic 4C-seq, we further uncover a complex network of candidate CREs and their downstream target genes, which supports the growth and self-renewal of mESCs. Notably, an essential enhancer, CRE111, and its target, Lrrc31, form the important switch to modulate the LIF-JAK1-STAT3 signaling pathway.

Original language	English (US)
Article number	108309
Journal	Cell reports
Volume	33
Issue number	4
DOIs	https://doi.org/10.1016/j.celrep.2020.108309
State	Published - Oct 27 2020

Keywords

CRISPR screen
JAK-STAT3
LRRC31
OCT4-bound
essential cis-regulatory elements
pluripotency
super-enhancer

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology

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@article{8b181525791542208160ec08117ccafd,

title = "Defining Essential Enhancers for Pluripotent Stem Cells Using a Features-Oriented CRISPR-Cas9 Screen",

abstract = "cis-regulatory elements (CREs) regulate the expression of genes in their genomic neighborhoods and influence cellular processes such as cell-fate maintenance and differentiation. To date, there remain major gaps in the functional characterization of CREs and the identification of their target genes in the cellular native environment. In this study, we perform a features-oriented CRISPR-utilized systematic (FOCUS) screen of OCT4-bound CREs using CRISPR-Cas9 to identify functional enhancers important for pluripotency maintenance in mESCs. From the initial 235 candidates tested, 16 CREs are identified to be essential stem cell enhancers. Using RNA-seq and genomic 4C-seq, we further uncover a complex network of candidate CREs and their downstream target genes, which supports the growth and self-renewal of mESCs. Notably, an essential enhancer, CRE111, and its target, Lrrc31, form the important switch to modulate the LIF-JAK1-STAT3 signaling pathway.",

keywords = "CRISPR screen, JAK-STAT3, LRRC31, OCT4-bound, essential cis-regulatory elements, pluripotency, super-enhancer",

author = "Wang, {Hao Fei} and Tushar Warrier and Farran, {Chadi A.} and Zheng, {Zi Hao} and Xing, {Qiao Rui} and Fullwood, {Melissa J.} and Zhang, {Li Feng} and Hu Li and Jian Xu and Lim, {Tit Meng} and Loh, {Yuin Han}",

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year = "2020",

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doi = "10.1016/j.celrep.2020.108309",

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AU - Wang, Hao Fei

AU - Warrier, Tushar

AU - Farran, Chadi A.

AU - Zheng, Zi Hao

AU - Xing, Qiao Rui

AU - Fullwood, Melissa J.

AU - Zhang, Li Feng

AU - Li, Hu

AU - Xu, Jian

AU - Lim, Tit Meng

AU - Loh, Yuin Han

PY - 2020/10/27

Y1 - 2020/10/27

N2 - cis-regulatory elements (CREs) regulate the expression of genes in their genomic neighborhoods and influence cellular processes such as cell-fate maintenance and differentiation. To date, there remain major gaps in the functional characterization of CREs and the identification of their target genes in the cellular native environment. In this study, we perform a features-oriented CRISPR-utilized systematic (FOCUS) screen of OCT4-bound CREs using CRISPR-Cas9 to identify functional enhancers important for pluripotency maintenance in mESCs. From the initial 235 candidates tested, 16 CREs are identified to be essential stem cell enhancers. Using RNA-seq and genomic 4C-seq, we further uncover a complex network of candidate CREs and their downstream target genes, which supports the growth and self-renewal of mESCs. Notably, an essential enhancer, CRE111, and its target, Lrrc31, form the important switch to modulate the LIF-JAK1-STAT3 signaling pathway.

AB - cis-regulatory elements (CREs) regulate the expression of genes in their genomic neighborhoods and influence cellular processes such as cell-fate maintenance and differentiation. To date, there remain major gaps in the functional characterization of CREs and the identification of their target genes in the cellular native environment. In this study, we perform a features-oriented CRISPR-utilized systematic (FOCUS) screen of OCT4-bound CREs using CRISPR-Cas9 to identify functional enhancers important for pluripotency maintenance in mESCs. From the initial 235 candidates tested, 16 CREs are identified to be essential stem cell enhancers. Using RNA-seq and genomic 4C-seq, we further uncover a complex network of candidate CREs and their downstream target genes, which supports the growth and self-renewal of mESCs. Notably, an essential enhancer, CRE111, and its target, Lrrc31, form the important switch to modulate the LIF-JAK1-STAT3 signaling pathway.

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KW - super-enhancer

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Defining Essential Enhancers for Pluripotent Stem Cells Using a Features-Oriented CRISPR-Cas9 Screen

Abstract

Keywords

ASJC Scopus subject areas

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