CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming

Yanxia Liu; Chen Yu; Timothy Patrick Daley; Fangyuan Wang; William S Cao; Salil Bhate; Xueqiu Lin; Chris Still 2nd; Honglei Liu; Dehua Zhao; Haifeng Wang; Xinmin S Xie; Sheng Ding; Wing Hung Wong; Marius Wernig; Lei S Qi

doi:10.1016/j.stem.2018.09.003

CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming

Cell Stem Cell. 2018 Nov 1;23(5):758-771.e8. doi: 10.1016/j.stem.2018.09.003. Epub 2018 Oct 11.

Authors

Yanxia Liu¹, Chen Yu², Timothy Patrick Daley³, Fangyuan Wang⁴, William S Cao⁵, Salil Bhate⁶, Xueqiu Lin¹, Chris Still 2nd⁷, Honglei Liu⁶, Dehua Zhao¹, Haifeng Wang¹, Xinmin S Xie⁵, Sheng Ding⁸, Wing Hung Wong⁹, Marius Wernig¹⁰, Lei S Qi¹¹

Affiliations

¹ Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA.
² The Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA.
³ Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Statistics & Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.
⁴ Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Shanghai Institute of Rheumatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
⁵ AfaSci Research Laboratories, Redwood City, CA 94063, USA.
⁶ Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
⁷ Graduate Program of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.
⁸ The Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.
⁹ Department of Statistics & Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.
¹⁰ Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA 94305, USA.
¹¹ Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA. Electronic address: stanley.qi@stanford.edu.

Abstract

Comprehensive identification of factors that can specify neuronal fate could provide valuable insights into lineage specification and reprogramming, but systematic interrogation of transcription factors, and their interactions with each other, has proven technically challenging. We developed a CRISPR activation (CRISPRa) approach to systematically identify regulators of neuronal-fate specification. We activated expression of all endogenous transcription factors and other regulators via a pooled CRISPRa screen in embryonic stem cells, revealing genes including epigenetic regulators such as Ezh2 that can induce neuronal fate. Systematic CRISPR-based activation of factor pairs allowed us to generate a genetic interaction map for neuronal differentiation, with confirmation of top individual and combinatorial hits as bona fide inducers of neuronal fate. Several factor pairs could directly reprogram fibroblasts into neurons, which shared similar transcriptional programs with endogenous neurons. This study provides an unbiased discovery approach for systematic identification of genes that drive cell-fate acquisition.

Keywords: CRISPR; CRISPR activation; CRISPRa screen; DNA-binding factor; cell-fate determination; genetic interaction; neuronal reprogramming; stem cell; transcription factor.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
CRISPR-Cas Systems / genetics*
Cells, Cultured
Cellular Reprogramming / genetics*
Female
Gene Editing*
Male
Mice
Mice, Inbred C57BL
Mutagenesis, Site-Directed / methods*
Neurons / cytology*
Neurons / metabolism*
Rats
Rats, Sprague-Dawley
Transcription Factors / genetics*
Transcription Factors / metabolism

Substances

Transcription Factors

Abstract

Publication types

MeSH terms

Substances

Grants and funding