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Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites.

Authors
  • Liu, Ying1, 2
  • Cao, Zhongzheng1, 2
  • Wang, Yinan1, 2
  • Guo, Yu1
  • Xu, Ping1
  • Yuan, Pengfei1
  • Liu, Zhiheng1, 2
  • He, Yuan1
  • Wei, Wensheng1
  • 1 Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China. , (China)
  • 2 Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China. , (China)
Type
Published Article
Journal
Nature Biotechnology
Publisher
Springer Nature
Publication Date
Nov 05, 2018
Identifiers
DOI: 10.1038/nbt.4283
PMID: 30395134
Source
Medline
Language
English
License
Unknown

Abstract

The functions of many long noncoding RNAs (lncRNAs) in the human genome remain unknown owing to the lack of scalable loss-of-function screening tools. We previously used pairs of CRISPR-Cas9 (refs. 1, 2, 3) single guide RNAs (sgRNAs) for small-scale functional screening of lncRNAs. Here we demonstrate genome-wide screening of lncRNA function using sgRNAs to target splice sites and achieve exon skipping or intron retention. Splice-site targeting outperformed a conventional CRISPR library in a negative selection screen targeting 79 ribosomal genes. Using a genome-scale library of splicing-targeting sgRNAs, we performed a screen covering 10,996 lncRNAs and identified 230 that are essential for cellular growth of chronic myeloid leukemia K562 cells. Screening GM12878 lymphoblastoid cells and HeLa cells with the same library identified cell-type-specific differences in lncRNA essentiality. Extensive validation confirmed the robustness of our approach.

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