CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

S John Liu; Max A Horlbeck; Seung Woo Cho; Harjus S Birk; Martina Malatesta; Daniel He; Frank J Attenello; Jacqueline E Villalta; Min Y Cho; Yuwen Chen; Mohammad A Mandegar; Michael P Olvera; Luke A Gilbert; Bruce R Conklin; Howard Y Chang; Jonathan S Weissman; Daniel A Lim

doi:10.1126/science.aah7111

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

Science. 2017 Jan 6;355(6320):aah7111. doi: 10.1126/science.aah7111. Epub 2016 Dec 15.

Authors

S John Liu^{1

2}, Max A Horlbeck^{3

4

5

6}, Seung Woo Cho⁷, Harjus S Birk^{1

2}, Martina Malatesta^{1

2}, Daniel He^{1

2}, Frank J Attenello^{1

2}, Jacqueline E Villalta^{3

4

5

6}, Min Y Cho^{3

4

5

6}, Yuwen Chen^{3

4

5

6}, Mohammad A Mandegar³, Michael P Olvera³, Luke A Gilbert^{3

4

5

6}, Bruce R Conklin^{3

8

9}, Howard Y Chang⁷, Jonathan S Weissman^{10

4

5

6}, Daniel A Lim^{11

2

12}

Affiliations

¹ Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA.
² Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA.
³ Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.
⁴ Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.
⁵ California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143, USA.
⁶ Center for RNA Systems Biology, University of California, San Francisco, CA 94143, USA.
⁷ Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
⁸ Deparment of Medicine, University of California, San Francisco, CA 94143, USA.
⁹ Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA.
¹⁰ Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA. daniel.lim@ucsf.edu jonathan.weissman@ucsf.edu.
¹¹ Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA. daniel.lim@ucsf.edu jonathan.weissman@ucsf.edu.
¹² San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA.

Abstract

The human genome produces thousands of long noncoding RNAs (lncRNAs)-transcripts >200 nucleotides long that do not encode proteins. Although critical roles in normal biology and disease have been revealed for a subset of lncRNAs, the function of the vast majority remains untested. We developed a CRISPR interference (CRISPRi) platform targeting 16,401 lncRNA loci in seven diverse cell lines, including six transformed cell lines and human induced pluripotent stem cells (iPSCs). Large-scale screening identified 499 lncRNA loci required for robust cellular growth, of which 89% showed growth-modifying function exclusively in one cell type. We further found that lncRNA knockdown can perturb complex transcriptional networks in a cell type-specific manner. These data underscore the functional importance and cell type specificity of many lncRNAs.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Cell Growth Processes / genetics
Cell Line
Clustered Regularly Interspaced Short Palindromic Repeats*
Gene Knockdown Techniques
Gene Regulatory Networks
Genetic Loci
Genetic Testing
Genome, Human*
Humans
Induced Pluripotent Stem Cells
Machine Learning
RNA Interference
RNA, Long Noncoding / genetics*
Transcription, Genetic
Transcriptome

Substances

RNA, Long Noncoding

Abstract

Publication types

MeSH terms

Substances

Grants and funding