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

• Published in: Science (American Association for the Advancement of Science) Vol. 355; no. 6320; p. 39
• Main Authors: Liu, S. John, Horlbeck, Max A., Cho, Seung Woo, Birk, Harjus S., Malatesta, Martina, He, Daniel, Attenello, Frank J., Villalta, Jacqueline E., Cho, Min Y., Chen, Yuwen, Mandegar, Mohammad A., Olvera, Michael P., Gilbert, Luke A., Conklin, Bruce R., Chang, Howard Y., Weissman, Jonathan S., Lim, Daniel A.
• Format: Journal Article
• Language: English
• Published: United States American Association for the Advancement of Science 06.01.2017; The American Association for the Advancement of Science
• Subjects: Biology; Biotechnology; Cell growth; Cell Growth Processes - genetics; Cell Line; Cell lines; Chromatin; Clustered Regularly Interspaced Short Palindromic Repeats; Coding; CRISPR; Depletion; Gene expression; Gene Knockdown Techniques; Gene regulation; Gene Regulatory Networks; Genes; Genetic Loci; Genetic Testing; Genome, Human; Genomes; Humans; Induced Pluripotent Stem Cells; Inhibitory postsynaptic potentials; Interference; Libraries; Loci; Machine Learning; Non-coding RNA; Nucleotides; Phenotypes; Pluripotency; Proteins; RESEARCH ARTICLE SUMMARY; Ribonucleic acid; Ribonucleic acids; RNA; RNA Interference; RNA, Long Noncoding - genetics; Robustness; Screening; Screening Tests; Stem cells; Transcription; Transcription, Genetic; Transcriptome; Transcriptomes; Transcripts (Written Records)
• ISSN: 0036-8075; 1095-9203; 1095-9203
• DOI: 10.1126/science.aah7111

The human genome generates many thousands of long noncoding RNAs (lncRNAs). A very small number of lncRNAs have been shown to be functional. Liu et al. carried out a large-scale CRISPR-based screen to assess the function of ∼17,000 lncRNAs in seven different human cell lines. A considerable number (∼500) of the tested lncRNAs influenced cell growth, suggesting biological function. In almost all cases, though, the function was highly cell type—specific, often limited to just one cell type. Science , this issue p. 10.1126/science.aah7111 A considerable fraction of long noncoding RNAs have highly cell type–specific biological functions. 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.