Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood
Author(s)
Verdine, Vanessa K.; Aguet, Francois; Fulco, Charles P.; Tseng, Yuen-Yi; Boehm, Jesse S.; Joung, Julia; Engreitz, Jesse Michael; Konermann, Silvana M; Gootenberg, Jonathan S; Sanjana, Neville E; Wright, Jason; Yoon, Charles; Lander, Eric Steven; Zhang, Feng; Abudayyeh, Omar O.; ... Show more Show less
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Mammalian genomes contain thousands of loci that transcribe long noncoding RNAs (lncRNAs), some of which are known to carry out critical roles in diverse cellular processes through a variety of mechanisms. Although some lncRNA loci encode RNAs that act non-locally (in trans), there is emerging evidence that many lncRNA loci act locally (in cis) to regulate the expression of nearby genes—for example, through functions of the lncRNA promoter, transcription, or transcript itself. Despite their potentially important roles, it remains challenging to identify functional lncRNA loci and distinguish among these and other mechanisms. Here, to address these challenges, we developed a genome-scale CRISPR–Cas9 activation screen that targets more than 10,000 lncRNA transcriptional start sites to identify noncoding loci that influence a phenotype of interest. We found 11 lncRNA loci that, upon recruitment of an activator, mediate resistance to BRAF inhibitors in human melanoma cells. Most candidate loci appear to regulate nearby genes. Detailed analysis of one candidate, termed EMICERI, revealed that its transcriptional activation resulted in dosage-dependent activation of four neighbouring protein-coding genes, one of which confers the resistance phenotype. Our screening and characterization approach provides a CRISPR toolkit with which to systematically discover the functions of noncoding loci and elucidate their diverse roles in gene regulation and cellular function.
Date issued
2017-08Department
Harvard University--MIT Division of Health Sciences and Technology; Massachusetts Institute of Technology. Department of Biological Engineering; Massachusetts Institute of Technology. Department of Biology; Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences; McGovern Institute for Brain Research at MITJournal
Nature
Publisher
Nature Publishing Group
Citation
Joung, Julia et al. “Genome-Scale Activation Screen Identifies a lncRNA Locus Regulating a Gene Neighbourhood.” Nature 548, 7667 (August 2017): 343–346
Version: Author's final manuscript
ISSN
0028-0836
1476-4687