Mammalian genomes contain thousands of loci that transcribe long noncoding RNAs (lncRNAs)1,2, some of which are known to carry out critical roles in diverse cellular processes through a variety of mechanisms3,4,5,6,7,8. Although some lncRNA loci encode RNAs that act non-locally (in trans)5, 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 itself3,6,7,8. 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.
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Gene Expression Omnibus
We thank M. Guttman, C. M. Johannessen and M. Ghandi for helpful discussions and insights; A. Sayeed, R. Deasy, A. Rotem and B. Izar for generating the primary patient melanoma cell lines; and R. Belliveau, R. Macrae and the Zhang laboratory for support and advice. J.M.E. is supported by the Fannie and John Hertz Foundation. O.A.A. is supported by a Paul and Daisy Soros Fellowship and National Defense Science and Engineering Fellowship. J.S.G. is supported by a DOE Computational Science Graduate Fellowship. N.E.S. is supported by the NIH through NHGRI (R00-HG008171). J.B.W. is supported by the NIH through NIDDK (F32-DK096822). C.P.F. is supported by the National Defense Science and Engineering Graduate Fellowship. E.S.L. is supported by UM1HG008895 and funds from the Broad Institute. F.Z. is a New York Stem Cell Foundation-Robertson Investigator. F.Z. is supported by the NIH through NIMH (5DP1-MH100706 and 1R01-MH110049), NSF, Howard Hughes Medical Institute, the New York Stem Cell, Simons, Paul G. Allen Family, and Vallee Foundations; and James and Patricia Poitras, Robert Metcalfe, and David Cheng.
Extended data figures
This file contains Supplementary Tables 1-10 and a Supplementary Table guide.
About this article
Nature Reviews Molecular Cell Biology (2019)