Letter | Published:

Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood

Nature volume 548, pages 343346 (17 August 2017) | Download Citation

  • An Erratum to this article was published on 20 September 2017


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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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.

Author information

Author notes

    • Silvana Konermann
    •  & Neville E. Sanjana

    Present addresses: Salk Institute for Biological Studies, La Jolla, California, USA (S.K.); New York Genome Center, New York, New York, USA (N.E.S.); Department of Biology, New York University, New York, New York, USA (N.E.S.).


  1. Department of Biological Engineering, MIT, Cambridge, Massachusetts 02139, USA

    • Julia Joung
    •  & Feng Zhang
  2. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA

    • Julia Joung
    • , Jesse M. Engreitz
    • , Silvana Konermann
    • , Omar O. Abudayyeh
    • , Vanessa K. Verdine
    • , Francois Aguet
    • , Jonathan S. Gootenberg
    • , Neville E. Sanjana
    • , Jason B. Wright
    • , Charles P. Fulco
    • , Yuen-Yi Tseng
    • , Jesse S. Boehm
    • , Eric S. Lander
    •  & Feng Zhang
  3. McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts 02139, USA

    • Julia Joung
    • , Silvana Konermann
    • , Omar O. Abudayyeh
    • , Vanessa K. Verdine
    • , Jonathan S. Gootenberg
    • , Neville E. Sanjana
    • , Jason B. Wright
    •  & Feng Zhang
  4. Department of Brain and Cognitive Science, MIT, Cambridge, Massachusetts 02139, USA

    • Julia Joung
    • , Silvana Konermann
    • , Omar O. Abudayyeh
    • , Jonathan S. Gootenberg
    • , Neville E. Sanjana
    • , Jason B. Wright
    •  & Feng Zhang
  5. Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, USA

    • Omar O. Abudayyeh
  6. Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Jonathan S. Gootenberg
    • , Charles P. Fulco
    •  & Eric S. Lander
  7. Department of Surgery, Brigham and Women’s Hospital, Boston, Massachusetts 02115, USA

    • Charles H. Yoon
  8. Department of Biology, MIT, Cambridge, Massachusetts 02139, USA

    • Eric S. Lander


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J.J., S.K. and F.Z. conceived and designed the study. J.J. and S.K. conducted the screen. J.J., V.K.V. and J.S.G. performed validation experiments. N.E.S. and J.B.W. performed ATAC–seq and ChIP experiments. J.J. analysed data. O.O.A. and F.A. analysed clinical datasets. J.M.E., C.P.F. and E.S.L. helped with lncRNA experimental design and interpretation. Y.-Y.T., C.H.Y. and J.S.B. generated primary patient melanoma cell lines. J.J., J.M.E., E.S.L. and F.Z. wrote the paper with help from all authors.

Competing interests

The authors have filed a patent application related to this work. F.Z. is an advisor for Editas Medicine and Horizon Discovery.

Corresponding authors

Correspondence to Eric S. Lander or Feng Zhang.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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    This file contains data blots for figure 3b, and for extended data figures 7a-c and 9a.

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