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

Nature. 2017 Aug 17;548(7667):343-346. doi: 10.1038/nature23451. Epub 2017 Aug 11.

Abstract

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • CRISPR-Cas Systems / genetics
  • Cell Line, Tumor
  • Drug Resistance, Neoplasm / drug effects
  • Drug Resistance, Neoplasm / genetics*
  • Genetic Loci / drug effects
  • Genetic Loci / genetics*
  • Genome, Human / genetics*
  • Humans
  • Indoles / pharmacology*
  • Indoles / therapeutic use
  • Melanoma / drug therapy
  • Melanoma / genetics*
  • Microtubule-Associated Proteins / genetics
  • Microtubule-Associated Proteins / metabolism
  • Phenotype
  • Promoter Regions, Genetic / genetics
  • Protein Kinase Inhibitors / pharmacology
  • Protein Kinase Inhibitors / therapeutic use
  • Protein-Serine-Threonine Kinases / metabolism
  • Proto-Oncogene Proteins B-raf / antagonists & inhibitors
  • RNA, Long Noncoding / genetics*
  • Signal Transduction / drug effects
  • Sulfonamides / pharmacology*
  • Sulfonamides / therapeutic use
  • Transcription Initiation Site
  • Transcriptional Activation / genetics*
  • Vemurafenib

Substances

  • Indoles
  • MOB3B protein, human
  • Microtubule-Associated Proteins
  • Protein Kinase Inhibitors
  • RNA, Long Noncoding
  • Sulfonamides
  • Vemurafenib
  • BRAF protein, human
  • Hippo protein, human
  • Protein-Serine-Threonine Kinases
  • Proto-Oncogene Proteins B-raf