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

Science. 2017 Jan 6;355(6320):aah7111. doi: 10.1126/science.aah7111. Epub 2016 Dec 15.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Cell Growth Processes / genetics
  • Cell Line
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • Gene Knockdown Techniques
  • Gene Regulatory Networks
  • Genetic Loci
  • Genetic Testing
  • Genome, Human*
  • Humans
  • Induced Pluripotent Stem Cells
  • Machine Learning
  • RNA Interference
  • RNA, Long Noncoding / genetics*
  • Transcription, Genetic
  • Transcriptome


  • RNA, Long Noncoding