Genome-Wide CRISPR Screening to Identify Mammalian Factors that Regulate Intron Retention

Anna M. Scarborough, Ashwin Govindan, Nicholas K. Conrad

Research output: Chapter in Book/Report/Conference proceedingChapter


Intron retention (IR) regulates gene expression to control fundamental biological processes like metabolism, differentiation, and cell cycle. Despite a wide variety of genes controlled by IR, few techniques are available to identify regulators of IR in an unbiased manner. Here, we describe a CRISPR knockout screening method that can be applied to uncover regulators of IR. This method uses GFP reporter constructs containing a retained intron from a gene of interest such that GFP signal is regulated by IR in the same fashion as the endogenous gene. The GFP levels are then used as a readout for genome-wide CRISPR screening. We have successfully used this approach to identify novel regulator of IR of the MAT2A transcript and propose that similar screens will be broadly applicable for the identification of novel factors that control IR of specific transcripts.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages22
StatePublished - 2022

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • CRISPR screens
  • Intron detention
  • Intron retention
  • MAT2A
  • OGT
  • Posttranscriptional regulation
  • Splicing

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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