CRISPR-mediated genetic interaction profiling identifies RNA binding proteins controlling metazoan fitness

Elife. 2017 Jul 18;6:e28129. doi: 10.7554/eLife.28129.


Genetic interaction screens have aided our understanding of complex genetic traits, diseases, and biological pathways. However, approaches for synthetic genetic analysis with null-alleles in metazoans have not been feasible. Here, we present a CRISPR/Cas9-based Synthetic Genetic Interaction (CRISPR-SGI) approach enabling systematic double-mutant generation. Applying this technique in Caenorhabditis elegans, we comprehensively screened interactions within a set of 14 conserved RNA binding protein genes, generating all possible single and double mutants. Many double mutants displayed fitness defects, revealing synthetic interactions. For one interaction between the MBNL1/2 ortholog mbl-1 and the ELAVL ortholog exc-7, double mutants displayed a severely shortened lifespan. Both genes are required for regulating hundreds of transcripts and isoforms, and both may play a critical role in lifespan extension through insulin signaling. Thus, CRISPR-SGI reveals a rich genetic interaction landscape between RNA binding proteins in maintaining organismal health, and will serve as a paradigm applicable to other biological questions.

Keywords: C. elegans; RNA binding proteins; RNA processing; chromosomes; evolutionary biology; genes; genomics; lifespan and fitness; synthetic genetic interactions.

Publication types

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

MeSH terms

  • Animals
  • Caenorhabditis elegans / genetics*
  • Caenorhabditis elegans / growth & development
  • Caenorhabditis elegans Proteins / genetics*
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • Epistasis, Genetic
  • High-Throughput Screening Assays / methods*
  • Mutation*
  • Phenotype
  • RNA Interference*
  • RNA-Binding Proteins / genetics*


  • Caenorhabditis elegans Proteins
  • EXC-7 protein, C elegans
  • RNA-Binding Proteins
  • mbl-1 protein, C elegans