Sequence determinants of improved CRISPR sgRNA design

The CRISPR/Cas9 system has revolutionized mammalian somatic cell genetics. Genome-wide functional screens using CRISPR/Cas9-mediated knockout or dCas9 fusion-mediated inhibition/activation (CRISPRi/a) are powerful techniques for discovering phenotype-associated gene function. We systematically assessed the DNA sequence features that contribute to single guide RNA (sgRNA) efficiency in CRISPR-based screens. Leveraging the information from multiple designs, we derived a new sequence model for predicting sgRNA efficiency in CRISPR/Cas9 knockout experiments. Our model confirmed known features and suggested new features including a preference for cytosine at the cleavage site. The model was experimentally validated…

• NS
  National Science Foundation

  Awards: 1120368, DMS-1120368
• DC
  Dana-Farber Cancer Institute
• NI
  National Institute for Health and Care Research

  Awards: U01 CA180980, R01 GM113242-01