RNAi/CRISPR Screens: from a Pool to a Valid Hit

Trends Biotechnol. 2019 Jan;37(1):38-55. doi: 10.1016/j.tibtech.2018.08.002. Epub 2018 Aug 31.


High-throughput genetic screens interfering with gene expression are invaluable tools to identify gene function and phenotype-to-genotype interactions. Implementing such screens in the laboratory is challenging, and the choice between currently available technologies based on RNAi and CRISPR/Cas9 (CRISPR-associated protein 9) is not trivial. Identifying reliable candidate hits requires a streamlined experimental setup adjusted to the specific biological question. Here, we provide a critical assessment of the various RNAi/CRISPR approaches to pooled screens and discuss their advantages and pitfalls. We specify a set of best practices for key parameters enabling a reproducible screen and provide a detailed overview of analysis methods and repositories for identifying the best candidate gene hits.

Keywords: CRISPR/Cas9; CRISPRa; CRISPRi; RNAi; essential genes; library pooled screens.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • Computational Biology / methods
  • Gene Knock-In Techniques / methods*
  • Gene Knockdown Techniques / methods*
  • Gene Knockout Techniques / methods*
  • Genetic Association Studies*
  • Genetic Testing / methods*
  • High-Throughput Screening Assays
  • RNA Interference*