RNA virus interference via CRISPR/Cas13a system in plants

Genome Biol. 2018 Jan 4;19(1):1. doi: 10.1186/s13059-017-1381-1.


Background: CRISPR/Cas systems confer immunity against invading nucleic acids and phages in bacteria and archaea. CRISPR/Cas13a (known previously as C2c2) is a class 2 type VI-A ribonuclease capable of targeting and cleaving single-stranded RNA (ssRNA) molecules of the phage genome. Here, we employ CRISPR/Cas13a to engineer interference with an RNA virus, Turnip Mosaic Virus (TuMV), in plants.

Results: CRISPR/Cas13a produces interference against green fluorescent protein (GFP)-expressing TuMV in transient assays and stable overexpression lines of Nicotiana benthamiana. CRISPR RNA (crRNAs) targeting the HC-Pro and GFP sequences exhibit better interference than those targeting other regions such as coat protein (CP) sequence. Cas13a can also process pre-crRNAs into functional crRNAs.

Conclusions: Our data indicate that CRISPR/Cas13a can be used for engineering interference against RNA viruses, providing a potential novel mechanism for RNA-guided immunity against RNA viruses and for other RNA manipulations in plants.

Keywords: CRISPR/Cas systems; CRISPR/Cas13a; Molecular immunity; RNA interference; RNA knockdown; Transcriptome regulation; Virus interference.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • CRISPR-Associated Proteins / metabolism
  • CRISPR-Cas Systems*
  • Genetic Engineering
  • Green Fluorescent Proteins / genetics
  • Potyvirus / genetics*
  • RNA / metabolism
  • RNA Interference
  • Ribonucleases / metabolism
  • Tobacco / genetics*
  • Tobacco / metabolism


  • CRISPR-Associated Proteins
  • Green Fluorescent Proteins
  • RNA
  • Ribonucleases

Supplementary concepts

  • Turnip mosaic virus