CRISPR-based tools for targeted transcriptional and epigenetic regulation in plants

PLoS One. 2019 Sep 26;14(9):e0222778. doi: 10.1371/journal.pone.0222778. eCollection 2019.


Programmable gene regulators that can modulate the activity of selected targets in trans are a useful tool for probing and manipulating gene function. CRISPR technology provides a convenient method for gene targeting that can also be adapted for multiplexing and other modifications to enable strong regulation by a range of different effectors. We generated a vector toolbox for CRISPR/dCas9-based targeted gene regulation in plants, modified with the previously described MS2 system to amplify the strength of regulation, and using Golden Gate-based cloning to enable rapid vector assembly with a high degree of flexibility in the choice of promoters, effectors and targets. We tested the system using the floral regulator FLOWERING LOCUS T (FT) as a target and a range of different effector domains including the transcriptional activator VP64, the H3K27 acetyltransferase p300 and the H3K9 methyltransferase KRYPTONITE. When transformed into Arabidopsis thaliana, several of the constructs caused altered flowering time phenotypes that were associated with changes in FT expression and/or epigenetic status, thus demonstrating the effectiveness of the system. The MS2-CRISPR/dCas9 system can be used to modulate transcriptional activity and epigenetic status of specific target genes in plants, and provides a versatile tool that can easily be used with different targets and types of regulation for a range of applications.

Publication types

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

MeSH terms

  • Arabidopsis / genetics
  • Arabidopsis Proteins / genetics
  • CRISPR-Cas Systems / genetics*
  • Epigenesis, Genetic / genetics*
  • Feasibility Studies
  • Gene Expression Regulation, Plant*
  • Genetic Engineering / methods*
  • Genetic Vectors / genetics
  • Histone Code / genetics
  • Plants, Genetically Modified / genetics
  • Promoter Regions, Genetic / genetics
  • Transcriptional Activation*


  • Arabidopsis Proteins
  • FT protein, Arabidopsis

Grant support

This work was supported by the Knut and Alice Wallenberg Foundation grant KAW 2016.0025 to MS. ( The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.