Repurposing the CRISPR-Cas9 system for targeted DNA methylation

Nucleic Acids Res. 2016 Jul 8;44(12):5615-28. doi: 10.1093/nar/gkw159. Epub 2016 Mar 11.


Epigenetic studies relied so far on correlations between epigenetic marks and gene expression pattern. Technologies developed for epigenome editing now enable direct study of functional relevance of precise epigenetic modifications and gene regulation. The reversible nature of epigenetic modifications, including DNA methylation, has been already exploited in cancer therapy for remodeling the aberrant epigenetic landscape. However, this was achieved non-selectively using epigenetic inhibitors. Epigenetic editing at specific loci represents a novel approach that might selectively and heritably alter gene expression. Here, we developed a CRISPR-Cas9-based tool for specific DNA methylation consisting of deactivated Cas9 (dCas9) nuclease and catalytic domain of the DNA methyltransferase DNMT3A targeted by co-expression of a guide RNA to any 20 bp DNA sequence followed by the NGG trinucleotide. We demonstrated targeted CpG methylation in a ∼35 bp wide region by the fusion protein. We also showed that multiple guide RNAs could target the dCas9-DNMT3A construct to multiple adjacent sites, which enabled methylation of a larger part of the promoter. DNA methylation activity was specific for the targeted region and heritable across mitotic divisions. Finally, we demonstrated that directed DNA methylation of a wider promoter region of the target loci IL6ST and BACH2 decreased their expression.

MeSH terms

  • Basic-Leucine Zipper Transcription Factors / genetics*
  • CRISPR-Cas Systems / genetics*
  • Cytokine Receptor gp130 / genetics*
  • DNA (Cytosine-5-)-Methyltransferases / genetics*
  • DNA Methylation / genetics*
  • DNA Methyltransferase 3A
  • Epigenesis, Genetic / genetics
  • Gene Expression Regulation / genetics
  • Promoter Regions, Genetic
  • RNA, Guide / genetics


  • BACH2 protein, human
  • Basic-Leucine Zipper Transcription Factors
  • DNMT3A protein, human
  • IL6ST protein, human
  • RNA, Guide
  • Cytokine Receptor gp130
  • DNA (Cytosine-5-)-Methyltransferases
  • DNA Methyltransferase 3A