Targeted DNA demethylation of the <i>Arabidopsis</i> genome using the human TET1 catalytic domain.

Abstract

DNA methylation is an important epigenetic modification involved in gene regulation and transposable element silencing. Changes in DNA methylation can be heritable and, thus, can lead to the formation of stable epialleles. A well-characterized example of a stable epiallele in plants is <i>fwa</i>, which consists of the loss of DNA cytosine methylation (5mC) in the promoter of the <i>FLOWERING WAGENINGEN</i> (<i>FWA</i>) gene, causing up-regulation of <i>FWA</i> and a heritable late-flowering phenotype. Here we demonstrate that a fusion between the catalytic domain of the human demethylase TEN-ELEVEN TRANSLOCATION1 (TET1cd) and an artificial zinc finger (ZF) designed to target the <i>FWA</i> promoter can cause highly efficient targeted demethylation, <i>FWA</i> up-regulation, and a heritable late-flowering phenotype. Additional ZF-TET1cd fusions designed to target methylated regions of the <i>CACTA1</i> transposon also caused targeted demethylation and changes in expression. Finally, we have developed a CRISPR/dCas9-based targeted demethylation system using the TET1cd and a modified SunTag system. Similar to the ZF-TET1cd fusions, the SunTag-TET1cd system is able to target demethylation and activate gene expression when directed to the <i>FWA</i> or <i>CACTA1</i> loci. Our study provides tools for targeted removal of 5mC at specific loci in the genome with high specificity and minimal off-target effects. These tools provide the opportunity to develop new epialleles for traits of interest, and to reactivate expression of previously silenced genes, transgenes, or transposons.