Versatile molecular tools enabling customizable DNA methylation editing in Arabidopsis

Tools to edit DNA methylation in a targeted manner are vital for establishing causal relationships between DNA methylation and its function, as well as for plant breeding and gene therapy. Here, by constructing dCas9 fusions to a panel of effectors and cofactors, we develop a range of highly effective tools for editing DNA methylation in Arabidopsis, including five tools for DNA methylation and six tools for DNA demethylation. Our tools show a diversity of performance features in terms of specificity and efficiency, offering either the capacity to edit DNA methylation in a target-specific manner or the ability to edit DNA methylation genome-wide due to potent off-target effect. Importantly, DNA methylation edited by these tools is inherited in the absence of transgene. These versatile tools pave the way for diverse applications of DNA methylation editing in not only research but also epigenetic breeding of crops. Targeted DNA methylation editing is critical for establishing the causal relationship between DNA methylation and its function as well as for epigenetic crop breeding. Here, the authors develop a CRISPR/dCas9-based fusion protein strategy for DNA methylation and demethylation editing in Arabidopsis.