Transgenic dCas9-DNMT3A mouse lines enable ex vivo and in vivo methylation editing with locus-dependent transcriptional effects

Abstract The number of epigenome-wide association studies linking CpG DNA methylation with disease, traits and exposures, continues to rise. Despite the rapid development of epigenome editing tools, establishing causation remains challenging, particularly in vivo . In this study, we developed and characterized three Cre-dependent CRISPR-based mouse lines that enable locus-specific DNA methylation deposition by either constitutive or inducible dCas9-DNMT3A expression. We demonstrate robust highly locus-specific DNA methylation deposition at MHC class II ( H2-Ab1) and interleukin 6 ( Il6) genes in bone marrow-derived myeloid cells ex vivo . Moreover, neuron-specific methylation targeting resulted in reduced cannabinoid receptor 1 ( Cnr1 ) expression in striatal neurons in vivo . Notably, we demonstrate that the causal effect of DNA methylation on gene expression is locus-dependent, reinforcing the necessity of such editing tools for detailed understanding of the role of DNA methylation and for addressing the causality of disease-associated CpGs.