The anti-DNA methylation mark histone H3 lysine 4 methylation recruits DNA demethylases in Arabidopsis [ChIP-seq]

Patterning of DNA methylation in eukaryotic genomes is shaped by de novo methylation, maintenance mechanisms, and demethylation pathways, but how these processes interface with epigenetic modification of histones is poorly understood. We found that the targeting of histone H3 lysine four trimethylation (H3K4me3) with the catalytic domain of the SDG2 histone methyltransferase potently erased DNA methylation and gene silencing at FWA and other genes, and also erased CG DNA methylation in the transcribed region of genes. This methylation erasure was completely blocked in the ros1 dml2 dml3 triple mutant which eliminates DNA demethylation enzymes, showing that H3K4me3 promotes the active removal of DNA methylation rather than preventing CG methylation maintenance. We also found that targeting the removal of H3K4me3 with the novel protein TRBIP1, which acts in part by recruiting the H3K4me3 demethylase JMJ14, causes potent gene silencing. Furthermore, using a CRISPR-based system to simultaneously target both TRBIP1 and a CG specific DNA methyltransferase, we observed more potent establishment of DNA methylation and gene silencing than targeting the DNA methyltransferase by itself. These results highlight H3K4me3 as a potent anti-DNA methylation mark, and reveal potent and specific tools for epigenome engineering. Overall design: To investigate the genes that can be upregulated by SDG2-ZF, RNA-seq of SDG2-ZF in both Col-0 background and rdd mutant background versus Col-0 and rdd mutant were performed. Chromatin immunoprecipitation sequencing (ChIP-seq) of myc-ROS1, Histone H3K4me3, H3K14ad, H2A.Z and ect was performed in the SDG2-ZF. Whole genome bisulfite sequencing (WGBS) was also performed to evaluate the genoe wide DNA methylation level of SDG2-ZF, TRBIP1-dCAS9-MQ1v, SunTag-TRBIP1-MQ1v, SunTag-StykC-TRBIP1-MQ1v and ect. Bifulfite PCR sequencing (BS-PCR-seq) was also performed to measure the DNA methylation level of Arabidopsis FWA gene promoter.