<i>Arabidopsis</i> EDM2 promotes <i>IBM1</i> distal polyadenylation and regulates genome DNA methylation patterns

Significance The histone 3 lysine 9 demethylase Increase in BONSAI Methylation 1 (IBM1) is critical for preventing CHG (H=A, T, or C) methylation in plant genes. We found that the putative chromatin regulator Enhanced Downy Mildew 2 (EDM2) controls genome CHG methylation and transgene silencing by regulating alternative polyadenylation of IBM1 . EDM2 contains a composite plant homeo domain that simultaneously recognizes both repressive and active histone marks, allowing it to associate specifically with the intronic heterochromatin of IBM1 and other plant genes so that it may affect polyadenylation by methylating the RNA through an N6-adenine methyltransferase-like activity. This work significantly advances our understanding of the regulation of DNA methylome and mechanisms of antisilencing and alternative polyadenylation of intronic heterochromatin-containing genes.