Histone acetylation recruits the SWR1 complex to regulate active DNA demethylation in Arabidopsis

The eukaryotic genome is divided into regions of heterochromatin and euchromatin. The histone variant H2A.Z specifically localizes at euchromatin and displays a genome-wide anti-correlation with DNA methylation. DNA methylation plays a central role in the epigenetic regulation of many eukaryotic genomes. Active DNA demethylation is critical for controlling the epigenome in plants and mammals. Yet, little is known about how DNA demethylases are recruited to target loci. Here we report that SWR1, a conserved histone H2A.Z deposition complex, regulates DNA demethylation in Arabidopsis thaliana by recruiting the plant DNA demethylase ROS1. A forward genetic screen for anti-silencing mutants identified two SWR1 components, PIE1 and ARP6, as cellular factors required for ROS1-mediated DNA demethylation. We further discovered two bromodomain-containing proteins, the methyl-DNA-binding protein AtMBD9, and NPX1, a plant homolog of ScBDF1 in yeast, as components of the SWR1 complex in Arabidopsis. AtMBD9 and NPX1 function redundantly in preventing DNA hypermethylation and transcriptional gene silencing by recognizing histone acetylation marks established by IDM1, a known regulator of DNA demethylation. We show that IDM1 is required for H2A.Z deposition in many genomic regions targeted for active DNA demethylation. We found that H2A.Z interacts with ROS1 and is required for locus-specific DNA demethylation and antisilencing. Our results reveal a role of H2A.Z in active DNA demethylation, and a mechanism through which DNA demethylases can be recruited to target regions by specific histone acetylation marks. Overall design: MethylC-Seq: 18 samples examined: 35S:SUC2 WT (6 replicates); mutants: h2a.z-2, arp6-4, idm1-9, pie1-6, ros1-14, and atmbd9-4npx1-4 (each mutant has 2 replicates). H2A.Z ChIP-Seq: 35S:SUC2 WT, arp6-4, pie1-6, idm1-9, ros1-14 (each genotype has 2 ChIP replicates and one Input control). H3K18Ac/H3K23Ac ChIP-Seq: 35S:SUC2 WT, arp6-4, idm1-9, atmbd9-4npx1-4 (each genotype has 2 ChIP replicates for H3K18Ac and H3K23Ac and one Input control)