Arabidopsis HDA6 Regulates Locus-Directed Heterochromatin Silencing In Cooperation With MET1

Abstract

In Arabidopsis, RNA-directed DNA methylation is involved in heterochromatin silencing. Histone deacetylase HDA6 has been identified as a component of such machinery. Genome-wide transcript profiling revealed that HDA6 and the CG DNA methyltransferase MET1 share common target loci for epigenetic silencing. The loci silenced by HDA6 carried abundant sequences corresponding to the RDR2-dependent 24nt siRNAs, however, their transcripts were mostly unaffected in the rdr2 mutant. The hda6 mutation caused the transition of epigenetic histone marks, such as histone acetylations on its directly targeted loci. Interestingly, we observed two different CG methylation statuses in the hda6 mutant. CG methylation was sustained at some loci where they were surrounded by flanking DNA-methylated regions. In contrast, CG methylation was lost where isolated from flanking DNA methylation. In both cases, loss of CHG and CHH methylation and transcriptional derepression occurred in the hda6 mutant. We also show that HDA6 specifically binds to its target loci, not the flanking methylated DNA. We propose that HDA6 regulates locus-directed heterochromatin silencing in cooperation with MET1.