HDA6 mediated gene silencing mechanism is independent of RDR2 and DDC

Abstract

Epigenetic mechanisms involving histone modifications, DNA methylation and siRNA regulate gene silencing and heterochromatin formation in eukaryotes. In Arabidopsis, a RNA-dependent RNA polymerase gene RDR2, DNA methyltransferase genes DRM1, DRM2, CMT3, and a histone deacetylase gene HDA6 are involved in siRNA-mediated epigenetic gene silencing.
We identified the genes that were upregulated in hda6 by tiling-array-based transcriptome analysis. Those genes showed considerable overlap with the mapping sites of siRNA and DNA methylation. Surprisingly, the transcriptome analyses using the mutants of hda6, rdr2 and ddc (triple mutant of drm1, drm2, and cmt3) revealed the upregulated genes in hda6 hardly overlapped with those regulated by RDR2 and DDC. These data suggest that HDA6 regulates the gene silencing independently of RDR2 and DDC.