POWERDERESS and HDA9 interact and promote histone H3 deacetylation at specific lysine residues in Arabidopsis. [RNA-Seq]

Histone acetylation is a major epigenetic control mechanism that is tightly linked to the promotion of gene expression. Histone acetylation levels are balanced through the opposing activities of histone acetyltransferases (HATs) and histone deacetylases (HDACs). Arabidopsis HDAC genes (AtHDACs) compose a large gene family, and distinct phenotypes among AtHDAC mutants reflect the functional specificity of individual AtHDACs. However, the mechanisms underlying this functional diversity are largely unknown. Here, we show that POWERDRESS (PWR), a positive regulator of floral stem cell maintenance, interacts with HDA9 and promotes histone H3 deacetylation possibly by facilitating HDA9 function at target chromatin. The PWR SANT2 domain, which is homologous to that of subunits in animal HDAC complexes, showed specific binding affinity to acetylated histone H3. Three lysine residues (K9, K14 and K27) of H3 retained hyperacetylation status in both pwr and hda9 mutants. Genome wide H3K9 and H3K14 acetylation levels were generally elevated, and a large portion of acetylated targets overlapped between the pwr and hda9 mutants. Comparative analysis revealed a correlation between gene expression and histone H3 acetylation status in the pwr and hda9 mutants. In addition, PWR and HDA9 modulated the AGAMOUS-LIKE 19 (AGL19)-mediated flowering time pathway through histone H3 deacetylation. Finally, PWR was shown to physically interact with HDA9. We therefore propose that PWR acts as a subunit in a complex with HDA9 to negatively regulate the acetylation of specific lysine residues of histone H3 at genomic targets.