The HDA9-HY5 module epigenetically regulates flowering time in Arabidopsis thaliana.

Histone deacetylases (HDACs) play important roles in the repression of gene expression. Our previous study revealed that HISTONE DEACETYLASE 9 (HDA9) interacts with ELONGATED HYPOCOTYL 5 (HY5) and is involved in regulating plant autophagy in response to the light-to-dark transition and nitrogen starvation. In this study, we observed that the hda9-1 and hy5-215 single mutants flowered earlier compared with the wild-type Col-0; in addition, the hda9-1 hy5-215 double mutant flowered earlier than each single mutant. The expression of several positive flowering time genes was upregulated in the hda9-1, hy5-215, and hda9-1 hy5-215 mutants. Chromatin immunoprecipitation analysis demonstrated that HDA9 and HY5 bound directly to the promoter regions of PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) and CONSTANS-LIKE 5 (COL5) and repressed their expression through H3K9 and H3K27 deacetylation. Taken together, our results reveal the epigenetic mechanism explaining how the HDA9-HY5 module functions in controlling flowering time.