Arabidopsis histone deacetylase HDA15 directly represses plant response to elevated ambient temperature

Elevated ambient temperatures affect plant growth and substantially impact biomass and crop yield. Recent results have indicated that chromatin remodelling is critical in plant thermal responses but how histone modification dynamics affects plant thermal response has not been clearly demonstarted. Here we show that Arabidopsis histone deacetylase genes HDA9, HDA15 and HDA19 play distinct roles in plant response to elevated ambient temperature. hda9 and hda19 mutants showed a warm-temperature-insensitive phenotype at 27°C, whereas hda15 plants displayed a constitutive warm-temperature-induced phenotype at 20°C and an enhanced thermal response at 27°C. The hda19 mutation led to upregulation of genes mostly related to stress response at both 20 and 27°C. The hda15 mutation resulted in upregulation of many warm temperature-responsive as well as metabolic genes at 20 and 27°C, while hda9 led to differential expression of a large number of genes at 20°C and impaired induction of warm-temperature-responsive genes at 27°C. HDA15 is associated with thermosensory mark genes at 20°C and that the association is decreased after shifting to 27°C, indicating that HDA15 is a direct repressor of plant thermal-responsive genes at normal temperature. In addition, as hda9, the hda15 mutation also led to upregulation of many metabolic genes and accumulation of primary metabolites. Furthermore, we show that HDA15 interacts with the transcription factor HFR1 (long Hypocotyl in Far Red1) to cooperatively repress warm-temperature response. Our study demonstrates that the histone deacetylases target to different sets of genes and play distinct roles in plant response to elevated ambient temperature.