Recent advances in the regulation of histone lysine methylation in plants and the role of this modification in the developmental programming of Arabidopsis are discussed.

BackgroundHistone deacetylases (HDACs) function as key epigenetic factors in repressing the expression of genes in multiple aspects of plant growth, development and plant response to abiotic or biotic stresses. To date, the molecular function of HDACs is well described in Arabidopsis thaliana, but no systematic analysis of this gene family in soybean (Glycine max) has been reported.ResultsIn this study, 28 HDAC genes from soybean genome were identified, which were asymmetrically distributed on 12 chromosomes. Phylogenetic analysis demonstrated that GmHDACs fall into three major groups previously named RPD3/HDA1, SIR2, and HD2. Subcellular localization analysis revealed that YFP-tagged GmSRT4, GmHDT2 and GmHDT4 were predominantly localized in the nucleus, whereas GmHDA6, GmHDA13, GmHDA14 and GmHDA16 were found in both the cytoplasm and nucleus. Real-time quantitative PCR showed that GmHDA6, GmHDA13, GmHDA14, GmHDA16 and GmHDT4 were broadly expressed across plant tissues, while GmHDA8, GmSRT2, GmSRT4 and GmHDT2 showed differential expression across various tissues. Interestingly, we measured differential changes in GmHDACs transcripts accumulation in response to several abiotic cues, indicating that these epigenetic modifiers could potentially be part of a dynamic transcriptional response to stress in soybean. Finally, we show that the levels of histone marks previously reported to be associated with plant HDACs are modulated by cold and heat in this legume.ConclusionWe have identified and classified 28 HDAC genes in soybean. Our data provides insights into the evolution of the HDAC gene family and further support the hypothesis that these genes are important for the plant responses to environmental stress.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1454-7) contains supplementary material, which is available to authorized users.

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.