DNA methylation and lipid metabolism are involved in GA-induced maize aleurone layers PCD as revealed by transcriptome analysis.

BACKGROUND: The aleurone layer is a part of many plant seeds, and during seed germination, aleurone cells undergo PCD, which is promoted by GA from the embryo. However, the numerous components of the GA signaling pathway that mediate PCD of the aleurone layers remain to be identified. Few genes and transcriptomes have been studied thus far in aleurone layers to improve our understanding of how PCD occurs and how the regulatory mechanism functions during PCD. Our previous studies have shown that histone deacetylases (HDACs) are required in GA-induced PCD of aleurone layer. To further explore the molecular mechanisms by which epigenetic modifications regulate aleurone PCD, we performed a global comparative transcriptome analysis of embryoless aleurones treated with GA or histone acetylase (HAT) inhibitors. RESULTS: In this study, a total of 7,919 differentially expressed genes (DEGs) were analyzed, 2,554 DEGs of which were found to be common under two treatments. These identified DEGs were involved in various biological processes, including DNA methylation, lipid metabolism and ROS signaling. Further investigations revealed that inhibition of DNA methyltransferases prevented aleurone PCD, suggesting that active DNA methylation plays a role in regulating aleurone PCD. GA or HAT inhibitor induced lipoxygenase gene expression, leading to lipid degradation, but this process was not affected by DNA methylation. However, DNA methylation inhibitor could regulate ROS-related gene expression and inhibit GA-induced production of hydrogen peroxide (H2O2). CONCLUSION: Overall, linking of lipoxygenase, DNA methylation, and H2O2 may indicate that GA-induced higher HDAC activity in aleurones causes breakdown of lipids via regulating lipoxygenase gene expression, and increased DNA methylation positively mediates H2O2 production; thus, DNA methylation and lipid metabolism pathways may represent an important and complex signaling network in maize aleurone PCD.

The histone deacetylase 1/GSK3/SHAGGY-like kinase 2/BRASSINAZOLE-RESISTANT 1 module controls lateral root formation in rice.

Lateral roots (LRs) are a main component of the root system of rice (Oryza sativa) that increases root surface area, enabling efficient absorption of water and nutrients. However, the molecular mechanism regulating LR formation in rice remains largely unknown. Here, we report that histone deacetylase 1 (OsHDAC1) positively regulates LR formation in rice. Rice OsHDAC1 RNAi plants produced fewer LRs than wild-type plants, whereas plants overexpressing OsHDAC1 exhibited increased LR proliferation by promoting LR primordia formation. Brassinosteroid treatment increased the LR number, as did mutation of GSK3/SHAGGY-like kinase 2 (OsGSK2), whereas overexpression of OsGSK2 decreased the LR number. Importantly, OsHDAC1 could directly interact with and deacetylate OsGSK2, inhibiting its activity. OsGSK2 deacetylation attenuated the interaction between OsGSK2 and BRASSINAZOLE-RESISTANT 1 (OsBZR1), leading to accumulation of OsBZR1. The overexpression of OsBZR1 increased LR formation by regulating Auxin/IAA signaling genes. Taken together, the results indicate that OsHDAC1 regulates LR formation in rice by deactivating OsGSK2, thereby preventing degradation of OsBZR1, a positive regulator of LR primordia formation. Our findings suggest that OsHDAC1 is a breeding target in rice that can improve resource capture.

Characteristic and evolution of HAT and HDAC genes in Gramineae genomes and their expression analysis under diverse stress in Oryza sativa.

MAIN CONCLUSION: Comprehensive characterization of Gramineae HATs and HDACs reveals their conservation and variation. The recent WGD/SD gene pairs in the CBP and RPD/HDA1 gene family may confer specific adaptive evolutionary changes. Expression of OsHAT and OsHDAC genes provides a new vision in different aspects of development and response to diverse stress. The histone acetylase (HAT) and histone deacetylase (HDAC) have been proven to be tightly linked to play a crucial role in plant growth, development and response to abiotic stress by regulating histone acetylation levels. However, the evolutionary dynamics and functional differentiation of HATs and HDACs in Gramineae remain largely unclear. In the present study, we identified 37 HAT genes and 110 HDAC genes in seven Gramineae genomes by a detailed analysis. Phylogenetic trees of these HAT and HDAC proteins were constructed to illustrate evolutionary relationship in Gramineae. Gene structure, protein property and protein motif composition illustrated the conservation and variation of HATs and HDACs in Gramineae. Gene duplication analysis suggested that recent whole genome duplication (WGD)/segmental duplication (SD) events contributed to the diversification of the CBP and RPD3/HDA1 gene family in Gramineae. Furthermore, promoter cis-element prediction indicated that OsHATs and OsHDACs were likely functional proteins and involved in various signaling pathways. Expression analysis by RNA-seq data showed that all OsHAT and OsHDAC genes were expressed in different tissues or development stages, revealing that they were ubiquitously expressed. In addition, we found that their expression patterns were altered in response to cold, drought, salt, light, abscisic acid (ABA), and indole-3-acetic acid (IAA) treatments. These findings provide the basis for further identification of candidate OsHAT and OsHDAC genes that may be utilized in regulating growth and development and improving crop tolerance to abiotic stress.