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

Hou, Jiaqi; Ren, Ruifei; Xiao, Huangzhuo; Chen, Zhenfei; Yu, Jun; Zhang, Haorui; Shi, Qipeng; Hou, Hanxue; He, Shibin; Li, Lijia

doi:10.1007/s00425-021-03589-1

Cited by 20 publications

(18 citation statements)

References 83 publications

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“…The histone deacetylation site, enzyme, and potential function are summarized, and are then associated with transcriptional activation, histone deposition, and DNA repair [ 8 ]. HDACs have been characterized in multiple plants, such as in Marchantia polymorpha [ 9 ], Arabidopsis [ 10 ], Zea mays [ 11 ], Oryza sativa [ 12 , 13 ], Camellia sinensis [ 14 ] and Gossypium spp. [ 15 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of the HDAC Gene Family and Its Functional Characterization at Low Temperatures in Tartary Buckwheat (Fagopyrum tataricum)

Hou

et al. 2022

IJMS

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Histone deacetylases (HDACs), widely found in various types of eukaryotic cells, play crucial roles in biological process, including the biotic and abiotic stress responses in plants. However, no research on the HDACs of Fagopyrum tataricum has been reported. Here, 14 putative FtHDAC genes were identified and annotated in Fagopyrum tataricum. Their gene structure, motif composition, cis-acting elements, phylogenetic relationships, protein structure, alternative splicing events, subcellular localization and gene expression pattern were investigated. The gene structure showed FtHDACs were classified into three subfamilies. The promoter analysis revealed the presence of various cis-acting elements responsible for hormone, abiotic stress and developmental regulation for the specific induction of FtHDACs. Two duplication events were identified in FtHDA6-1, FtHDA6-2, and FtHDA19. The expression patterns of FtHDACs showed their correlation with the flavonoid synthesis pathway genes. In addition, alternative splicing, mRNA enrichment profiles and transgenic analysis showed the potential role of FtHDACs in cold responses. Our study characterized FtHDACs, providing a candidate gene family for agricultural breeding and crop improvement.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of the HDAC Gene Family and Its Functional Characterization at Low Temperatures in Tartary Buckwheat (Fagopyrum tataricum)

Hou

et al. 2022

IJMS

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“…Recent evidence shows that drought stress induces different expression patterns of HAT genes, resulting in changes in the levels of histone acetylation of drought response genes. In rice, the expression of OsHAG702, OsHAG703 and OsHAM701 was significantly increased after drought treatment [59]. In Chinese cabbage, the expression of BraHAC1, BraHAC2, BraHAC3, BraHAC4, BraHAC7, BraHAG2, BraHAG5, BraHAG7 and BraHAF1 was increased after drought treatment [48].…”

Section: Hatsmentioning

confidence: 98%

“…Yang et al revealed that the expression levels of nine examined GmHDACs (GmHDA6, GmHDA8, GmHDA13, GmHDA14, GmHDA16, GmSRT2, GmSRT4, GmHDT2, GmHDT4) were decreased by drought treatment in soybean [60]. In rice, the transcriptional levels of two HDAC genes (OsHDA703, OsHDA710) were significantly decreased, while OsHDA704, OsHDA705, OsHDA706, OsHDA711, OsHDA712, OsHDA713, OsHDT701 and OsSRT702 were significantly increased [59]. In Dendrobium officinale, HDAC genes displayed different expression patterns in different tissues.…”

Section: Hdacsmentioning

confidence: 99%

Histone Acetylation Changes in Plant Response to Drought Stress

Gao

et al. 2021

Genes

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Drought stress causes recurrent damage to a healthy ecosystem because it has major adverse effects on the growth and productivity of plants. However, plants have developed drought avoidance and resilience for survival through many strategies, such as increasing water absorption and conduction, reducing water loss and conversing growth stages. Understanding how plants respond and regulate drought stress would be important for creating and breeding better plants to help maintain a sound ecosystem. Epigenetic marks are a group of regulators affecting drought response and resilience in plants through modification of chromatin structure to control the transcription of pertinent genes. Histone acetylation is an ubiquitous epigenetic mark. The level of histone acetylation, which is regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), determines whether the chromatin is open or closed, thereby controlling access of DNA-binding proteins for transcriptional activation. In this review, we summarize histone acetylation changes in plant response to drought stress, and review the functions of HATs and HDACs in drought response and resistance.

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“…In Arabidopsis thaliana , 18 HDACs were identified, i.e., 12 in the HDA1/RPD3 family, 4 in the HD2 family, and 2 in the SIR family [ 13 ]. The HDACs family has also been detected in rice ( Oryza sativa japonica) [ 14 ], poplar ( Populus trichocarpa ) [ 15 ], and other plants [ 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 ]. However, it is unclear how frequently they occur in ornamental plants.…”

Section: Introductionmentioning

confidence: 99%

HDACs Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in Prunus mume

Meng

Wen

et al. 2022

IJMS

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Histone deacetylases (HDACs) play important roles in plant growth, development, and stress response. However, the pattern of how they are expressed in response to cold stress in the ornamental woody plant Prunus mume is poorly understood. Here, we identify 121 RoHDACs from eight Rosaceae plants of which 13 PmHDACs genes are from P. mume. A phylogenetic analysis suggests that the RoHDACs family is classified into three subfamilies, HDA1/RPD3, HD2, and SIR2. We identify 11 segmental duplication gene pairs of RoHDACs and find, via a sequence alignment, that the HDACs gene family, especially the plant-specific HD2 family, has experienced gene expansion and contraction at a recent genome evolution history. Each of the three HDACs subfamilies has its own conserved domains. The expression of PmHDACs in mei is found to be tissue-specific or tissue-wide. RNA-seq data and qRT-PCR experiments in cold treatments suggest that almost all PmHDACs genes—especially PmHDA1/6/14, PmHDT1, and PmSRT1/2—significantly respond to cold stress. Our analysis provides a fundamental insight into the phylogenetic relationship of the HDACs family in Rosaceae plants. Expression profiles of PmHDACs in response to cold stress could provide an important clue to improve the cold hardiness of mei.

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

Cited by 20 publications

References 83 publications

Genome-Wide Analysis of the HDAC Gene Family and Its Functional Characterization at Low Temperatures in Tartary Buckwheat (Fagopyrum tataricum)

Genome-Wide Analysis of the HDAC Gene Family and Its Functional Characterization at Low Temperatures in Tartary Buckwheat (Fagopyrum tataricum)

Histone Acetylation Changes in Plant Response to Drought Stress

HDACs Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in Prunus mume

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