Involvement of Histone Modifications in Plant Abiotic Stress Responses

Yuan, Ling; Liu, Xuncheng; Luo, Ming; Yang, Shi-Nine; Wu, Keqiang

doi:10.1111/jipb.12060

Cited by 139 publications

(58 citation statements)

References 104 publications

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“…The changes in expression of EF‐hand domain and STr could have contributed to effective control of stomata opening for higher water use efficiency and more adequate carbon source transportation at the increased photosynthetic rate (Williams et al ; Day et al ). The increased expression of Methylase might have triggered epigenetic mechanisms that enriched the expression diversity of genes in response to the environmental change (Jaenisch and Bird ; Mirouze and Paszkowski ; Yuan et al ).…”

Section: Discussionmentioning

confidence: 99%

Population transcriptomics reveals a potentially positive role of expression diversity in adaptation

Xing

Zhu

et al. 2014

JIPB

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While it is widely accepted that genetic diversity determines the potential of adaptation, the role that gene expression variation plays in adaptation remains poorly known. Here we show that gene expression diversity could have played a positive role in the adaptation of Miscanthus lutarioriparius. RNA-seq was conducted for 80 individuals of the species, with half planted in the energy crop domestication site and the other half planted in the control site near native habitats. A leaf reference transcriptome consisting of 18,503 high-quality transcripts was obtained using a pipeline developed for de novo assembling with population RNA-seq data. The population structure and genetic diversity of M. lutarioriparius were estimated based on 30,609 genic single nucleotide polymorphisms. Population expression (E p ) and expression diversity (E d ) were defined to measure the average level and the magnitude of variation of a gene expression in the population, respectively. It was found that expression diversity increased while genetic diversity decreased after the species was transplanted from the native habitats to the harsh domestication site, especially for genes involved in abiotic stress resistance, histone methylation, and biomass synthesis under water limitation. The increased expression diversity could have enriched phenotypic variation directly subject to selections in the new environment.

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Section: Discussionmentioning

confidence: 99%

Population transcriptomics reveals a potentially positive role of expression diversity in adaptation

Xing

Zhu

et al. 2014

JIPB

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“…Epigenetic modifications are important regulatory mechanisms of gene transcription and play essential roles in plant development and stress responses (Yuan et al, 2013). The reversible process of histone acetylation and deacetylation by histone acetyltransferases (HATs) and histone deacetylases (HDACs) has been implicated in genome expression, chromatin structural organization, and gene function (Wang et al, 2014;Verdin and Ott, 2015).…”

Section: Introductionmentioning

confidence: 99%

Histone Deacetylase HDA9 With ABI4 Contributes to Abscisic Acid Homeostasis in Drought Stress Response

et al. 2020

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Drought stress, a major environmental factor, significantly affects plant growth and reproduction. Plants have evolved complex molecular mechanisms to tolerate drought stress. In this study, we investigated the function of the Arabidopsis thaliana RPD3-type HISTONE DEACETYLASE 9 (HDA9) in response to drought stress. The loss-of-function mutants hda9-1 and hda9-2 were insensitive to abscisic acid (ABA) and sensitive to drought stress. The ABA content in the hda9-1 mutant was reduced in wild type (WT) plant. Most histone deacetylases in animals and plants form complexes with other chromatin-remodeling components, such as transcription factors. In this study, we found that HDA9 interacts with the ABA INSENSITIVE 4 (ABI4) transcription factor using a yeast two-hybrid assay and coimmunoprecipitation. The expression of CYP707A1 and CYP707A2, which encode (+)-ABA 8′-hydroxylases, key enzymes in ABA catabolic pathways, was highly induced in hda9-1, hda9-2, abi4, and hda9-1 abi4 mutants upon drought stress. Chromatin immunoprecipitation and quantitative PCR showed that the HDA9 and ABI4 complex repressed the expression of CYP707A1 and CYP707A2 by directly binding to their promoters in response to drought stress. Taken together, these data suggest that HDA9 and ABI4 form a repressive complex to regulate the expression of CYP707A1 and CYP707A2 in response to drought stress in Arabidopsis.

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“…Epigenomic modifications modulate gene expression in response to environmental biotic and abiotic stimuli and developmental cues [1–3]. For example, covalent modifications of histone proteins have been demonstrated to be essential gene expression modulators [4].…”

Section: Introductionmentioning

confidence: 99%

Ethylene induces combinatorial effects of histone H3 acetylation in gene expression in Arabidopsis

et al. 2017

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BackgroundHistone acetylation and deacetylation are essential for gene regulation and have been implicated in the regulation of plant hormone responses. Many studies have indicated the role of histone acetylation in ethylene signaling; however, few studies have investigated how ethylene signaling regulates the genomic landscape of chromatin states. Recently, we found that ethylene can specifically elevate histone H3K14 acetylation and the non-canonical histone H3K23 acetylation in etiolated seedlings and the gene activation is positively associated with the elevation of H3K14Ac and H3K23Ac in response to ethylene. To assess the role of H3K9, H3K14, and H3K23 histone modifications in the ethylene response, we examined how ethylene regulates histone acetylation and the transcriptome at global level and in ethylene regulated genes both in wild type (Col-0) and ein2-5 seedlings.ResultsOur results revealed that H3K9Ac, H3K14Ac, and H3K23Ac are preferentially enriched around the transcription start sites and are positively correlated with gene expression levels in Col-0 and ein2-5 seedlings both with and without ethylene treatment. In the absence of ethylene, no combinatorial effect of H3K9Ac, H3K14Ac, and H3K23Ac on gene expression was detected. In the presence of ethylene, however, combined enrichment of the three histone acetylation marks was associated with high gene expression levels, and this ethylene-induced change was EIN2 dependent. In addition, we found that ethylene-regulated genes are expressed at medium or high levels, and a group of ethylene regulated genes are marked by either one of H3K9Ac, H3K14Ac or H3K23Ac. In this group of genes, the levels of H3K9Ac were altered by ethylene, but in the absence of ethylene the levels of H3K9Ac and peak breadths are distinguished in up- and down- regulated genes. In the presence of ethylene, the changes in the peak breadths and levels of H3K14Ac and H3K23Ac are required for the alteration of gene expressions.ConclusionsOur study reveals that the plant hormone ethylene induces combinatorial effects of H3K9Ac, K14Ac and K23Ac histone acetylation in gene expression genome widely. Further, for a group of ethylene regulated genes, in the absence of ethylene the levels and the covered breadths of H3K9Ac are the preexist markers for distinguishing up- and down- regulated genes, the change in the peak breadths and levels of H3K14Ac and H3K23Ac are required for the alteration of gene expression in the presence of ethylene.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3929-6) contains supplementary material, which is available to authorized users.

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Involvement of Histone Modifications in Plant Abiotic Stress Responses

Cited by 139 publications

References 104 publications

Population transcriptomics reveals a potentially positive role of expression diversity in adaptation

Population transcriptomics reveals a potentially positive role of expression diversity in adaptation

Histone Deacetylase HDA9 With ABI4 Contributes to Abscisic Acid Homeostasis in Drought Stress Response

Ethylene induces combinatorial effects of histone H3 acetylation in gene expression in Arabidopsis

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