Genome-wide profiling of histone H3K4-tri-methylation and gene expression in rice under drought stress. Plant Mol Biol

National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
Plant Molecular Biology (Impact Factor: 4.26). 11/2012; 81(1-2). DOI: 10.1007/s11103-012-9990-2
Source: PubMed


Histone modifications affect gene expression level. Several studies have shown that they may play key roles in regulating gene expression in plants under abiotic stress, but genome-wide surveys of such stress-related modifications are very limited, especially for crops. By using ChIP-Seq and RNA-Seq, we investigated the genome-wide distribution pattern of histone H3 lysine4 tri-methylation (H3K4me3) and the pattern's association with whole genome expression profiles of rice (Oryza sativa L.) under drought stress, one of the major and representative abiotic stresses. We detected 51.1 and 48 % of annotated genes with H3K4me3 modification in rice seedlings under normal growth (control) and drought stress conditions, respectively. By RNA-Seq, 76.7 and 79 % of annotated genes were detected with expression in rice seedlings under the control and drought stress conditions, respectively. Furthermore, 4,837 genes were differentially H3K4me3-modified (H3M), (3,927 genes with increased H3M; 910 genes with decreased H3M) and 5,866 genes were differentially expressed (2,145 up-regulated; 3,721 down-regulated) in drought stress. Differential H3K4me3 methylation only affects a small proportion of stress-responsive genes, and the H3K4me3 modification level was significantly and positively correlated with transcript level only for a subset of genes showing changes both in modification and expression with drought stress. Moreover, for the H3K4me3-regulated stress-related genes, the H3K4me3 modification level was mainly increased in genes with low expression and decreased in genes with high expression under drought stress. The comprehensive data of H3K4me3 and gene expression profiles in rice under drought stress provide a useful resource for future epigenomic regulation studies in plants under abiotic stresses.

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    • "The submergence of rice seedlings cause up-regulation of genes encoding both alcohol dehydrogenase and pyruvate decarboxylase, mainly due to the decrease of histone H3 Lys 4 trimethylation (H3K4me3) and histone H3 acetylation at these genes [15]. The droughtinduced expression of a number of stress-responsive genes is associated with the increase of H3K4me3 and histone H3 Lys 9 acetylation (H3K9ac) in Arabidopsis and rice [16] [21]. The functions of many epigenetic modifiers have been investigated, and some of them have been shown to be integrated in abiotic stress signaling pathways [22] [23] [24]. "
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    ABSTRACT: Plants have evolved a number of different mechanisms to respond and to adapt to abiotic stress for their survival. However, the regulatory mechanisms involved in coordinating abiotic stress tolerance and plant growth are not fully understood. Here, the function of OsMYB91, an R2R3-type MYB transcription factor of rice was explored. OsMYB91 was induced by abiotic stress, especially by salt stress. Analysis of chromatin structure of the gene revealed that salt stress led to rapid removal of DNA methylation from the promoter region and rapid changes of histone modifications in the locus. Plants over-expressing OsMYB91 showed reduced plant growth and accumulation of endogenous ABA under control conditions. Under salt stress, the over-expression plants showed enhanced tolerance with significant increases of proline levels and a highly enhanced capacity to scavenge active oxygen as well as the increased induction of OsP5CS1 and LOC_Os03g44130 compared to wild type, while RNAi plants were less sensitive. In addition, expression of OsMYB91 was also induced by other abiotic stresses and hormone treatment. More interestingly, SLR1, the rice homolog of Arabidopsis DELLA genes that have been shown to integrate endogenous developmental signals with adverse environmental conditions, was highly induced by OsMYB91 over-expression, while the salt-induction of SLR1 expression was impaired in the RNAi plants. These results suggested that OsMYB91 was a stress-responsive gene that might be involved in coordinating rice tolerance to abiotic stress and plant growth by regulating SLR1 expression. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
    Plant Science 07/2015; 236. DOI:10.1016/j.plantsci.2015.03.023 · 3.61 Impact Factor
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    • "Moreover, in the PEG2 line, several regions with enriched H3K4me3 binding corresponded with those found in the PEG1 line, further favoring the specificity of the PEG selection to fix certain epialleles. In plants, changes in histone methylation mark distribution have been implicated in response to a range of abiotic stresses, including drought, osmotic, and salt stresses (Sokol et al., 2007; van Dijk et al., 2010; Kim et al., 2012; Sani et al., 2013; Zong et al., 2013). In all these studies, histone mark changes resulted from sensitization for stress responsiveness. "
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    ABSTRACT: To increase both the yield potential and stability of crops, integrated breeding strategies are used that have mostly a direct genetic basis, but the utility of epigenetics to improve complex traits is unclear. A better understanding of the status of the epigenome and its contribution to the agronomic performance would help in developing approaches to incorporate the epigenetic component of complex traits into breeding programs. Starting from isogenic canola ( Brassica napus ) lines, epilines were generated by selecting, recurrently for three generations, lines with an increased energy use efficiency and drought tolerance. These epilines had an enhanced energy use efficiency, drought tolerance, nitrogen use efficiency, and yield under suboptimal conditions. Transcriptome analysis of the epilines and a line selected for its energy use efficiency solely revealed common differentially expressed genes related to the onset of stress tolerance-regulating signaling events. Genes related to responses to salt, osmotic, abscisic acid, and drought treatments were specifically differentially expressed in the drought-tolerant epilines. The status of the epigenome, scored as differential trimethylation of lysine 4 of histone 3, further supported the phenotype by targeting drought-responsive genes and facilitating the transcription of the differentially expressed genes. From these results, we conclude that the canola epigenome can be shaped by selection to increase yield and stress tolerance. Hence, these findings support the further development of strategies to incorporate epigenetics into breeding. Copyright © 2015, Plant Physiology.
    Plant physiology 06/2015; 168(4). DOI:10.1104/pp.15.00155 · 6.84 Impact Factor
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    • "Extensive studies on rice epigenetic regulation have been performed . For example, genome-wide distribution of histone modification in rice has been surveyed (Zong et al., 2013; Du et al., 2013; Malone et al., 2011; Li et al., 2008; Hu et al., 2012). Molecular and developmental function of many rice histone modification enzymes has been analyzed (Yokoo et al., 2014; Li et al., 2013; Cui et al., 2013; Chen et al., 2013; Sun et al., 2012; Ding et al., 2012; Li et al., 2011; Qin et al., 2010; Hu et al., 2009; Sun and Zhou, 2008; Huang et al., 2007). "
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    ABSTRACT: Histones, acting as the core of nucleosome, are the chief protein component of chromatin. They play an important role in gene regulation by covalent modification at several sites and histone variants replacement. Five major families of histones exist: H1, H2A, H2B, H3 and H4. The protein sequences within each family appear to be highly conserved. In this paper, we identified 60 histone proteins in rice (Oryza sativa) including 14 H2A, 15 H2B, 16 H3,11 H4 and 4 H1. Sequence analysis indicates that histone protein sequences in plant are more variable than in animal. Interestingly, we found a rice-specific H4 variant which showed several amino acid substitutions with canonical protein and was expressed in different tissues in a low level. Expression analysis indicates that a subset of histone genes were expressed in a similar pattern and many of them responded to stress conditions. Specifically, we found that two H2A.Z genes were down-regulated by stress in leaves but not in roots suggesting that they might be involved in stress response.
    Plant Physiology and Biochemistry 11/2014; 86. DOI:10.1016/j.plaphy.2014.11.012 · 2.76 Impact Factor
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