Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple.
Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple.
复制标题
单碱基甲基化组分析揭示了与苹果缺水相关的动态表观基因组差异
DOI：
10.1111/pbi.12820
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发表时间：
2018-03
影响因子：
13.8
通讯作者：
Guan Q
中科院分区：
文献类型：
--
作者：
Xu J;Zhou S;Gong X;Song Y;van Nocker S;Ma F;Guan Q
胞嘧啶甲基化是表观遗传调控的重要特征，参与多种生物过程。尽管已经在基因组规模上对几种植物物种的胞嘧啶甲基化进行了分析，但人们普遍缺乏对在生物和非生物胁迫环境下生长的植物的整体和基因 DNA 甲基化动态的了解。在这项研究中，我们以单碱基分辨率绘制了商业苹果（Malus x Domestica）基因组中的胞嘧啶甲基化图谱，并分析了代表性干旱敏感和耐旱品种中与水分亏缺相关的甲基化模式的变化。我们发现苹果基因组在 CG、CHG 和 CHH 序列背景下分别表现出约 54%、约 38% 和约 8.5% 的甲基化。我们还记录了与缺水相关的基因表达变化，试图将甲基化和基因表达变化联系起来。全局甲基化和转录分析表明，启动子非甲基化基因的表达水平高于启动子甲基化基因。基因体甲基化似乎与基因表达呈正相关。缺水胁迫与许多基因的甲基化变化有关，包括编码转录因子（TF）和转座元件（TE）的基因。这些结果呈现了苹果基因组的甲基化图谱，并揭示了响应缺水胁迫的广泛 DNA 甲基化改变。这些数据将有助于了解在自然环境中生长并受到非生物和生物胁迫挑战的植物中 DNA 甲基化和基因表达之间的潜在联系。
Cytosine methylation is an essential feature of epigenetic regulation and is involved in various biological processes. Although cytosine methylation has been analysed at the genomic scale for several plant species, there is a general lack of understanding of the dynamics of global and genic DNA methylation in plants growing in environments challenged with biotic and abiotic stresses. In this study, we mapped cytosine methylation at single‐base resolution in the genome of commercial apple (Malus x domestica), and analysed changes in methylation patterns associated with water deficit in representative drought‐sensitive and drought‐tolerant cultivars. We found that the apple genome exhibits ~54%, ~38% and ~8.5% methylation at CG, CHG and CHH sequence contexts, respectively. We additionally documented changes in gene expression associated with water deficit in an attempt to link methylation and gene expression changes. Global methylation and transcription analysis revealed that promoter‐unmethylated genes showed higher expression levels than promoter‐methylated genes. Gene body methylation appears to be positively correlated with gene expression. Water deficit stress was associated with changes in methylation at a multitude of genes, including those encoding transcription factors (TFs) and transposable elements (TEs). These results present a methylome map of the apple genome and reveal widespread DNA methylation alterations in response to water deficit stress. These data will be helpful for understanding potential linkages between DNA methylation and gene expression in plants growing in natural environments and challenged with abiotic and biotic stresses.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
14.9
作者：
Kanehisa M;Araki M;Goto S;Hattori M;Hirakawa M;Itoh M;Katayama T;Kawashima S;Okuda S;Tokimatsu T;Yamanishi Y
通讯作者：
Yamanishi Y
影响因子：
56.9
作者：
Jacobsen, SE;Meyerowitz, EM
通讯作者：
Meyerowitz, EM
影响因子：
7
作者：
Gent JI;Ellis NA;Guo L;Harkess AE;Yao Y;Zhang X;Dawe RK
通讯作者：
Dawe RK