Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa.
Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa.
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DOI：
10.1186/1471-2229-13-92
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发表时间：
2013-06-25
影响因子：
5.3
通讯作者：
Strauss SH
中科院分区：
文献类型：
--
作者：
Vining K;Pomraning KR;Wilhelm LJ;Ma C;Pellegrini M;Di Y;Mockler TC;Freitag M;Strauss SH
胞嘧啶 DNA 甲基化 (5mC) 是一种表观遗传修饰，对于基因组稳定性和基因表达调控非常重要。 5mC 的扰动被认为是通过体外培养系统再生的植物表型变异的原因。然而，在基因组规模上，人们对 5mC 的变化模式及其在基因表达方面的功能作用知之甚少。更全面地了解 5mC 在体外操作过程中如何变化可能有助于开发减少或放大体外培养和植物转化的诱变和表观遗传效应的方法。我们在模拟杨属再生和植物转化常规方法的系统中研究了模型树种毛果杨的体外甲基化组。使用甲基化 DNA 免疫沉淀和高通量测序 (MeDIP-seq)，我们比较了微繁殖外植体、去分化愈伤组织和再生植物节间茎段的甲基化。我们发现，超过一半（56%）的基因组甲基化部分在三种组织类型中似乎存在差异甲基化。令人惊讶的是，基因启动子甲基化在组织之间变化不大，然而，外植体和愈伤组织中体甲基化基因的百分比从9%增加到14%，然后在再生节间下降到8%。百分之四十五的差异甲基化基因经历短暂甲基化，在愈伤组织中甲基化，并在再生体中去甲基化。这些基因在基因密度较高的染色体区域中出现的频率更高。与表达微阵列数据集的比较表明，在所有三种组织中，启动子和基因体均甲基化的基因的表达低于未甲基化或仅启动子甲基化的基因。四种丰富的转座元件在再生的节间中表现出最高水平的5mC。在体外分化和再生过程中，DNA 甲基化以高度基因和染色体差异的方式变化。在研究期间，再分化组织中的 5mC 没有重置为原始外植体中的 5mC。去分化细胞中基因体的高甲基化不会干扰转录，并且可能对丰富的转座元件的激活起到保护作用。
Cytosine DNA methylation (5mC) is an epigenetic modification that is important to genome stability and regulation of gene expression. Perturbations of 5mC have been implicated as a cause of phenotypic variation among plants regenerated through in vitro culture systems. However, the pattern of change in 5mC and its functional role with respect to gene expression, are poorly understood at the genome scale. A fuller understanding of how 5mC changes during in vitro manipulation may aid the development of methods for reducing or amplifying the mutagenic and epigenetic effects of in vitro culture and plant transformation. We investigated the in vitro methylome of the model tree species Populus trichocarpa in a system that mimics routine methods for regeneration and plant transformation in the genus Populus (poplar). Using methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq), we compared the methylomes of internode stem segments from micropropagated explants, dedifferentiated calli, and internodes from regenerated plants. We found that more than half (56%) of the methylated portion of the genome appeared to be differentially methylated among the three tissue types. Surprisingly, gene promoter methylation varied little among tissues, however, the percentage of body-methylated genes increased from 9% to 14% between explants and callus tissue, then decreased to 8% in regenerated internodes. Forty-five percent of differentially-methylated genes underwent transient methylation, becoming methylated in calli, and demethylated in regenerants. These genes were more frequent in chromosomal regions with higher gene density. Comparisons with an expression microarray dataset showed that genes methylated at both promoters and gene bodies had lower expression than genes that were unmethylated or only promoter-methylated in all three tissues. Four types of abundant transposable elements showed their highest levels of 5mC in regenerated internodes. DNA methylation varies in a highly gene- and chromosome-differential manner during in vitro differentiation and regeneration. 5mC in redifferentiated tissues was not reset to that in original explants during the study period. Hypermethylation of gene bodies in dedifferentiated cells did not interfere with transcription, and may serve a protective role against activation of abundant transposable elements.
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影响因子：
4.5
作者：
Fukai E;Umehara Y;Sato S;Endo M;Kouchi H;Hayashi M;Stougaard J;Hirochika H
通讯作者：
Hirochika H
DOI：
10.1016/j.cub.2011.07.002
发表时间：
2011-08-23
期刊：
Current biology : CB
影响因子：
--
作者：
Jiang C;Mithani A;Gan X;Belfield EJ;Klingler JP;Zhu JK;Ragoussis J;Mott R;Harberd NP
通讯作者：
Harberd NP
影响因子：
6.9
作者：
Elhiti M;Tahir M;Gulden RH;Khamiss K;Stasolla C
通讯作者：
Stasolla C
影响因子：
6.2
作者：
Bao, Y.;Dharmawardhana, P.;Strauss, Steven H.
通讯作者：
Strauss, Steven H.
影响因子：
2.7
作者：
Grafi, Gideon;Ben-Meir, Hagit;Zemach, Assaf
通讯作者：
Zemach, Assaf