Widespread natural variation of DNA methylation within angiosperms.
Widespread natural variation of DNA methylation within angiosperms.
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DOI：
10.1186/s13059-016-1059-0
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发表时间：
2016-09-27
期刊：
影响因子：
12.3
通讯作者：
Schmitz RJ
中科院分区：
文献类型：
--
作者：
Niederhuth CE;Bewick AJ;Ji L;Alabady MS;Kim KD;Li Q;Rohr NA;Rambani A;Burke JM;Udall JA;Egesi C;Schmutz J;Grimwood J;Jackson SA;Springer NM;Schmitz RJ
DNA甲基化是植物表观基因组的一个重要特征，参与异染色质的形成并影响基因表达。从自然变异的研究中已经发现了物种内DNA甲基化模式的广泛变异。然而，DNA甲基化在开花植物物种之间的变化程度仍然不清楚。为了了解开花植物物种之间DNA甲基化基因组模式的变化，我们比较了34种不同被子植物物种的单碱基分辨率DNA甲基化组。通过分析全基因组亚硫酸氢盐测序数据的系统发育背景下，它变得很清楚，有广泛的变化，整个被子植物基因体DNA甲基化，常染色体沉默的转座子和重复，以及沉默异染色质转座子。紫云英科具有降低的CHG甲基化水平，并且CG基因体甲基化也降低或丧失。禾本科的特征在于异染色质CHH甲基化的缺乏或减少以及CHH甲基化在基因区域中的富集。此外，在许多物种中观察到低水平的CHH甲基化，特别是在克隆繁殖的物种中。这些结果揭示了DNA甲基化在被子植物中的变异程度，并表明DNA甲基化模式广泛地反映了植物物种的进化和生活史。本文的在线版本（doi：10.1186/s13059-016-1059-0）包含补充材料，可供授权用户使用。
DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species. By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species. These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species. The online version of this article (doi:10.1186/s13059-016-1059-0) contains supplementary material, which is available to authorized users.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
DOI：
10.1038/nrm4043
发表时间：
2015-09
期刊：
Nature reviews. Molecular cell biology
影响因子：
--
作者：
Du J;Johnson LM;Jacobsen SE;Patel DJ
通讯作者：
Patel DJ
影响因子：
16.6
作者：
Chavez Montes, Ricardo A.;de Fatima Rosas-Cardenas, Flor;de Folter, Stefan
通讯作者：
de Folter, Stefan
影响因子：
4.9
作者：
Bao W;Kojima KK;Kohany O
通讯作者：
Kohany O
影响因子：
64.5
作者：
Calarco JP;Borges F;Donoghue MT;Van Ex F;Jullien PE;Lopes T;Gardner R;Berger F;Feijó JA;Becker JD;Martienssen RA
通讯作者：
Martienssen RA