DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
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DOI：
10.7554/elife.05255
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发表时间：
2015-05-05
期刊：
影响因子：
7.7
通讯作者：
Nordborg M
中科院分区：
文献类型：
--
作者：
Dubin MJ;Zhang P;Meng D;Remigereau MS;Osborne EJ;Paolo Casale F;Drewe P;Kahles A;Jean G;Vilhjálmsson B;Jagoda J;Irez S;Voronin V;Song Q;Long Q;Rätsch G;Stegle O;Clark RM;Nordborg M
表观基因组调节可能为生物体在世代内和世代之间提供一种适应机制。然而，这种情况发生的程度和涉及的机制都不清楚。在这里，我们研究了在两种不同温度下生长的瑞典拟南芥材料的DNA甲基化变异。环境影响仅限于转座子，在转座子中发现CHH甲基化随着温度的升高而增加。全基因组关联研究显示，广泛的CHH甲基化变异与顺式和反式的遗传变异密切相关，包括接近DNA甲基转移酶CMT2的主要反式关联。与CHH甲基化不同，CpG基因体甲基化(GBM)不受生长温度的影响，而是与起源纬度相关。来自寒冷地区的材料在基因组的相当一部分中具有较高的GBM水平，这与受影响基因的转录增加有关。Gwas揭示，这种影响很大程度上是由于反式作用基因座，其中许多显示出局部适应的证据。DOI：http://dx.doi.org/10.7554/eLife.05255.001生物需要迅速适应环境的变化。基因DNA序列的突变可以导致新的适应，但这可能需要很多代人的时间。相反，通过改变DNA在细胞中的包装方式来改变基因的开启方式，可以使生物体在世代内和世代之间适应。在生物体中控制基因的一种方式是通过一种名为DNA甲基化的过程，即在DNA中添加甲基标签，作为参与激活基因的其他蛋白质的标记。DNA是由四个不同的称为核苷酸的分子组成的，它们以不同的顺序排列，产生各种各样的DNA序列。一种类型的DNA甲基化可能发生在名为胞嘧啶的核苷酸后面跟着另外两个非胞嘧啶核苷酸的位置。另一种类型的甲基化可以发生在胞嘧啶后面跟着鸟嘌呤核苷酸的位置。然而，目前还不清楚DNA甲基化在让生物体适应不断变化的环境方面起到了多大的作用。这里，Dubin，Zhang，Meng，Remigereau等人。研究了一种名为拟南芥的植物的DNA甲基化。来自瑞典的几个不同品种的柳杉在两种不同的温度下生长。实验表明，生长在较高温度下的拟南芥植株更有可能在称为转座子的DNA片段上贴上甲基标签，转座子能够在基因组中移动。在不同的植物中，这种DNA甲基化的水平有很多不同，其中一些被证明与参与DNA甲基化的基因的变异有关。然而，这些植物中并不是所有的DNA甲基化都对植物生长的温度敏感。Dubin，Zhang，Meng，Remigereau等人。结果表明，在基因中发现的一种DNA甲基化模式取决于植物祖先来自瑞典北部的多远，而不是植物生长的温度。起源于更寒冷地区、更靠北的植物，在许多基因中有更多的DNA甲基化，这些基因更活跃。这些发现表明，这些植物的遗传差异强烈地影响着DNA甲基化的水平，它们提供了DNA甲基化与环境适应之间的第一个直接联系。未来的研究应该会揭示DNA甲基化是如何在这些植物中受到调控的，以及它是在适应中发挥关键作用，还是仅仅反映了基因组的其他变化。DOI：http://dx.doi.org/10.7554/eLife.05255.002
Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent to which this occurs, nor the mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects were limited to transposons, where CHH methylation was found to increase with temperature. Genome-wide association studies (GWAS) revealed that the extensive CHH methylation variation was strongly associated with genetic variants in both cis and trans, including a major trans-association close to the DNA methyltransferase CMT2. Unlike CHH methylation, CpG gene body methylation (GBM) was not affected by growth temperature, but was instead correlated with the latitude of origin. Accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was associated with increased transcription for the genes affected. GWAS revealed that this effect was largely due to trans-acting loci, many of which showed evidence of local adaptation. DOI: http://dx.doi.org/10.7554/eLife.05255.001 Organisms need to adapt quickly to changes in their environment. Mutations in the DNA sequence of genes can lead to new adaptations, but this can take many generations. Instead, altering how genes are switched on by changing how the DNA is packaged in cells can allow organisms to adapt within and between generations. One way that genes are controlled in organisms is by a process known as DNA methylation, where ‘methyl’ tags are added to DNA and act as markers for other proteins involved in activating genes. DNA is made of four different molecules called ‘nucleotides’ that are arranged in different orders to produce a vast variety of DNA sequences. One type of DNA methylation can happen at sites where a nucleotide called cytosine is followed by two other non-cytosine nucleotides. Another type of methylation can take place at sites where a cytosine is followed by a guanine nucleotide. However, it is not clear how big a role DNA methylation plays in allowing organisms to adapt to their changing environment. Here, Dubin, Zhang, Meng, Remigereau et al. studied DNA methylation in a plant called Arabidopsis thaliana. Several different varieties of A. thaliana plants from Sweden were grown at two different temperatures. The experiments showed that the A. thaliana plants grown at higher temperatures were more likely to have methyl tags attached to sections of DNA called transposons, which are able to move around the genome. There was a lot of variety in the levels of this DNA methylation in the different plants, and some of it was shown to be associated with variation in a gene that is involved in DNA methylation. However, not all of the DNA methylation in these plants was sensitive to the temperature the plants were grown in. Dubin, Zhang, Meng, Remigereau et al. show that the pattern of a type of DNA methylation that is found within genes depends on how far north in Sweden the plants' ancestors came from rather than the temperature the plants were grown in. Plants that originated from colder regions, farther north, had more DNA methylation within many genes and these genes were more active. These findings suggest that genetic differences in these plants strongly influence the levels of DNA methylation, and they provide the first direct link between DNA methylation and adaption to the environment. Future studies should reveal how DNA methylation is regulated in these plants, and whether it plays a key role in adaptation, or merely reflects other changes in the genome. DOI: http://dx.doi.org/10.7554/eLife.05255.002