Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana.,PLOS Genetics

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Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana.
PLOS Genetics ( IF 4.0 ) Pub Date : 2019-12-30 , DOI: 10.1371/journal.pgen.1008492
Eriko Sasaki ₁ , Taiji Kawakatsu _{2,

3,

4} , Joseph R Ecker _{2,

3,

5} , Magnus Nordborg ₁

Affiliation

DNA cytosine methylation is an epigenetic mark associated with silencing of transposable elements (TEs) and heterochromatin formation. In plants, it occurs in three sequence contexts: CG, CHG, and CHH (where H is A, T, or C). The latter does not allow direct inheritance of methylation during DNA replication due to lack of symmetry, and methylation must therefore be re-established every cell generation. Genome-wide association studies (GWAS) have previously shown that CMT2 and NRPE1 are major determinants of genome-wide patterns of TE CHH methylation. Here we instead focus on CHH methylation of individual TEs and TE-families, allowing us to identify the pathways involved in CHH methylation simply from natural variation and confirm the associations by comparing them with mutant phenotypes. Methylation at TEs targeted by the RNA-directed DNA methylation (RdDM) pathway is unaffected by CMT2 variation, but is strongly affected by variation at NRPE1, which is largely responsible for the longitudinal cline in this phenotype. In contrast, CMT2-targeted TEs are affected by both loci, which jointly explain 7.3% of the phenotypic variation (13.2% of total genetic effects). There is no longitudinal pattern for this phenotype, however, because the geographic patterns appear to compensate for each other in a pattern suggestive of stabilizing selection.

中文翻译：

CMT2和NRPE1的常见等位基因是拟南芥CHH甲基化变异的主要决定因素。

DNA胞嘧啶甲基化是与转座因子（TEs）沉默和异染色质形成相关的表观遗传标记。在植物中，它以三种序列形式出现：CG，CHG和CHH（其中H是A，T或C）。由于缺乏对称性，后者不允许在DNA复制期间直接继承甲基化作用，因此必须在每一代细胞中重新建立甲基化作用。全基因组关联研究（GWAS）先前已显示CMT2和NRPE1是TE CHH甲基化的全基因组模式的主要决定因素。在这里，我们将注意力集中在单个TE和TE家族的CHH甲基化上，从而使我们能够简单地从自然变异中识别CHH甲基化所涉及的途径，并通过将其与突变表型进行比较来确认其关联。通过RNA定向DNA甲基化（RdDM）途径靶向的TE处的甲基化不受CMT2变异的影响，但受NRPE1变异的强烈影响，NRPE1很大程度上负责该表型的纵向表达。相比之下，靶向CMT2的TE受两个基因座的影响，共同解释了7.3％的表型变异（占总遗传效应的13.2％）。但是，此表型没有纵向模式，因为地理模式似乎在暗示稳定选择的模式中相互补偿。总遗传效应的2％）。但是，此表型没有纵向模式，因为地理模式似乎在暗示稳定选择的模式中相互补偿。总遗传效应的2％）。但是，此表型没有纵向模式，因为地理模式似乎在暗示稳定选择的模式中相互补偿。

更新日期：2019-12-31

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