DNA methylation and gene expression in Mimulus guttatus.
DNA methylation and gene expression in Mimulus guttatus.
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DOI：
10.1186/s12864-015-1668-0
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发表时间：
2015-07-07
期刊：
影响因子：
4.4
通讯作者：
Hileman LC
中科院分区：
文献类型：
--
作者：
Colicchio JM;Miura F;Kelly JK;Ito T;Hileman LC
在生物体基因组中胞嘧啶核苷酸上甲基的存在（甲基化）是基因组稳定性、交换和基因调控的主要调节因子。DNA甲基化的能力被环境条件改变，并可能在世代之间传递，使其成为跨代表观遗传的主要候选者。在这里，我们进行了第一次分析的Mimulus guttatus甲基化，重点是DNA甲基化和基因表达之间的关系。我们提出了一个全基因组甲基化的自交系铁山62（IM 62）。DNA甲基化在染色体、基因组区域和基因之间变化。我们开发了一个基于DNA甲基化（R2 = 0.2）预测基因表达的模型。该模型的事后分析证实了先前的关系，并确定了甲基化和基因表达之间的新关系。此外，我们发现，DNA甲基化是显着耗尽附近的基因转录起始位点，这可能解释了最近发现的重组率在这些相同的区域。参考甲基化组的建立将为M.作为一个模型系统。使用基于模型的方法，我们证明了甲基化模式是基因表达变异的重要预测因子。该模型为差异甲基化分析提供了一种新的方法，该方法可以产生关于基因表达的独特且可检验的假设。本文的在线版本（doi：10.1186/s12864-015-1668-0）包含补充材料，可供授权用户使用。
The presence of methyl groups on cytosine nucleotides across an organism’s genome (methylation) is a major regulator of genome stability, crossing over, and gene regulation. The capacity for DNA methylation to be altered by environmental conditions, and potentially passed between generations, makes it a prime candidate for transgenerational epigenetic inheritance. Here we conduct the first analysis of the Mimulus guttatus methylome, with a focus on the relationship between DNA methylation and gene expression. We present a whole genome methylome for the inbred line Iron Mountain 62 (IM62). DNA methylation varies across chromosomes, genomic regions, and genes. We develop a model that predicts gene expression based on DNA methylation (R2 = 0.2). Post hoc analysis of this model confirms prior relationships, and identifies novel relationships between methylation and gene expression. Additionally, we find that DNA methylation is significantly depleted near gene transcriptional start sites, which may explain the recently discovered elevated rate of recombination in these same regions. The establishment here of a reference methylome will be a useful resource for the continued advancement of M. guttatus as a model system. Using a model-based approach, we demonstrate that methylation patterns are an important predictor of variation in gene expression. This model provides a novel approach for differential methylation analysis that generates distinct and testable hypotheses regarding gene expression. The online version of this article (doi:10.1186/s12864-015-1668-0) contains supplementary material, which is available to authorized users.
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影响因子：
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