Watanabe seed Co., Ltd, Machiyashiki, Misato-cho, Miyagi 987-8607, Japan.
Gene. 2012 Sep 15;506(2):301-9. doi: 10.1016/j.gene.2012.07.003. Epub 2012 Jul 13.
Difference in the level of expression of genes is one of the factors contributing to plant phenotype. As well as being under genetic control, gene expression is regulated by epigenetic processes such as DNA methylation and histone modifications. We compared genome-wide gene expression between Arabidopsis thaliana and the related species Arabidopsis lyrata subsp. lyrata and Arabidopsis halleri subsp. gemmifera to understand which genes might contribute to species differences. Genes categorized into response to stress tended to show differential expression between species, suggesting that divergence of expression in these genes contributes to adaptation to environmental conditions following the divergence of species. Regions methylated in A. lyrata were identified from Methylated-DNA immunoprecipitation, and this DNA methylation profile together with transcriptome data revealed that gene body methylation was not associated with differential gene expression between A. thaliana and A. lyrata. The DNA methylation status of four putative imprinted genes of A. lyrata was examined and found to be conserved in vegetative tissues between A. thaliana and A. lyrata in FIS2, HDG3, and HDG9, but not in HDG8.
基因表达水平的差异是导致植物表型的因素之一。基因表达除了受遗传控制外，还受到表观遗传过程的调控，如 DNA 甲基化和组蛋白修饰。我们比较了拟南芥和相关物种拟南芥亚种 lyrata 和拟南芥亚种 gemmifera 的全基因组基因表达，以了解哪些基因可能导致物种差异。分类为对胁迫反应的基因在物种间表现出差异表达，表明这些基因表达的差异有助于物种分化后对环境条件的适应。从甲基化 DNA 免疫沉淀中鉴定出拟南芥中甲基化的区域，该 DNA 甲基化图谱与转录组数据一起表明，基因体甲基化与拟南芥和拟南芥亚种 lyrata 之间的差异基因表达无关。对拟南芥亚种 lyrata 的四个假定印记基因的 DNA 甲基化状态进行了检测，发现 FIS2、HDG3 和 HDG9 中的基因在拟南芥和拟南芥亚种 lyrata 的营养组织中是保守的，但在 HDG8 中则不是。
