Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
Genome Res. 2013 Oct;23(10):1651-62. doi: 10.1101/gr.153510.112. Epub 2013 Jun 5.
The maize genome, with its large complement of transposons and repeats, is a paradigm for the study of epigenetic mechanisms such as paramutation and imprinting. Here, we present the genome-wide map of cytosine methylation for two maize inbred lines, B73 and Mo17. CG (65%) and CHG (50%) methylation (where H = A, C, or T) is highest in transposons, while CHH (5%) methylation is likely guided by 24-nt, but not 21-nt, small interfering RNAs (siRNAs). Correlations with methylation patterns suggest that CG methylation in exons (8%) may deter insertion of Mutator transposon insertion, while CHG methylation at splice acceptor sites may inhibit RNA splicing. Using the methylation map as a guide, we used low-coverage sequencing to show that parental methylation differences are inherited by recombinant inbred lines. However, frequent methylation switches, guided by siRNA, persist for up to eight generations, suggesting that epigenetic inheritance resembling paramutation is much more common than previously supposed. The methylation map will provide an invaluable resource for epigenetic studies in maize.
玉米基因组含有大量的转座子和重复序列，是研究表观遗传机制（如基因印迹和位置效应）的典范。在这里，我们呈现了两个玉米自交系 B73 和 Mo17 的全基因组胞嘧啶甲基化图谱。CG（65%）和 CHG（50%）甲基化（其中 H = A、C 或 T）在转座子中含量最高，而 CHH（5%）甲基化可能由 24 个核苷酸而不是 21 个核苷酸的小干扰 RNA（siRNA）指导。与甲基化模式的相关性表明，外显子中的 CG 甲基化（8%）可能阻止 Mutator 转座子的插入，而剪接受体位点的 CHG 甲基化可能抑制 RNA 剪接。我们利用甲基化图谱作为指导，使用低覆盖度测序表明，重组自交系继承了亲本的甲基化差异。然而，在多达 8 代的时间里，siRNA 引导的频繁甲基化开关仍然存在，这表明类似于位置效应的表观遗传遗传比之前认为的要普遍得多。该甲基化图谱将为玉米的表观遗传学研究提供宝贵的资源。
