背景回顾：Parent-of-origin–dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin–specific expression. 

研究目的和材料：To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. 

结果1：Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling.

结果2：However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. 

结果3：However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. 

结果4：Correlating epigenetic and genetic variation occurred at key regulatory regions—the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. 

结论：Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution.

 摘 要 

哺乳动物和有花植物中依赖于亲本起源的基因表达是由遗传自父本和母本等位基因上的染色质印记差异所导致的。在种子的胚乳组织中，印记基因的表达与遗传自母本DNA的局部低甲基化有关，而与父本无关，其中某些小RNAs也表现出亲本起源的特异性基因表达。为了理解水稻中基因组印记机制的演化，作者分析了四个水稻栽培种之间的印记分化，这四个水稻栽培种囊括了粳稻（日本晴和Kitaake）和籼稻亚种（93-11和IR64）。大多数的印记基因在不同栽培种中均表现出印记表达，并且显著富集于染色质和转录调控、发育和信号转导。但是，4%～11%的印记基因表现出分化印记的现象。通过对DNA甲基化和小RNAs的分析，作者发现那些能够形成胚乳特异性24nt小RNA的位点表现出更低水平的RNA指导的DNA甲基化，经常重叠基因区域，并且印记是基因的四倍左右。但是，印记分化多与局部DNA甲基化表观突变有关（17个位点中，9个位点具有此特征），这些表观突变在亚种内较为稳定。这9个局部表观突变的位点中有4个存在小片段的插入/缺失事件和转座因子插入事件，并其余8个位点中的另外4个位点与印记分化相关。表观遗传变异与遗传变异的相关性主要出现在关键调控区，偏母系表达基因主要在启动子和转录起始位点，而偏父系表达基因主要在启动子和基因区。本文的研究结果进一步揭示了母系特异性DNA低甲基化在母系和父系偏向表达基因印记中的作用模型，并突出了转座和表观突变在水稻印记演化中的作用。