Methylated CHH (mCHH) islands are peaks of CHH methylation that occur primarily upstream to genes. These regions are actively targeted by the methylation machinery, occur at boundaries between heterochromatin and euchromatin, and tend to be near highly expressed genes. Here we took an evolutionary perspective by studying upstream mCHH islands across a sample of eight grass species. Using a statistical approach to define mCHH islands as regions that differ from genome-wide background CHH methylation levels, we demonstrated that mCHH islands are common and associate with 39% of genes, on average. We hypothesized that islands should be more frequent in genomes of large size, because they have more heterochromatin and hence more need for defined boundaries. We found, however, that smaller genomes tended to have a higher proportion of genes associated with 5′ mCHH islands. Consistent with previous work suggesting that islands reflect the silencing of the edge of transposable elements (TEs), genes with nearby TEs were more likely to have mCHH islands. However, the presence of mCHH islands was not a function solely of TEs, both because the underlying sequences of islands were often not homologous to TEs and because genic properties also predicted the presence of 5′ mCHH islands. These genic properties included length and gene-body methylation (gbM); in fact, in three of eight species, the absence of gbM was a stronger predictor of a 5′ mCHH island than TE proximity. In contrast, gene expression level was a positive but weak predictor of the presence of an island. Finally, we assessed whether mCHH islands were evolutionarily conserved by focusing on a set of 2,720 orthologs across the eight species. They were generally not conserved across evolutionary time. Overall, our data establish additional genic properties that are associated with mCHH islands and suggest that they are not just a consequence of the TE silencing machinery.

中文翻译：

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CHH 甲基化岛：草基因组的非保守特征，与转座元件正相关，但与基因体甲基化负相关


甲基化 CHH (mCHH) 岛是主要发生在基因上游的 CHH 甲基化峰。这些区域是甲基化机制的主动目标，出现在异染色质和常染色质之间的边界处，并且往往靠近高表达基因。在这里，我们通过研究八种草类样本的上游 mCHH 岛屿，从进化的角度进行了研究。使用统计方法将 mCHH 岛定义为与全基因组背景 CHH 甲基化水平不同的区域，我们证明 mCHH 岛很常见，平均与 39% 的基因相关。我们假设岛屿在大基因组中应该更常见，因为它们有更多的异染色质，因此更需要明确的边界。然而，我们发现较小的基因组往往具有较高比例的与 5' mCHH 岛相关的基因。与之前的研究一致，表明岛反映了转座元件 (TE) 边缘的沉默，TE 附近的基因更有可能具有 mCHH 岛。然而，mCHH 岛的存在不仅仅是 TE 的函数，因为岛的底层序列通常与 TE 不同源，而且基因特性也预测了 5' mCHH 岛的存在。这些基因特性包括长度和基因体甲基化（gbM）；事实上，在八个物种中的三个中，gbM 的缺失比 TE 邻近性更能预测 5' mCHH 岛的存在。相比之下，基因表达水平是岛屿存在的积极但较弱的预测因子。最后，我们通过关注 8 个物种的 2,720 个直系同源物来评估 mCHH 岛在进化上是否保守。它们在整个进化过程中通常不保守。 总的来说，我们的数据建立了与 mCHH 岛相关的额外基因特性，并表明它们不仅仅是 TE 沉默机制的结果。