PNAS|DNA甲基化相关的染色质可及性影响拟南芥的基因组结构

DNA甲基化是一种跨物种的主要表观遗传修饰，对许多生物过程有着深远的影响。然而，它对染色质可及性和高阶基因组组织的影响还不清楚，特别是在植物中。本文，我们介绍了18个在CG、CHG或CHH DNA甲基化缺陷的拟南芥突变体的全基因组染色质可及性图谱。我们发现，在所有三种序列背景下的DNA甲基化都会影响异染色质中染色质的可及性。当DNA甲基化仅在一个或两个序列环境中丢失时，许多染色质区域保持不可及性，当DNA甲基化在所有环境中都减少时，可及性特征尤其受到影响，这表明不同类型的DNA甲基化之间存在相互作用。此外，我们发现染色质可及性的增加并不总是伴随着转录的增加，这表明DNA甲基化可以通过其他机制直接影响染色质结构。我们还观察到染色质可及性的增加伴随着染色质长程相互作用的增强。

总之，这些结果为染色质结构和DNA甲基化分析提供了有价值的资源，并揭示了甲基化在维持异染色质不可及性中的关键作用。

DNA methylation is a major epigenetic modification found across species and has a profound impact on many biological processes. However, its influence on chromatin accessibility and higher-order genome organization remains unclear, particularly in plants. Here, we present genome-wide chromatin accessibility profiles of 18 Arabidopsis mutants that are deficient in CG, CHG, or CHH DNA methylation. We find that DNA methylation in all three sequence contexts impacts chromatin accessibility in heterochromatin. Many chromatin regions maintain inaccessibility when DNA methylation is lost in only one or two sequence contexts, and signatures of accessibility are particularly affected when DNA methylation is reduced in all contexts, suggesting an interplay between different types of DNA methylation. In addition, we found that increased chromatin accessibility was not always accompanied by increased transcription, suggesting that DNA methylation can directly impact chromatin structure by other mechanisms. We also observed that an increase in chromatin accessibility was accompanied by enhanced long-range chromatin interactions. Together, these results provide a valuable resource for chromatin architecture and DNA methylation analyses and uncover a pivotal role for methylation in the maintenance of heterochromatin inaccessibility.

https://www.pnas.org/content/pnas/118/5/e2023347118.full.pdf

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