2018年5月21日，Nature Reviews Molecular Cell Biology在线发表了中国科学院上海植物逆境生物学研究中心朱健康研究员、张惠明研究员与郎曌博研究员共同完成的题为“Dynamics and function of DNA methylation in plants”的综述文章。本博客将持续解读该文章，本文为连载第三期，包括第一章节DNA甲基化动态的第二部分内容：DNA甲基化维持。

Dynamics and function of DNA methylation in plants

First author: Huiming Zhang; Affiliations: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences (中国科学院上海植物逆境生物学研究中心): Shanghai, China

Corresponding author: Jian- Kang Zhu

Maintenance of DNA methylation

Maintenance of plant DNA methylation depends on the cytosine sequence context and is catalysed by DNA methyltransferases that are regulated by different mechanisms (Fig. 2). CG cytosine methylation is maintained by METHYLTRANSFERASE 1 (MET1) (Fig. 2a). MET1 is an orthologue of the mammalian DNA (cytosine-5)-methyltransferase 1 (DNMT1), which recognizes hemi-methylated CG dinucleotides following DNA replication and methylates the unmodified cytosine in the daughter strand^9,56. Compared with mouse and human DNMT1, A. thalianaMET1 lacks the cysteine-rich CXXC domain that is thought to help DNMT1 distinguish a hemi-methylated CG from a non-methylated CG^57,58. Similar to the model in which DNMT1 is recruited by the E3 ubiquitin-protein ligase UHRF1^59,60, MET1 has been proposed to be recruited to DNA by VARIANT IN METHYLATION proteins, which are UHRF1 orthologues required to maintain CG methylation^61,62.

植物甲基化的维持取决于胞嘧啶序列的组成，由受到不同机制调控的DNA甲基化转移酶催化（图2）。CG胞嘧啶甲基化由MET1维持（图2a）。MET1是哺乳动物DNA胞嘧啶-5-甲基转移酶DNMT1的同源物，主要在DNA复制后识别半甲基化的CG二核苷酸，并且甲基化子链上未被修饰的胞嘧啶。与人类和老鼠的DNMT1相比，拟南芥的MET1缺少富含半胱氨酸的CXXC结构域，该结构域被认为有助于帮助DNMT1区分半甲基化CG和未甲基化CG。哺乳动物中，DNMT1由E3泛素蛋白连接酶UHRF1所招募，与此类似，植物中的MET1由VARIANT IN METHYLATION蛋白招募到DNA上，该蛋白是UHRF1的同源物，对于维持CG甲基化是必需的。

Maintenance of CHG methylation in A. thaliana is catalysed by the DNA methyltransferase CHROMOMETHYLASE 3 (CMT3) and to a much lesser extent by CMT2^63,64 (Fig. 2a). The protein structure of the maize CMT3 homologue CHROMOMETHYLASE 1 (MET2A) demonstrated that its bromo-adjacent homology (BAH) and chromo domains bind to H3K9me2⁶⁵. Preventing the CMT3-H3K9me2 interaction not only disrupts the binding of CMT3 to the nucleosome but also leads to a complete loss of CMT3 activity⁶⁵. Mutations in the A. thalianaH3K9-specific methyltransferase SUVH4 and its paralogues SUVH5 and SUVH6 abolish H3K9me2 and substantially reduce CHG methylation^66-71. Methylated CHG is bound by the SRA domain of SUVH4 and recruits it to carry out H3K9 methylation⁷². Therefore, the methylated CHG and H3K9me2 modifications reinforce each other through regulatory feedback loops (Fig. 2a).

拟南芥中CHG甲基化的维持由DNA甲基转移酶CMT3所催化，另还有少部分由CMT2所催化（Fig2a）。玉米CMT3同源物MET2A的蛋白结构显示其bromo毗邻同源域（BAH）及chromo域结合到H3K9me2。阻止CMT3-H3K9me2之间的互作不仅能破坏CMT3结合到核小体上，还能导致CMT3活性的完全缺失。拟南芥H3K9特异性甲基转移酶SUVH4及其SUVH5、SUVH6的突变会基本废除H3K9me2，并大幅降低CHG甲基化水平。甲基化的CHG由SUVH4的SRA结构域所结合，并招募它进行H3K9甲基化。因此，甲基化的CHG和H3K9me2修饰通过反馈调节通路相互增强（图2a）。

CHH methylation is maintained by DRM2 or CMT2, depending on the genomic region. Through RdDM, DRM2 maintains CHH methylation at RdDM target regions, which are preferentially located at evolutionarily young transposons and short transposons and at other repeat sequences in euchromatic chromosome arms as well as at the edges of long transposons, which are usually located in heterochromatin^36,73,74. By contrast, CMT2 catalyses CHH methylation at histone H1-containing heterochromatin, where RdDM is inhibited. Methylation by CMT2 is impaired by mutations in DECRESED DNA METHYLATION 1 (DDM1), which is a chromatin-remodelling protein that is also required for maintaining DNA methylation in symmetric cytosine sequencecontexts^74,75. Maintenance of asymmetric methylation may also be affected by MET1 and CMT3 because MET1-dependent methylation can be recognized by SUVH2 and SUVH9 for recruitment of POL V at some RdDM loci³⁷ and because CMT3-dependent CHG methylation increases H3K9me2 levels, which facilitates CMT2-catalysed non-CG methylation⁶⁴. Although CHH cytosines can be methylated only by DRM2 and CMT2, these two enzymes can also methylate cytosines in other contexts.

CHH甲基化由DRM2或者CMT2所维持，取决于所处的基因组区域。DRM2维持RdDM靶向区域的CHH甲基化，这些区域主要集中在演化上比较年轻的转座子、短转座子以及一些常染色体臂上的其他重复序列，同时还有通常出现在异染色质区域的长转座子的边缘区域。相反，由CMT2催化的CHH甲基化主要在含组蛋白H1异染色质区域，而这些区域不存在RdDM。DDM1的突变会破坏由CMT2催化的CHH甲基化，DDM1是一种染色质重塑蛋白，该蛋白同时对于维持对称胞嘧啶序列处的DNA甲基化也是必需的。非对称甲基化的维持可能也会受到MET1和CMT3的影响，因为MET1依赖性的甲基化同样可以被SUVH2和SUVH9所识别以在某些RdDM位点招募POL V，另外CMT3依赖性的CHG甲基化增加了H3K9me2的水平，进而促进了CMT2催化的非CG类型甲基化。尽管CHH胞嘧啶仅仅可以被DRM2和CMT2所甲基化，但这两个酶也可以在其他序列类型上甲基化胞嘧啶。

doi: https://doi.org/10.1038/s41580-018-0016-z

Journal: Nature Reviews Molecular Cell Biology

Published date: 21 May, 2018