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，本文为连载第一期，包括摘要和引言。

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

• Abstract

DNA methylation is a conserved epigenetic modification that is important for gene regulation and genome stability. Aberrant (异常的) patterns of DNA methylation can lead to plant developmental abnormalities (不正常). A specific DNA methylation state is an outcome of dynamic regulation by de novo methylation, maintenance of methylation and active demethylation, which are catalysed by various enzymes that are targeted by distinct regulatory pathways. In this Review , we discuss DNA methylation in plants, including methylating and demethylating enzymes and regulatory factors, and the coordination of methylation and demethylation activities by a so-called methylstat mechanism; the functions of DNA methylation in regulating transposon silencing, gene expression and chromosome interactions; the roles of DNA methylation in plant development; and the involvement of DNA methylation in plant responses to biotic and abiotic stress conditions.

摘要| DNA甲基化是非常保守的表观修饰，对于基因调控及基因组稳定性十分重要。异常的DNA甲基化模式会导致植物的发育缺陷。一个特定的DNA甲基化状态是由从头甲基化、甲基化维持以及主动去甲基化的动态调控所实现的，这些过程受到多个酶的催化，并且受到不同调控通路的调控。本综述主要讨论了植物中的DNA甲基化，包括甲基化和去甲基化酶以及调控因子，还有一个甲基化和去甲基化共同协作的机制（甲基化稳态调控）；DNA甲基化对于转座沉默、基因表达及染色体互作的作用；DNA甲基化在植物发育中所扮演的角色；以及DNA甲基化参与植物对生物及非生物胁迫的响应。

• Introduction

  
  

DNA methylation at the 5ʹ position of cytosine contributes to the epigenetic regulation of nuclear gene expression and to genome stability (Robertson, 2005; Slotkin & Martienssen, 2007). Epigenetic changes, including DNA methylation, histone modifications and histone variants and some non-coding RNA (ncRNA) changes, influence chromatin structure and, in turn, the accessibility of genetic information. As a result, DNA methylation is important to many biological processes, and disruption of DNA methylation can lead to developmental abnormalities in plants and mammals, such as failure in tomato fruit ripening and embryo lethality in mice (Robertson, 2005; Lang et al., 2017; Cortellino et al., 2011).

5号位置胞嘧啶的DNA甲基化作用于核基因表达的表观调控及基因组稳定性。包括DNA甲基化、组蛋白修饰、组蛋白变异及一些非编码RNA改变在内的表观变化会影响染色质结构，进而影响遗传信息的可接近性。因此，DNA甲基化对于许多生物学过程是非常重要的，破坏DNA甲基化能够导致动植物发育不正常，比如西红柿果实成熟、老鼠胚胎致死等。

DNA methylation is conserved in plants and mammals, and precise patterns of genomic DNA methylation are crucial for development. In both plants and mammals, DNA methylation is catalysed by conserved DNA methyltransferases using S-adenosyl-l-methionine (S-腺苷-L-蛋氨酸) as the methyl donor, whereas active DNA demethylation involves a base excision (切除) repair pathway (Zhu, 2009; Wu & Zhang, 2010; Law & Jacobsen, 2010; Zhang & Zhu, 2012; He et al., 2011). An RNA-directed DNA methylation pathway is crucial for de novo methylation in plants but is less important in mammals (Watanabe et al., 2011; Matzke & Mosher, 2014). In contrast to mammals, which initiate active DNA demethylation with oxidation and/or deamination (脱氨作用) of 5-methylcytosine (5-mC; 5-甲基胞嘧啶), plants directly excise the 5-mC base utilizing 5-mC DNA glycosylases 糖基酶 (Zhu, 2009; Wu & Zhang, 2010; Zhang & Zhu, 2012).

DNA甲基化在动植物中十分保守，基因组DNA甲基化精细模式对于发育是非常重要的。在动植物中，DNA甲基化由保守的DNA甲基化转移酶利用S-腺苷甲硫氨酸作为甲基供体进行催化，而主动DNA去甲基化则涉及到一个碱基切除修复机制。一个由RNA指导的DNA甲基化通路对于植物中的从头甲基化至关重要，但在哺乳动物中却不是很重要。与哺乳动物相反，哺乳动物中的主动DNA去甲基化由5-甲基胞嘧啶（5-mC）的氧化作用和脱氨作用起始，而植物则利用5-mC DNA糖基酶直接切除5-mC碱基。

In this Review, we discuss recent discoveries and the current understanding of the regulation and function of DNA methylation in plants. The mechanisms underlying the generation of specific DNA methylation patterns are best understood in the model plant Arabidopsis thaliana, in which mutations in components of the DNA methylation and demethylation machineries and regulatory factors are generally not lethal. However, DNA methylation appears to be more crucial for development and environmental- stress responses in plants that have more complex genomes. Recent findings have uncovered important regulatory mechanisms of plant DNA methylation, such as the initial triggering of de novo DNA methylation by ncRNA, the targeting of active DNA demethylation by the novel protein complex IDM (increased DNA methylation) and the balancing of DNA methylation and demethylation by a methylation-sensing genetic element. We also discuss the important roles of DNA methylation dynamics in regulating transposon silencing, in gene expression, in chromosome interactions, in plant development and in plant responses to biotic and abiotic environmental stimuli, as well as in fruit ripening, root nodulation and other developmental processes.

本综述中，作者讨论了近来有关植物DNA甲基化调控和功能的最新研究进展。模式植物拟南芥中特异性DNA甲基化模式产生的潜在机制研究的最清楚，拟南芥中DNA甲基化和去甲基化组份和调控因子的突变通常并不致死。然而，DNA甲基化对于植物的发育和环境胁迫响应显得更加重要，植物拥有更加复杂的基因组。最新的研究发现了一些植物DNA甲基化重要的调控机制，比如由ncRNA诱导的从头DNA甲基化起始，由蛋白复合体IDM靶向的主动DNA去甲基化以及由一个甲基化感应遗传元件所介导的DNA甲基化和去甲基化之间的平衡。作者同时还讨论了DNA甲基化动态调控转座子沉默、基因表达、染色体互作、植物发育、植物响应生物和非生物环境刺激、果实成熟、根结瘤和其他发育过程的重要作用。

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

Journal: Nature Reviews Molecular Cell Biology

Published date: 21 May, 2018