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Colloquium(座谈会) RNA-directed DNA methylation in Arabidopsis(在拟南芥中由 RNA指导的DNA甲基化) Werner Aufsatz*, M. Florian Mette*, Johannes van der Winden, Antonius J. M. Matzke, and Marjori Matzke? Institute of Molecular Biology(分子生物研究所), Austrian Academy of Sciences(奥地利科学院), Billrothstrasse 11, A-5020 Salzburg, Austria In plants, double-stranded RNA that is processed to short RNAs_21–24 nt in length can trigger two types of epigenetic gene Silencing(在植物中,双链RNA可以使RNA链缩短为21-24个碱 基的长度,以引发两种表观基因沉默). Posttranscriptional gene silencing, which is related to RNA interference in animals and quelling in fungi, involves targeted elimination of homologous mRNA in the cytoplasm (转录后的基因沉默, 关系到动物中RNA 干涉和对真菌的平息, 包括细胞质中同源RNA的目标性消除) . ) RNAdirected DNA methylation involves de novo methylation of almost all cytosine residues within a region of RNA–DNA sequence identity(包括在RNA-DNA序列标识区域,几乎所有的 胞嘧啶残基重新甲基化). RNA-directed DNA methylation is presumed to be responsible

for the methylation observed in protein coding regions of posttranscriptionally silenced genes(RNA指导的DNA甲基化可 能与转录后沉默基因对应的蛋白质编码区的甲基化有关). Moreover, a type of transcriptional gene silencing and de novo methylation of homologous promoters in trans can occur if a double-stranded RNA contains promoter sequences. (而且,如 果双链RNA中存在启动子序列,在转录过程中转录基因沉默和 同源启动子的甲基化会发生)Although RNA-directed DNA methylation has been described so far only in plants, there is increasing evidence that RNA can also target genome modifications in other organisms(尽管RNA指导的DNA甲基化 目前只在植物中有描述,但越来越多的证据表明RNA也能在其 他生物中进行针对性基因修改) To understand how RNA directs methylation to identical DNA sequences and how changes in chromatin configuration contribute to initiating or maintaining DNA methylation induced by RNA, a promoter double-stranded RNA-mediated transcriptional gene silencing system has been established in Arabidopsis(为了理解 RNA如何指导同一性DNA序列甲基化以及在染色体组配中的变 化如何推动启动或维护由RNA引发的DNA甲基化,在拟南芥中

双链RNA指导的转录基因沉默系统的启动子已经建立). A genetic analysis of this system is helping to unravel (阐明)the relationships among RNA signals, DNA methylation, and chromatin structure (这个系统的基因分析有助于阐明RNA信号,DNA甲基化及染 色体结构之间的关系). The term ‘‘RNA silencing’’ refers to epigeneticgene silencing effects that are initiated by double-stranded RNA (dsRNA)(RNA沉 默是指遗传学上的基因沉默效应,它是由双链RNA引起的) (1). Discovered independently in plants, fungi, and animals, RNA silencing phenomena are revealing new ways to repress gene expression and to subdue transposable elements and viruses that produce dsRNA during their replication cycle)(2–8) (分别在 植物, 真菌和动物研究中的发现表明, RNA沉默现象反映了抑制 基因表达和抑制在复制周期中制造双链RNA的转化因子和病毒 的新方法). A fundamental step in RNA silencing pathways is cleavage of dsRNA into short RNAs (9), which are believed to act as guides for enzyme complexes that either degrade or modify homologous nucleic acids(在RNA沉默的过程中最根本的一步是将双链RNA 裂解成短的RNA序列, 这一步被认为复合性酶降解或修饰同源核

酸的指导). The most familiar type of RNA silencing occurs primarily in the cytoplasm and is termed posttranscriptional gene silencing (PTGS) in plants quelling in Neurospora, and RNA interference (RNAi) in animals 最熟悉的RNA沉默类型首先发生在细胞质中, ( 称为转录后基因沉默,平息脉胞菌和动物中RNA干涉). PTGS_RNAi involves a dsRNA that is processed by an RNase III (RNA酶Ⅲ)-like enzyme(酶) called Dicer into short interfering (si) RNAs21–22 nt in length(长度为21-22的小片段干扰RNA). The antisense siRNAs associate with a ribonuclease complex and guide sequencespecific degradation of complementary mRNAs (5–8)(反义RNA与核糖核 酸酶复合体相联系并且指导mRNA的互补序列降解). A second form of RNA silencing involves sequence-specific changes at the genome level(RNA沉默的第二种方式是基因组水 平特定序列的变化). RNA-directed DNA methylation (RdDM) (10), which has been described so far only in plants, leads to de novo methylation of almost all cytosine residues within the region of sequence identity between the triggering RNA and the target DNA (RNA指导的DNA甲基化目前仅在植物中进行过描述,它导致 引发体RNA和目标DNA序列区域的几乎所有的胞嘧啶残基重新 甲基化). Similarly to PTGS_RNAi, RdDM requires a dsRNA that

is cleaved to short RNAs _21–24 nt in length (11)(和PTGS_RNAi相似,RdDM需要一个能断裂成21-24 个碱基长度的短RNA片段的双链RNA, ). It is not yet certain whether the short RNAs or dsRNA guide methylation of homologous DNA sequences, although the length of short RNAs is consistent with the minimum DNA target size of RdDM (_30 bp) (12)(目前还不确定是短RNA片段RdDM还是双链RNA指导同源 DNA序列的甲基化,尽管短RNA片段和目标DNA的最小幅度相 一致). RdDM is assumed to be the source of methylation observed in protein coding regions in many cases of PTGS, where it can contribute in an unknown way to the maintenance of silencing(13, 14) RdDM被认为是在许多情况下观察到的蛋白质编码区甲基化 ( 的来源,该文现就实验所取得的,它可以以某种未知的方式保持基 因沉默). In addition, RdDM has been implicated in a type of transcriptional gene silencing (TGS) that is initiated by dsRNAs containing promoter sequences(此外,RdDM已经涉及到一种转录 基因沉默(TGS),这是由双链RNA发起的包含启动子的序列). Promoter dsRNAs that trigger TGS and RdDM of homologous promoters in trans can be produced in the nucleus by transcription through inverted repeats (IRs) of promoter sequences (11, 15) or in the cytoplasm by a replicating RNA virus that is engineered to

contain sequences identical to the promoter of a nuclear gene (16, 17)(双链 RNAs启动子触发TGS ,并且转录过程中RdDM同源启动子在细 胞核中由反转录序列的启动子转录而成或在细胞质RNA病毒复 制产生该病毒包含和细胞核基因相同的启动子序列). Although the phenomenon of RdDM is well established in plants, a number of questions remain. (尽管RdDM 现象在植物中 已很好地确立,但仍然存在很多问题)One concerns the identity of the DNA methyltransferases (MTases) that are required for establishing and maintaining the unusual pattern of methylation characteristic of RdDM.(其中一个问题涉及到DNA甲基转移酶的 识别,它需要确立和保持RdDM甲基化的特征) A second issue concerns the relationship between DNA methylation and changes in chromatin structure(另一个问题涉及到DNA甲基化和和染色质结构变化的 关系). Given the close links between DNA methylation, chromatin remodeling (18–20), and histone modifications, such as acetylation (21) and methylation (22, 23), it might be anticipated that alterations in chromatin structure would be required to initiate and_or retain methylation induced by RdDM(根据DNA甲基化、 染色质重塑和想乙酰基化和甲基化的组蛋白构建之间的紧密联 系, 可以推断染色质结构的变化是引发或保持由双链RNA引起的

甲基化所需要的). To address these questions, we carried out a genetic analysis of a promoter dsRNA-mediated TGS system that we have established in Arabidopsis(为了解决这些问题,我们对在拟南芥建 立起的由双链RNA主导的TGS系统的启动子进行了遗传分析). In this paper, we describe this system and the impact of several mutations that impair DNA methylation and_or possible chromatin remodeling processes(在本文中,我们描述了这个系统和几个突 变的影响,这些突变可能影响染色质DNA甲基化及染色质的重 建) We discuss whether RdDM might occur in animals and whether . RNA might direct chromatin modifications in organisms that do not methylate their DNA(我们还讨论了RdDM是否会在动物上发 生,RNA是否可以不使DNA甲基化就能直接控制生物的染色质 构建).


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