Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America.
PLoS Genet. 2010 Oct 28;6(10):e1001182. doi: 10.1371/journal.pgen.1001182.
Eukaryotic DNA cytosine methylation can be used to transcriptionally silence repetitive sequences, including transposons and retroviruses. This silencing is stable between cell generations as cytosine methylation is maintained epigenetically through DNA replication. The Arabidopsis thaliana Dnmt3 cytosine methyltransferase ortholog DOMAINS rearranged methyltransferase2 (DRM2) is required for establishment of small interfering RNA (siRNA) directed DNA methylation. In mammals PIWI proteins and piRNA act in a convergently evolved RNA-directed DNA methylation system that is required to repress transposon expression in the germ line. De novo methylation may also be independent of RNA interference and small RNAs, as in Neurospora crassa. Here we identify a clade of catalytically mutated DRM2 paralogs in flowering plant genomes, which in A.thaliana we term domains rearranged methyltransferase3 (DRM3). Despite being catalytically mutated, DRM3 is required for normal maintenance of non-CG DNA methylation, establishment of RNA-directed DNA methylation triggered by repeat sequences and accumulation of repeat-associated small RNAs. Although the mammalian catalytically inactive Dnmt3L paralogs act in an analogous manner, phylogenetic analysis indicates that the DRM and Dnmt3 protein families diverged independently in plants and animals. We also show by site-directed mutagenesis that both the DRM2 N-terminal UBA domains and C-terminal methyltransferase domain are required for normal RNA-directed DNA methylation, supporting an essential targeting function for the UBA domains. These results suggest that plant and mammalian RNA-directed DNA methylation systems consist of a combination of ancestral and convergent features.
真核生物 DNA 胞嘧啶甲基化可用于转录沉默重复序列，包括转座子和逆转录病毒。这种沉默在细胞世代之间是稳定的，因为胞嘧啶甲基化通过 DNA 复制在表观遗传上得以维持。拟南芥 Dnmt3 胞嘧啶甲基转移酶同源物 DOMAINS rearranged methyltransferase2 (DRM2) 是小干扰 RNA (siRNA) 指导的 DNA 甲基化建立所必需的。在哺乳动物中，PIWI 蛋白和 piRNA 作用于一个趋同进化的 RNA 指导的 DNA 甲基化系统，该系统需要抑制生殖系中转座子的表达。从头甲基化也可能独立于 RNA 干扰和小 RNA，就像在粗糙脉孢菌中一样。在这里，我们在开花植物基因组中鉴定出一个催化突变 DRM2 同源物的分支，在拟南芥中，我们称之为 DOMAINS rearranged methyltransferase3 (DRM3)。尽管 DRM3 发生了催化突变，但它仍然是正常维持非 CG DNA 甲基化、重复序列触发的 RNA 指导的 DNA 甲基化建立以及重复相关小 RNA 积累所必需的。尽管哺乳动物无催化活性的 Dnmt3L 同源物以类似的方式起作用，但系统发育分析表明，DRM 和 Dnmt3 蛋白家族在植物和动物中是独立进化的。我们还通过定点突变表明，DRM2 的 N 端 UBA 结构域和 C 端甲基转移酶结构域都需要正常的 RNA 指导的 DNA 甲基化，这支持了 UBA 结构域的基本靶向功能。这些结果表明，植物和哺乳动物的 RNA 指导的 DNA 甲基化系统由祖先和趋同特征的组合组成。
