Short RNAs can identify new candidate transposable element families in Arabidopsis
Short RNAs can identify new candidate transposable element families in Arabidopsis
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DOI：
10.1104/pp.007047
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发表时间：
2002-09-01
期刊：
影响因子：
7.4
通讯作者：
Matzke, AJM
中科院分区：
文献类型：
--
作者：
Mette, MF;van der Winden, J;Matzke, AJM
通过DNA序列相似性搜索和分析方案挖掘拟南芥基因组中的转座因子（TE），揭示了先前未鉴定的TE家族，并提供了对TE结构、移动性、分布和多样性的见解（Le et al.，2000）。我们在这里建议可以通过涉及克隆和分析短RNA的替代方法来识别新的推定TE家族和部分分歧的TE样序列，这是RNA沉默机制的标志。RNA沉默由dsRNA触发，dsRNA被称为Dicer的RNA酶III样酶切割成长度为21至24个核苷酸（nts）的短RNA（Matzke et al. 2001; Hutvágner等人，2002年）。短RNA被认为可以引导酶复合物降解细胞质中的互补RNA（这一过程在植物中称为转录后基因沉默，在动物中称为RNA干扰[RNAi]），或者修饰细胞核中的同源DNA序列（RNA指导的DNA甲基化[RdDM]）。在植物中，如果dsRNA含有启动子序列，则RdDM可导致转录基因沉默（Matzke等人，2001年）。在许多情况下可能由RdDM引起的转录后基因沉默/RNAi和DNA甲基化的主要功能是限制TE的增殖（Matzke等人，2000）。RNA沉默的宿主防御作用通过RNAi缺陷的秀丽隐杆线虫突变体中的一些TE的移动来证明（Ketting等人，1999; Tabara等人，1999）和在DNA甲基化或染色质结构的某些方面缺陷的拟南芥突变体中（Miura等人，2001; Okamoto和Hirochika，2001; Singer等人，2001; Tomba等人，2002年）。RNA沉默在TE控制中的作用也得到了与从不同来源克隆的短RNA集合中的各种TE同源的序列的发现的支持（Rehkeng等人，2001; Lagos-Quintana等人，2001年）。已知TE序列在短RNA群体中的富集，这可能是Dicer样酶的切割产物，表明未识别的TE可能通过它们在短RNA文库中的存在而被检测到。在一个正在进行的项目，克隆和测序短RNA约17至27个核苷酸长度从拟南芥叶，我们已经分离出短RNA，似乎是来自以前未知的TE家族和TE样序列。
Mining the Arabidopsis genome for transposable elements (TEs) by DNA sequence similarity searches and analysis protocols is revealing previously unidentified families of TEs and providing insights into TE structure, mobility, distribution, and diversity (Le et al., 2000). We suggest here that new putative TE families and partially diverged TE-like sequences can be identified by an alternate approach involving cloning and analyzing short RNAs, which are a hallmark of RNA silencing mechanisms. RNA silencing is triggered by dsRNA that is cleaved to short RNAs 21 to 24 nucleotides (nts) in length by an RNase III-like enzyme termed Dicer (Matzke et al., 2001; Hutvágner et al., 2002). The short RNAs are thought to guide enzyme complexes that either degrade complementary RNAs in the cytoplasm (a process termed posttranscriptional gene silencing in plants and RNA interference [RNAi] in animals), or modify homologous DNA sequences in the nucleus (RNA-directed DNA methylation [RdDM]). In plants, RdDM can lead to transcriptional gene silencing if dsRNAs contain promoter sequences (Matzke et al., 2001). A major function of posttranscriptional gene silencing/RNAi and DNA methylation, which may result from RdDM in many cases, is to limit the proliferation of TEs (Matzke et al., 2000). The host defense role of RNA silencing is evidenced by the mobilization of some TEs in Caenorhabditis elegans mutants defective in RNAi (Ketting et al., 1999; Tabara et al., 1999) and in Arabidopsis mutants deficient in some aspect of DNA methylation or chromatin structure (Miura et al., 2001; Okamoto and Hirochika, 2001; Singer et al., 2001; Tomba et al., 2002). A role for RNA silencing in TE control is also supported by findings of sequences homologous to various TEs in collections of short RNAs cloned from different sources (Djikeng et al., 2001; Lagos-Quintana et al., 2001). The enrichment of known TE sequences in populations of short RNAs, which are presumably cleavage products of a Dicer-like enzyme, suggests that unidentified TEs might be detected through their presence in short RNA libraries. In an ongoing project to clone and sequence short RNAs approximately 17 to 27 nts in length from Arabidopsis leaves, we have isolated short RNAs that appear to be derived from previously unknown TE families and from TE-like sequences.