Repertoire and evolution of miRNA genes in four divergent nematode species
Repertoire and evolution of miRNA genes in four divergent nematode species
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DOI：
10.1101/gr.093781.109
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发表时间：
2009-11-01
期刊：
影响因子：
7
通讯作者：
Berezikov, Eugene
中科院分区：
文献类型：
--
作者：
de Wit, Elzo;Linsen, Sam E. V.;Berezikov, Eugene
mirna类似于22-nt RNA分子，在转录后调控中发挥重要作用。我们对秀丽隐杆线虫、C. briggsae、C. remanei和太平洋隐杆线虫进行了小RNA测序，这些线虫在4亿年前就已经分化，以建立这些物种的microrna库和进化动力学。除了已知的秀丽隐杆线虫和c.b briggsae的miRNA基因外，我们还发现了许多它们的同源基因在C. remanei和p.p pacificus中表达，并鉴定了100多个新的表达miRNA基因，其中大部分属于p.p pacificus。有趣的是，在所有四种线虫物种中，超过一半已鉴定的miRNA基因在种子水平上是保守的，而只有少数miRNA似乎是物种特异性的。在我们的miRNA纲要中，我们观察到miRNA进化的已知机制的证据，包括反义转录和臂切换，以及miRNA家族通过基因复制扩增。此外，我们发现了一种新的miRNA进化模式，称为“发夹移动”，在这种模式中，一个替代的发夹与上行或下行序列形成，导致发夹的移动和新的miRNA*物种的产生。最后，我们在所有四种线虫中都鉴定了21U-RNA，其中包括太平洋线虫，其中上游21U-RNA基序更加分化。本文描述的四种线虫小RNA库的鉴定和系统分析为理解mirna介导的基因调控的进化动力学提供了宝贵的资源。
miRNAs are similar to 22-nt RNA molecules that play important roles in post-transcriptional regulation. We have performed small RNA sequencing in the nematodes Caenorhabditis elegans, C. briggsae, C. remanei, and Pristionchus pacificus, which have diverged up to 400 million years ago, to establish the repertoire and evolutionary dynamics of miRNAs in these species. In addition to previously known miRNA genes from C. elegans and C. briggsae we demonstrate expression of many of their homologs in C. remanei and P. pacificus, and identified in total more than 100 novel expressed miRNA genes, the majority of which belong to P. pacificus. Interestingly, more than half of all identified miRNA genes are conserved at the seed level in all four nematode species, whereas only a few miRNAs appear to be species specific. In our compendium of miRNAs we observed evidence for known mechanisms of miRNA evolution including antisense transcription and arm switching, as well as miRNA family expansion through gene duplication. In addition, we identified a novel mode of miRNA evolution, termed "hairpin shifting,'' in which an alternative hairpin is formed with up-or downstream sequences, leading to shifting of the hairpin and creation of novel miRNA* species. Finally, we identified 21U-RNAs in all four nematodes, including P. pacificus, where the upstream 21U-RNA motif is more diverged. The identification and systematic analysis of small RNA repertoire in four nematode species described here provides a valuable resource for understanding the evolutionary dynamics of miRNA-mediated gene regulation.