Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs.
Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs.
复制标题
恒河猴核仁小RNA的系统鉴定及进化特征
DOI：
10.1186/1471-2164-11-61
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发表时间：
2010-01-25
期刊：
影响因子：
4.4
通讯作者：
Zhu D
中科院分区：
文献类型：
--
作者：
Zhang Y;Liu J;Jia C;Li T;Wu R;Wang J;Chen Y;Zou X;Chen R;Wang XJ;Zhu D
近年来的研究表明，非蛋白质编码RNA（npcRNA/ncRNA）在真核生物的发育、物种进化和疾病的病因学中发挥着重要作用。恒河猴是生物医学研究和灵长类进化研究中应用最广泛的灵长类动物模型。然而，大多数关于这些动物的报道都集中在蛋白质编码序列的功能作用上，而对猕猴的ncRNA知之甚少。在本研究中，我们通过构建cDNA文库对恒河猴的中等大小ncRNA（50至500 nt）进行了首次系统性分析。我们鉴定了117种恒河猴ncRNA，包括80种小核仁RNA（snoRNA），29种其他类型的已知RNA（snRNA，Y RNA等）和8种未分类的ncRNA。比较基因组分析和北方印迹杂交表明，一些snoRNA的谱系或物种特异性。旁系同源序列被发现的大多数恒河猴snoRNA，其表达可能是由于广泛的复制恒河猴基因组内。对snoRNA侧翼序列的进一步研究表明，一些恒河猴snoRNA是来自L1介导的整合的逆转录基因。最后，系统发育分析表明，鸟类和灵长类动物共享一些snoRNA及其宿主基因，这表明相关的宿主基因和其中包含的snoRNA可能遗传自共同的祖先。然而，在鸟类和哺乳动物之间进化分歧之后，出现了一些由非核糖体相关基因宿主的恒河猴snoRNA。我们提供了第一个实验来源的恒河猴ncRNA目录，并揭示了一些有趣的基因组和进化特征。这些发现为进一步研究snoRNA在灵长类进化中的功能提供了重要信息。
Recent studies have demonstrated that non-protein-coding RNAs (npcRNAs/ncRNAs) play important roles during eukaryotic development, species evolution, and in the etiology of disease. Rhesus macaques are the most widely used primate model in both biomedical research and primate evolutionary studies. However, most reports on these animals focus on the functional roles of protein-coding sequences, whereas very little is known about macaque ncRNAs. In the present study, we performed the first systematic profiling of intermediate-size ncRNAs (50 to 500 nt) from the rhesus monkey by constructing a cDNA library. We identified 117 rhesus monkey ncRNAs, including 80 small nucleolar RNAs (snoRNAs), 29 other types of known RNAs (snRNAs, Y RNA, and others), and eight unclassified ncRNAs. Comparative genomic analysis and northern blot hybridizations demonstrated that some snoRNAs were lineage- or species-specific. Paralogous sequences were found for most rhesus monkey snoRNAs, the expression of which might be attributable to extensive duplication within the rhesus monkey genome. Further investigation of snoRNA flanking sequences showed that some rhesus monkey snoRNAs are retrogenes derived from L1-mediated integration. Finally, phylogenetic analysis demonstrated that birds and primates share some snoRNAs and host genes thereof, suggesting that both the relevant host genes and the snoRNAs contained therein may be inherited from a common ancestor. However, some rhesus monkey snoRNAs hosted by non-ribosome-related genes appeared after the evolutionary divergence between birds and mammals. We provide the first experimentally-derived catalog of rhesus monkey ncRNAs and uncover some interesting genomic and evolutionary features. These findings provide important information for future functional characterization of snoRNAs during primate evolution.
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