National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, PR China.
BMC Genomics. 2010 Jan 25;11:61. doi: 10.1186/1471-2164-11-61.
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.
最近的研究表明，非蛋白编码 RNA（npcRNA/ncRNA）在真核生物发育、物种进化以及疾病病因中发挥着重要作用。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，而对猴类 ncRNA 知之甚少。
本研究通过构建 cDNA 文库，首次对恒河猴中等大小 ncRNA（50 至 500 个核苷酸）进行了系统分析。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 northern blot 杂交表明，一些 snoRNA 具有谱系或种特异性。大多数恒河猴 snoRNA 都存在同源基因，它们的表达可能归因于恒河猴基因组中的广泛重复。进一步研究 snoRNA 侧翼序列表明，一些恒河猴 snoRNA 是由 L1 介导的整合产生的返座基因。最后，系统发育分析表明，鸟类和灵长类动物共享一些 snoRNA 和其宿主基因，这表明相关的宿主基因及其内含的 snoRNA 可能是从一个共同的祖先遗传而来的。然而，一些由非核糖体相关基因承载的恒河猴 snoRNA 出现在鸟类和哺乳动物的进化分歧之后。
我们提供了恒河猴 ncRNA 的首个实验性目录，并揭示了一些有趣的基因组和进化特征。这些发现为今后在灵长类进化过程中对 snoRNA 的功能特征进行研究提供了重要信息。
