Glazov Evgeny A, Kongsuwan Kritaya, Assavalapsakul Wanchai, Horwood Paul F, Mitter Neena, Mahony Timothy J
Diamantina Institute for Cancer, Immunology and Metabolic Medicine, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia.
PLoS One. 2009 Jul 27;4(7):e6349. doi: 10.1371/journal.pone.0006349.
MicroRNA (miRNA) and other types of small regulatory RNAs play a crucial role in the regulation of gene expression in eukaryotes. Several distinct classes of small regulatory RNAs have been discovered in recent years. To extend the repertoire of small RNAs characterized in mammals and to examine relationship between host miRNA expression and viral infection we used Illumina's ultrahigh throughput sequencing approach. We sequenced three small RNA libraries prepared from cell line derived from the adult bovine kidney under normal conditions and upon infection of the cell line with Bovine herpesvirus 1. We used a bioinformatics approach to distinguish authentic mature miRNA sequences from other classes of small RNAs and short RNA fragments represented in the sequencing data. Using this approach we detected 219 out of 356 known bovine miRNAs and 115 respective miRNA* sequences. In addition we identified five new bovine orthologs of known mammalian miRNAs and discovered 268 new cow miRNAs many of which are not identifiable in other mammalian genomes and thus might be specific to the ruminant lineage. In addition we found seven new bovine mirtron candidates. We also discovered 10 small nucleolar RNA (snoRNA) loci that give rise to small RNA with possible miRNA-like function. Results presented in this study extend our knowledge of the biology and evolution of small regulatory RNAs in mammals and illuminate mechanisms of small RNA biogenesis and function. New miRNA sequences and the original sequencing data have been submitted to miRNA repository (miRBase) and NCBI GEO archive respectively. We envisage that these resources will facilitate functional annotation of the bovine genome and promote further functional and comparative genomics studies of small regulatory RNA in mammals.
微小RNA（miRNA）和其他类型的小调控RNA在真核生物基因表达调控中发挥着关键作用。近年来已发现了几类不同的小调控RNA。为了扩展哺乳动物中已鉴定的小RNA种类，并研究宿主miRNA表达与病毒感染之间的关系，我们采用了Illumina的超高通量测序方法。我们对三个小RNA文库进行了测序，这些文库分别来自正常条件下的成年牛肾细胞系以及感染了牛疱疹病毒1的该细胞系。我们使用生物信息学方法从测序数据中代表的其他小RNA类别和短RNA片段中区分出真正的成熟miRNA序列。通过这种方法，我们在356个已知牛miRNA中检测到了219个以及115个相应的miRNA*序列。此外，我们鉴定出了5个已知哺乳动物miRNA的新牛直系同源物，并发现了268个新的牛miRNA，其中许多在其他哺乳动物基因组中无法识别，因此可能是反刍动物谱系特有的。此外，我们还发现了7个新的牛mirtron候选物。我们还发现了10个小核仁RNA（snoRNA）位点，它们产生具有可能类似miRNA功能的小RNA。本研究的结果扩展了我们对哺乳动物中小调控RNA生物学和进化的认识，并阐明了小RNA生物合成和功能的机制。新的miRNA序列和原始测序数据已分别提交至miRNA数据库（miRBase）和NCBI GEO存档。我们设想这些资源将有助于牛基因组的功能注释，并促进哺乳动物中小调控RNA的进一步功能和比较基因组学研究。
