Khan Shahid Y, Hackett Sean F, Riazuddin S Amer
The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
Exp Eye Res. 2016 Apr;145:347-351. doi: 10.1016/j.exer.2016.01.010. Epub 2016 Jan 22.
Non-coding RNAs (ncRNAs) are emerging as an important player in the regulation of genome integrity and gene expression, and they have been implicated in the pathogenesis of many diseases. The aim of the present study is to identify the repertoire of ncRNAs expressed in the developing mouse lens. We previously reported the mouse lens transcriptome, including mRNA and microRNA (miRNA) profiling at two embryonic (E15 and E18) and four postnatal (P0, P3, P6, and P9) time points. We analyzed the data from small RNA-Seq and mRNA-Seq libraries to investigate the ncRNA profile. Our analysis revealed expression of 12 different classes of ncRNA in the murine lens at six developmental time points. Annotation of small RNA data showed expression of 1,756 antisense ncRNA (asncRNA) in the mouse lens transcriptome. Likewise, we identified 82 P-element-induced wimpy testis (PIWI)-interacting RNA (piRNA), 345 transfer RNA (tRNA), 12 small nuclear RNA (snRNA), 167 small nucleolar RNA (snoRNA), 19 small Cajal body-specific RNA (scaRNA), six ribosomal RNA (rRNA), 18 tRNA-like structures, one MALAT1-associated small cytoplasmic RNA (mascRNA), one Vault RNA (vtRNA), and one Y RNA expressed in the developing mouse lens. In parallel, bioinformatic investigation of mRNA-Seq data identified expression of 1,952 long intergenic ncRNA (lincRNA) in the developing mouse lens. In conclusion, we report a comprehensive ncRNA profile in the murine lens at six developmental time points. To the best of our knowledge, this is first report investigating different classes of ncRNAs in the developing mouse lens and will be monumental in elucidating processes essential for the development of the ocular lens and the maintenance of its transparency.
非编码RNA（ncRNAs）正成为基因组完整性和基因表达调控中的重要参与者，并且它们与许多疾病的发病机制有关。本研究的目的是鉴定发育中的小鼠晶状体中表达的ncRNA种类。我们之前报道过小鼠晶状体转录组，包括在两个胚胎期（E15和E18）以及四个出生后（P0、P3、P6和P9）时间点的mRNA和微小RNA（miRNA）谱。我们分析了来自小RNA测序和mRNA测序文库的数据，以研究ncRNA谱。我们的分析揭示了在六个发育时间点的小鼠晶状体中12种不同类型ncRNA的表达。小RNA数据注释显示在小鼠晶状体转录组中有1756种反义ncRNA（asncRNA）表达。同样，我们鉴定出82种与P元件诱导的弱精睾丸（PIWI）相互作用的RNA（piRNA）、345种转运RNA（tRNA）、12种小核RNA（snRNA）、167种小核仁RNA（snoRNA）、19种小卡哈尔体特异性RNA（scaRNA）、6种核糖体RNA（rRNA）、18种tRNA样结构、1种与MALAT1相关的小细胞质RNA（mascRNA）、1种穹窿体RNA（vtRNA）以及1种在发育中的小鼠晶状体中表达的Y RNA。同时，对mRNA测序数据的生物信息学研究确定了在发育中的小鼠晶状体中有1952种长链基因间ncRNA（lincRNA）表达。总之，我们报道了在六个发育时间点的小鼠晶状体中的全面ncRNA谱。据我们所知，这是首次关于发育中的小鼠晶状体中不同类型ncRNAs的研究报告，对于阐明晶状体发育及其透明度维持所必需的过程将具有重要意义。
