Non-coding RNA profiling of the developing murine lens.
Non-coding RNA profiling of the developing murine lens.
复制标题
DOI：
10.1016/j.exer.2016.01.010
复制
发表时间：
2016-04
影响因子：
3.4
通讯作者：
Riazuddin SA
中科院分区：
文献类型：
--
作者：
Khan SY;Hackett SF;Riazuddin SA
非编码 RNA (ncRNA) 正在成为基因组完整性和基因表达调控的重要参与者，并且与许多疾病的发病机制有关。本研究的目的是确定发育中的小鼠晶状体中表达的 ncRNA 库。我们之前报道了小鼠晶状体转录组，包括两个胚胎（E15 和 E18）和四个出生后（P0、P3、P6 和 P9）时间点的 mRNA 和 microRNA (miRNA) 分析。我们分析了小型 RNA-Seq 和 mRNA-Seq 文库的数据，以研究 ncRNA 图谱。我们的分析揭示了小鼠晶状体在六个发育时间点表达了 12 种不同类别的 ncRNA。小 RNA 数据注释显示小鼠晶状体转录组中表达了 1,756 个反义 ncRNA (asncRNA)。同样，我们鉴定了 82 个 P 元件诱导的弱睾丸 (PIWI) 相互作用 RNA (piRNA)、345 个转移 RNA (tRNA)、12 个小核 RNA (snRNA)、167 个小核仁 RNA (snoRNA)、19 个小卡哈尔体特异性 RNA (scaRNA)、6 个核糖体 RNA (rRNA)、18 个 tRNA 样结构、1 个 MALAT1 相关小 RNA细胞质 RNA (mascRNA)、一种 Vault RNA (vtRNA) 和一种 Y RNA 在发育中的小鼠晶状体中表达。与此同时，对 mRNA-Seq 数据的生物信息学研究确定了发育中的小鼠晶状体中 1,952 个长基因间 ncRNA (lincRNA) 的表达。总之，我们报告了小鼠晶状体在六个发育时间点的全面 ncRNA 谱。据我们所知，这是第一份研究发育中的小鼠晶状体中不同类别的 ncRNA 的报告，对于阐明眼晶状体发育和维持其透明度所必需的过程具有里程碑意义。
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.