Systematic identification of intergenic long-noncoding RNAs in mouse retinas using full-length isoform sequencing
Systematic identification of intergenic long-noncoding RNAs in mouse retinas using full-length isoform sequencing
复制标题
使用全长同工型测序系统鉴定小鼠视网膜中基因间长非编码 RNA
DOI：
10.1186/s12864-019-5903-y
复制
发表时间：
2019-07-08
期刊：
影响因子：
4.4
通讯作者：
Gan, Lin
中科院分区：
文献类型：
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作者：
Wan, Ying;Liu, Xiaoyang;Gan, Lin
背景在小鼠基因组中发现了大量的长链非编码RNA（longnoncodingRNA，lncRNA），近几十年来越来越多的证据表明它们在多种生物学过程中发挥着重要作用。然而，由于缺乏对视网膜中表达的lncRNA的全面注释，lncRNA在小鼠视网膜中的生物学作用在很大程度上仍然未知。结果在这项研究中，我们应用长读段测序策略来解开发育中小鼠视网膜的转录组，并鉴定了总共940个基因间lncRNA在胚胎和新生儿视网膜中，约13%的lincRNA转录自未注释的基因位点。随后的分析显示，在小鼠视网膜中表达的lincRNA的功能与该组织的生理作用密切相关，包括在视网膜神经节细胞（RGC）分化的关键调节因子的功能丧失后差异表达的90种lincRNA。原位杂交结果表明，富集的IV类POU同源盒基因lincRNA（linc-3a，linc-3bandlinc-3c）在神经节细胞层，并表明他们是潜在的RGC-specific.ConclusionsIn总结，这项研究系统地注释了lincRNA在胚胎和新生小鼠视网膜中表达，并暗示其在视网膜发育，如RGC分化的重要调控作用。
BackgroundA great mass of long noncoding RNAs (lncRNAs) have been identified in mouse genome and increasing evidences in the last decades have revealed their crucial roles in diverse biological processes. Nevertheless, the biological roles of lncRNAs in the mouse retina remains largely unknown due to the lack of a comprehensive annotation of lncRNAs expressed in the retina.ResultsIn this study, we applied the long-reads sequencing strategy to unravel the transcriptomes of developing mouse retinas and identified a total of 940 intergenic lncRNAs (lincRNAs) in embryonic and neonatal retinas, including about 13% of them were transcribed from unannotated gene loci. Subsequent analysis revealed that function of lincRNAs expressed in mouse retinas were closely related to the physiological roles of this tissue, including 90 lincRNAs that were differentially expressed after the functional loss of key regulators of retinal ganglion cell (RGC) differentiation. In situ hybridization results demonstrated the enrichment of three class IV POU-homeobox genes adjacent lincRNAs (linc-3a,linc-3bandlinc-3c) in ganglion cell layer and indicated they were potentially RGC-specific.ConclusionsIn summary, this study systematically annotated the lincRNAs expressed in embryonic and neonatal mouse retinas and implied their crucial regulatory roles in retinal development such as RGC differentiation.