Identification and characterization of long intergenic non-coding RNAs related to mouse liver development
Identification and characterization of long intergenic non-coding RNAs related to mouse liver development
复制标题
与小鼠肝脏发育相关的长基因间非编码RNA的鉴定和表征
DOI：
10.1007/s00438-014-0882-9
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发表时间：
2014-12-01
影响因子：
3.1
通讯作者：
Wu, Qiong
中科院分区：
文献类型：
--
作者：
Lv, Jie;Huang, Zhijun;Wu, Qiong
长链非编码RNA（lncRNA）在过去几年中得到了广泛的研究。肝脏是一个重要的器官，在葡萄糖代谢和稳态中起着至关重要的作用，然而，很少有报道的lncRNA的识别和功能特性的重要作用，在肝脏发育。因此，有必要系统地鉴定参与肝脏发育的lncRNA。在这篇论文中，我们使用已发表的RNA-seq数据在三个小鼠肝脏发育阶段组装了转录组，并鉴定了4，882个在至少一个研究阶段表达的推定长基因间非编码RNA（lincRNA）。将这些与Ensembl lincRNA结合，我们建立了小鼠肝脏中6，602个转录lincRNA的参考目录。然后，我们系统地分析了该参考目录中的所有lincRNA，并揭示了肝脏lincRNA携带来自蛋白质编码基因的不同基因组特征，而推定的lincRNA通常与已知的Ensembl lincRNA相当。此外，lincRNA与RNA剪接、蛋白质定位和脂肪酸代谢等重要生物学过程相关，可能在肝脏发育中发挥重要作用。在发育中的肝组织中特异性表达的选定lincRNA的验证进一步表明了我们方法的有效性。我们的研究表明，在肝脏发育的三个阶段中差异表达的lincRNA可能在肝脏发育中具有重要的调节作用。鉴定的推定lincRNA是用于进一步功能研究的有价值的资源。
Long non-coding RNAs (lncRNAs) have been studied extensively over the last few years. Liver is an important organ that plays a crucial role in glucose metabolism and homeostasis; however, there are few reports of the identification and functional characterization of lncRNAs with important roles in liver development. Therefore, it is necessary to systematically identify lncRNAs that are involved in liver development. In this paper, we assembled the transcriptome using published RNA-seq data across three mouse liver developmental stages and identified 4,882 putative long intergenic non-coding RNAs (lincRNAs) expressed in at least one of the investigated stages. Combining these with Ensembl lincRNAs, we established a reference catalog of 6,602 transcribed lincRNAs in the mouse liver. We then analyzed all the lincRNAs in this reference catalog systematically and revealed that liver lincRNAs carry different genomic signatures from protein-coding genes, while the putative lincRNAs are generally comparable with known Ensembl lincRNAs. In addition, putative lincRNAs are functionally associated with essential biological processes, including RNA splicing, protein localization and fatty acid metabolic process, implying that they may play an important role in regulating liver development. The validation of selected lincRNAs that are specifically expressed in developing liver tissues further suggested the effectiveness of our approach. Our study shows that lincRNAs that are differentially expressed during three liver developmental stages could have important regulatory roles in liver development. The identified putative lincRNAs are a valuable resource for further functional studies.