Zhao Weimin, Mu Yulian, Ma Lei, Wang Chen, Tang Zhonglin, Yang Shulin, Zhou Rong, Hu Xiaoju, Li Meng-Hua, Li Kui
The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
1] CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100049, China.
Sci Rep. 2015 Mar 10;5:8957. doi: 10.1038/srep08957.
Long intergenic non-coding RNAs (lincRNAs) play important roles in many cellular processes. Here, we present the first systematic identification and characterization of lincRNAs in fetal porcine skeletal muscle. We obtained a total of 55.02 million 90-bp paired-end reads and assembled 54,550 transcripts using cufflinks. We developed a pipeline to identify 570 multi-exon lincRNAs by integrating a set of previous approaches. These putative porcine lincRNAs share many characteristics with mammalian lincRNAs, such as a relatively short length, small number of exons and low level of sequence conservation. We found that the porcine lincRNAs were preferentially located near genes mediating transcriptional regulation rather than those with developmental functions. We further experimentally analyzed the features of a conserved mouse lincRNA gene and found that isoforms 1 and 4 of this lincRNA were enriched in the cell nucleus and were associated with polycomb repressive complex 2 (PRC2). Our results provide a catalog of fetal porcine lincRNAs for further experimental investigation of the functions of these genes in the skeletal muscle developmental process.
长链基因间非编码RNA（lincRNAs）在许多细胞过程中发挥着重要作用。在此，我们首次对猪胎儿骨骼肌中的lincRNAs进行了系统的鉴定和特征分析。我们共获得了5502万个90碱基对的双端 reads，并使用cufflinks组装了54550个转录本。我们开发了一个流程，通过整合一系列先前的方法来鉴定570个多外显子lincRNAs。这些推测的猪lincRNAs与哺乳动物lincRNAs具有许多共同特征，如相对较短的长度、较少的外显子数量和较低的序列保守水平。我们发现猪lincRNAs优先位于介导转录调控的基因附近，而非具有发育功能的基因附近。我们进一步通过实验分析了一个保守的小鼠lincRNA基因的特征，发现该lincRNA的亚型1和4在细胞核中富集，并与多梳抑制复合物2（PRC2）相关。我们的结果提供了一份猪胎儿lincRNAs目录，用于进一步实验研究这些基因在骨骼肌发育过程中的功能。
