Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development

• DOI: 10.1038/srep08957
• Publication Date: 2015-03-10T10:47:21Z
• Authors: Weimin Zhao; Yulian Mu; Lei Ma; Chen Wang; Zhonglin Tang; Shulin Yang; Rong Zhou; Xiaoju Hu; Meng-Hua Li; Kui Li
• Keywords: 0301 basic medicine; Mice; 03 medical and health sciences; Swine; Animals; Gene Expression Regulation, Developmental; RNA, Long Noncoding; Exons; Muscle Development; Muscle, Skeletal; Article; Conserved Sequence

AbstractLong 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.