Abstract
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.
Highlights
Long intergenic non-coding RNAs play important roles in many cellular processes
We developed a highly stringent filtering pipeline (Figure 1) to identify porcine lincRNAs using an integrated experimental and computational approach
We found that our lincRNA genes contained canonical splice sites (GT-AG); these lincRNAs were distributed in all chromosomes except the Y chromosome
Summary
Long intergenic non-coding RNAs (lincRNAs) play important roles in many cellular processes. Several studies in the past decade, have revealed that most of these regions may represent novel transcribed regions[2,3,4], where transcripts longer than 200 nucleotides in length are localized Much of this newly discovered major class of transcripts has very weak or no protein-coding potential and, was defined as long intergenic non-coding RNAs (lincRNAs)[5]. Previous investigations found that polycomb repressive complex 2 (PRC2) plays a key role in regulating myogenesis[33] and that approximately 20% of lincRNAs are bound by PRC234. These findings indicate that lincRNAs are most likely involved in the development of skeletal muscle. The 50–75 dpc period is a critical stage of fetal skeletal muscle development
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