Identification of Large Intergenic Non-Coding RNAs in Bovine Muscle Using Next-Generation Transcriptomic Sequencing

The advent of large-scale gene expression technologies has helped to reveal in eukaryotic cells, the existence of thousands of non-coding transcripts, whose function and significance remain mostly poorly understood. Among these non-coding transcripts, long non-coding RNAs are the least well-studied but are emerging as key regulators of diverse cellular processes. Thousands of these loci have been identified in a variety of species, from flies to humans. However, only a handful of lncRNAs have been identified in farm animals, including in cattle. In the present study, we performed a survey in bovine Longissimus thoraci of lincRNAs (long intergenic non-coding RNAs).

To identify lincRNAs, we used paired-end RNA-Seq to explore the transcriptomes of Longissimus thoraci from nine Limousin bull calves. Approximately 14-46 million paired-end reads were obtained per library. A total of 30,548 different transcripts were identified. Using a computational pipeline, we defined a stringent set of 417 different lincRNAs with 249 lincRNAs found in all nine muscle samples. None of these lincRNAs have been previously identified in cattle. Bovine lincRNAs share characteristics seen in mammalian counterparts: relatively short length, low exon number and low expression. Eighteen lincRNAs have been selected for validation by RT-PCR. Some of the lincRNAs expressed in muscle are located within quantitative trait loci for meat quality traits. Our study will facilitate future experimental studies to unravel the function of these molecules.