Open Access Research article

Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing

Coline Billerey1234, Mekki Boussaha12, Diane Esquerré56, Emmanuelle Rebours12, Anis Djari7, Cédric Meersseman12, Christophe Klopp7, Daniel Gautheret34 and Dominique Rocha12*

Author Affiliations

1 INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France

2 AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France

3 Institut de Génétique et Microbiologie, Université Paris-Sud, UMR8621, F-91405 Orsay, France

4 CNRS, UMR8621, Institut de Génétique et Microbiologie, F-91405 Orsay, France

5 INRA, UMR 444, Laboratoire de Génétique Cellulaire, INRA Auzeville, BP 52627, F-31326 Castanet-Tolosan Cedex, France

6 GeT-PlaGe, Genotoul, INRA Auzeville, BP 52627, F-31362 Castanet-Tolosan Cedex, France

7 INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, F-31326 Castanet-Tolosan Cedex, France

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BMC Genomics 2014, 15:499  doi:10.1186/1471-2164-15-499

Published: 19 June 2014

Abstract

Background

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 (lncRNAs) are the least well-studied but are emerging as key regulators of diverse cellular processes. In the present study, we performed a survey in bovine Longissimus thoraci of lincRNAs (long intergenic non-coding RNAs not overlapping protein-coding transcripts). To our knowledge, this represents the first such study in bovine muscle.

Results

To identify lincRNAs, we used paired-end RNA sequencing (RNA-Seq) to explore the transcriptomes of Longissimus thoraci from nine Limousin bull calves. Approximately 14–45 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 584 different lincRNAs with 418 lincRNAs found in all nine muscle samples. Bovine lincRNAs share characteristics seen in their mammalian counterparts: relatively short transcript and gene lengths, low exon number and significantly lower expression, compared to protein-encoding genes. As for the first time, our study identified lincRNAs from nine different samples from the same tissue, it is possible to analyse the inter-individual variability of the gene expression level of the identified lincRNAs. Interestingly, there was a significant difference when we compared the expression variation of the 418 lincRNAs with the 10,775 known selected protein-encoding genes found in all muscle samples. In addition, we found 2,083 pairs of lincRNA/protein-encoding genes showing a highly significant correlated expression. Fourteen lincRNAs were selected and 13 were validated by RT-PCR. Some of the lincRNAs expressed in muscle are located within quantitative trait loci for meat quality traits.

Conclusions

Our study provides a glimpse into the lincRNA content of bovine muscle and will facilitate future experimental studies to unravel the function of these molecules. It may prove useful to elucidate their effect on mechanisms underlying the genetic variability of meat quality traits. This catalog will complement the list of lincRNAs already discovered in cattle and therefore will help to better annotate the bovine genome.

Keywords:
Cattle; Muscle; RNA-Seq; Beef; Long non-coding RNA