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

Abstract

BackgroundThe 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.ResultsTo 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-499) contains supplementary material, which is available to authorized users.

Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat

“…In agreement with similar studies on different organisms, the identified putative lncRNAs had fewer exon numbers, shorter transcript lengths, and lower expression levels than protein-coding genes [11, 48, 49]. The number of putative lncRNAs detected in this study was more than that reported in previous studies in cattle and goat [9, 52]. Six randomly selected differentially expressed lncRNA transcripts were validated using qPCR, and the results were consistent with the results from the RNA-seq data.…”

Long noncoding RNA repertoire in chicken liver and adipose tissue

“…These numbers of long noncoding genes are consistent with other studies that focus on a single tissue, even if the number of replicates, the sequencing depth and the criteria used to consider that a long noncoding gene is expressed, differ between studies. For example, Wang et al [33] reported 2805 lncRNA transcripts in the pig endometrium (using 12 porcine samples and 85–105 million reads per sample), and Billerey et al [34] reported approximately 1300 lncRNA transcripts in bovine muscle (using nine samples with 15 million to 45 million reads per sample). In contrast, multi-tissue studies reported a larger number of lncRNA transcripts, generally above 10,000, with a wide variation depending on the sequenced tissues and the tools used for the lncRNA detection (9778 lncRNA transcripts reported by Koufariotis et al [16] in 18 bovine tissues (using 1.87 million 120-bp stranded paired-end reads and CPC/CNCI tools for lncRNA prediction [24, 35]), and 20,163 lncRNA transcripts reported by Li et al [36] in 13 maize tissues (using 1.17 million 35- to 110-bp unstranded paired- and single-end reads and the CPC tool for lncRNA prediction [24]).…”

Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications

“…References for lncRNA genes amounts are as follow: human, Gencode v19, Dec 2013, GRCh37 - Ensembl 74 [2] and [3, 164]; chimpanzee, macaque [3]; mouse, Gencode v2, Dec 2013, GRCm38 - Ensembl 74 [2] and [3, 164]; rat and cow lncRNA content was estimated to be similar to related organisms based on consistent amounts from single tissue analyses (liver for rat [63], skin [165] and muscle [166] for cow [see also 167]) and data for the organs of other mammals [3]; opossum [3]; chicken [3, 167]; frog [3]; zebrafish [12, 164, 167, 168]; nematode [167, 169]; Drosophila [5, 6]; in mosquito, 633 lncRNAs were identified with a very strict cut offs for identification. Therefore, given these first estimations for lncRNA content in drosophila, on the figure mosquito lncRNA content is represented as >1000 lncRNA genes (based on a set of 633 lncRNAs with very strict cut-offs [199]); yeast [167]; Ganoderma lucidum [170]; plasmodium [171]; Arabidopsis [7]; maize [8, 9].…”