An atlas and analysis of bovine skeletal muscle long noncoding RNAs

Abstract

Long noncoding RNAs (lncRNAs) have various biological functions and have been extensively studied in recent years. However, the identification and characterization of bovine lncRNAs in skeletal muscle has been very limited compared with that of lncRNAs in other model organisms. In this study, 7188 bovine skeletal muscle lncRNAs were identified by RNA-Seq and a stringent screening procedure in four different muscle tissues. These lncRNAs shared many characteristics with other mammalian lncRNAs, such as a shorter open reading frame and lower expression level than for mRNAs. Furthermore, the chromosomal locations and global expression patterns for these lncRNAs are also described in detail. More importantly, we detected the important interaction relationships of lncRNAs-miRNAs-mRNAs related to muscle development among 36 lncRNAs, 62 miRNAs and 12 mRNAs. Our results provide a global expression pattern of lncRNAs specific to bovine skeletal muscle and provide important targets for revealing the function of bovine muscle development by thoroughly studying the interaction relationships of lncRNAs-miRNAs-mRNAs.

Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

“…Eight of the cis target protein-coding genes enriched in GO term associated with skeletal muscle cell differentiation (BCL9L, HIVEP3, MEF2D, RB1, MAFF, EMD, BTG2 and ASB2), indicating the important roles of lncRNAs in skeletal muscle development. It was consistent with previous studies that lncRNAs regulated nearby protein-coding genes to involve in muscle development and diseases (Zhan et al 2016;Liu et al 2017;Yue et al 2019). For example, the most recent study reported that the bovine lncKBTBD10 affect its proximity gene KBTBD10 to involve in myogensis (Chen et al 2019).…”

“…lncRNAs are known to be shorter transcript lengths and fewer exon numbers than mRNAs (Wang et al 2018;Sulayman et al 2019). Approximately 80.51% of our 4155 lncRNAs was shorter than 2800 bp and 87.32% of them had 2-4 exons, which was in agreement with previous studies in cattle (Billerey et al 2014;Liu et al 2017;Choi et al 2019;Yue et al 2019). These investigations provide valuable information about the characteristics of lncRNAs in bovine.…”

“…Thus, we only chose multi-exonic lncRNAs for further analysis, as was done in other studies (Tong et al 2017;Kern et al 2018;Yang et al 2018;Yue et al 2019), and depends on a highly stringent filtering pipeline to minimise the number of false-positive lncRNAs. Consequently, 4155 non-protein coding transcripts were considered as highly reliable lncRNAs, which was less than previous studies due to our stringent criteria (Billerey et al 2014;Liu et al 2017;Choi et al 2019;Yue et al 2019). These lncRNAs have different expression distribution in different chromosomes.…”

“…Koufariotis et al (2015) captured 9778 high-confidence putative lncRNAs from RNA-Seq data across 18 tissues of a single cow. Liu et al (2017) identified 7188 bovine skeletal muscle lncRNAs by RNA-Seq. Kern et al (2018) identified 7235 lncRNAs in cattle using RNA-seq from eight tissue types.…”

Assembly and validation of conserved long non-coding RNAs in the ruminant transcriptome

“…6-40 million reads each) [32], and horse (8 tissues, sequenced at approx. 20-200 million reads each) [33], complementing tissue-specific lncRNA catalogues of, for example, cattle muscle [34, 35] and skin [36], and pig adipose [37, 38], liver [39] and testis [40].…”