Abstract
Alternative splicing is a ubiquitous regulatory mechanism in gene expression that allows a single gene generating multiple messenger RNAs (mRNAs). Significant differences in fat deposition ability and meat quality traits have been reported between Japanese black cattle (Wagyu) and Chinese Red Steppes, which presented a unique model for analyzing the effects of transcriptional level on marbling fat in livestock. In previous studies, the differentially expressed genes (DGEs) in longissimus dorsi muscle (LDM) samples between Wagyu and other breeds of beef cattle have been reported. In this study, we further investigated the differences in alternative splicing in LDM between Wagyu and Chinese Red Steppes cattle. We identified several alternative splicing types including cassette exon, mutually exclusive exons, alternative 5′ splice site, alternative 3′ splice site, alternative start exon, and intron retention. In total, 115 differentially expressed alternatively spliced genes were obtained, of which 17 genes were enriched in the metabolic pathway. Among the 17 genes, 5 genes, including MCAT, CPT1B, HADHB, SIRT2, and DGAT1, appeared to be the novel spliced candidates that affect the lipid metabolism in cattle. Additionally, another 17 genes were enriched in the Gene Ontology (GO) terms related to muscle development, such as NR4A1, UQCC2, YBX3/CSDA, ITGA7, etc. Overall, altered splicing and expression levels of these novel candidates between Japanese black cattle and Chinese Red Steppes revealed by RNA-seq suggest their potential involvement in the muscle development and fat deposition of beef cattle.
Highlights
Alternative splicing or alternative RNA splicing is a method to create different proteins from the same strand of DNA in mammalian cell
The mechanisms and outcomes of alternative splicing of individual transcripts are relatively well-understood in dairy and beef cattle, such as angiopoietin like 6 (ANGPTL6) [23], transmembrane protein 95 (TMEM95) [24], and calpain 3 (CAPN3) [25], the scopes and exact functions of this regulatory mechanism still remain to be investigated on novel transcripts and alternative splicing networks
The present study found that many genes have novel transcripts with different expression levels, the specific genetic functions and regulation mechanisms of translated proteins by these messenger RNAs (mRNAs) of the same gene on bovine muscle development, fat deposition, and meat quality traits still require further study
Summary
Alternative splicing or alternative RNA splicing is a method to create different proteins from the same strand of DNA in mammalian cell. Pan et al [7] analyzed alternative splicing complexity in human tissues showing transcripts from ∼95% of multiexon genes undergo alternative splicing by combining mRNA-Seq with expressed sequence tag (EST)-complementary DNA (cDNA) sequence data. The data of 15 diverse human tissue and cell line transcriptomes indicated that 92–94% of human genes undergo alternative splicing, and most alternative splicing and alternative cleavage events vary between tissues [8]. These results demonstrate the universality and utility of alternative splicing in mammal, and to further understand the alternative splicing will be a crucial effective method in the study of formation of human disease or perfect economic traits in livestock
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