The developmental transcriptome landscape of bovine skeletal muscle defined by Ribo-Zero ribonucleic acid sequencing1

Abstract

Ribonucleic acid sequencing (RNA-Seq) libraries are normally prepared with oligo(dT) selection of poly(A)+ mRNA, but it depends on intact total RNA samples. Recent studies have described Ribo-Zero technology, a novel method that can capture both poly(A)+ and poly(A)- transcripts from intact or fragmented RNA samples. We report here the first application of Ribo-Zero RNA-Seq for the analysis of the bovine embryonic, neonatal, and adult skeletal muscle whole transcriptome at an unprecedented depth. Overall, 19,893 genes were found to be expressed, with a high correlation of expression levels between the calf and the adult. Hundreds of genes were found to be highly expressed in the embryo and decreased at least 10-fold after birth, indicating their potential roles in embryonic muscle development. In addition, we present for the first time the analysis of global transcript isoform discovery in bovine skeletal muscle and identified 36,694 transcript isoforms. Transcriptomic data were also analyzed to unravel sequence variations; 185,036 putative SNP and 12,428 putative short insertions-deletions (InDel) were detected. Specifically, many stop-gain, stop-loss, and frameshift mutations were identified that probably change the relative protein production and sequentially affect the gene function. Notably, the numbers of stage-specific transcripts, alternative splicing events, SNP, and InDel were greater in the embryo than in the calf and the adult, suggesting that gene expression is most active in the embryo. The resulting view of the transcriptome at a single-base resolution greatly enhances the comprehensive transcript catalog and uncovers the global trends in gene expression during bovine skeletal muscle development.

Transcriptome and DNA Methylation Analyses of the Molecular Mechanisms Underlying with Longissimus dorsi Muscles at Different Stages of Development in the Polled Yak

“…In the present study, three significant expression profiles were identified and combined into two clusters, class I profiles (profiles 1 and 0) with downregulated patterns and a class II profile (profile 6) with an upregulated pattern. According to the results of the STEM software analysis, it was found that there were cases in which genes were downregulated in the class I profiles, for example, PAX7, Col4A1, Col4A2, IGF2R, IGF2, FN1, MYL4, and MYL7, consistent with research on cattle and goats [46,47]. In the class II profile, many upregulated genes were observed, including LMOD2, MUSTN1, XIRP2, PDLIM5, MYF6, and TNNT1, also in accordance with a previous report on cows [47].…”

“…According to the results of the STEM software analysis, it was found that there were cases in which genes were downregulated in the class I profiles, for example, PAX7, Col4A1, Col4A2, IGF2R, IGF2, FN1, MYL4, and MYL7, consistent with research on cattle and goats [46,47]. In the class II profile, many upregulated genes were observed, including LMOD2, MUSTN1, XIRP2, PDLIM5, MYF6, and TNNT1, also in accordance with a previous report on cows [47]. For instance, many MYL protein family members were found in this study.…”

Transcriptome analysis of the pectoral muscles of local chickens and commercial broilers using Ribo-Zero ribonucleic acid sequencing

“…A transcript represents a mature RNA molecule, and "gene" refers to one or more transcript subtypes of a common exon in a mature cut form. When the transcription factor expression level changes, genes with different subtypes can encode the same protein, which helps maintain the gene expression at a certain level[ 27 ]. In addition, different subtypes of the same gene can also encode different proteins, which may have specific functions in different breeds.…”

Transcriptome analysis of differential gene expression in the longissimus dorsi muscle from Debao and landrace pigs based on RNA-sequencing

“…The growth ratio of the longissimus dorsi muscle is relatively more stable than that of other muscles. Thus, a previous study focused on and revealed mRNA or miRNA expression levels in longissimus dorsi muscle using high-throughput RNA-seq analysis of animals during growth and development periods [19,20]. On the other hand, RNA-seq is an efficient way to map and quantify the transcriptome and to analyze differentially expressed genes (DEGs) in different breeds.…”