Development-related expression patterns of protein-coding and miRNA genes involved in porcine muscle growth

Abstract

ABSTRACT. Muscle growth and development is associated with remarkable changes in protein-coding and microRNA (miRNA) gene expression. To determine the expression patterns of genes and miRNAs related to muscle growth and development, we measured the expression levels of 25 protein-coding and 16 miRNA genes in skeletal and cardiac muscles throughout 5 developmental stages by quantitative reverse transcription-polymerase chain reaction. The Short Time-Series Expression Miner (STEM) software clustering results showed that growth-related genes were downregulated at all developmental stages in both the psoas major and longissimus dorsi muscles, indicating their involvement in early developmental stages. Furthermore, genes related to muscle atrophy, such as forkhead box 1 and muscle ring finger, showed unregulated expression with increasing age, suggesting a decrease in protein synthesis during the later stages of skeletal muscle development. We found that development of the cardiac muscle was a complex process in which growth-related genes were highly expressed during embryonic development, but they did not show uniform postnatal expression patterns. Moreover, the expression level of miR-499, which enhances the expression of the β-myosin heavy chain, was significantly different in the psoas major and longissimus dorsi muscles, suggesting the involvement of miR-499 in the determination of skeletal muscle fiber types. We also performed correlation analyses of messenger RNA and miRNA expression. We found negative relationships between miR-486 and forkhead box 1, and miR-133a and serum response factor at all developmental stages, suggesting that forkhead box 1 and serum response factor are potential targets of miR-486 and miR-133a, respectively.

Comparative analyses of longissimus muscle miRNAomes reveal microRNAs associated with differential regulation of muscle fiber development between Tongcheng and Yorkshire pigs

“…MiR-499-5p was a breed-DE miRNA found at 40, 55, 70, and 90 dpc in the present study, and its expression level gradually down-regulated over time. A recent study showed that miR-499 exhibits a greater expression level in psoas major muscle compared with the longissimus muscle, which respectively have higher proportions of red and white skeletal muscle in pigs [ 55 ]. And there was a substantial loss of type I muscle fibers and a concomitant increase in the expression of faster types IIx and IIb muscle fiber in the soleus of double knockout mice for miR-208b -/- and miR-499 -/- ; while the overexpression of miRNA-499 resulted in higher proportions of type I muscle fiber [ 22 ].…”

miR-434-3p and DNA hypomethylation co-regulate eIF5A1 to increase AChRs and to improve plasticity in SCT rat skeletal muscle

“…In addition to miR-434-3p, other miRNAs that play important roles in skeletal muscle have also been identified using miRNA microarrays. Among these miRNAs, miR-499 enhances the expression of the β-myosin heavy chain, which promotes muscle development 39 . Let-7 mutants exhibit temporal misregulation of NMJ maturation 40 .…”

Dynamic transcriptome profiles of postnatal porcine skeletal muscle growth and development

“…To investigate the dynamic genetic changes starting from newborn to two months old, STEM analysis was performed using the transcriptomic data of the LD muscle samples at the four time points. The STEM analysis provides a new approach to cluster, compare and visualize gene expression data from short-time series RNA-seq or microarray experiments [ 27 ], which has been widely used in studying the dynamic transcriptomic changes during development in pigs [ 28 – 30 ]. After adjusting a series of parameters, we found that setting the maximum number of model profiles to 2 and retaining the default values of the other parameters were optimal, as eight significantly different expression profiles were found to contain most of the DEGs.…”