Transcriptome and proteomics analysis revealed key genes in rabbit skeletal muscle after weight loss

Skeletal muscle is one of the important organs of energy metabolism and is closely related to insulin secretion. Its metabolic characteristics have a major influence on fat distribution in various body tissues. However, rabbit skeletal muscle has lower intramuscular fat content, and its metabolic mechanism is still unclear. We investigated skeletal muscle growth and metabolic differences among rabbits using a comparative multi-omics approach after a 14-day weight loss by a restricted diet. Rabbit body weight and perirenal fat were significantly reduced after the weight loss. Transcriptomics data revealed 917 differentially expressed genes in skeletal muscle primarily enriched in the FOXO signaling, Glutathione metabolism, and AMPK signaling pathways. Proteomics data found 127 differential proteins concentrated in protein metabolism and immunoinflammatory pathways. Conbined analysis demonstrated that eight genes (ATP2A2, PDLIM3, GPX7, FKBP5, MYL3, COL5A2, UCHL1, and COL3A1) were strongly correlated at the transcriptional and translational levels. These results provide a good reference for further revealing the mechanism of skeletal muscle metabolism in rabbits.

Morphological changes and functional circRNAs screening of rabbit skeletal muscle development

Background The temporal expression pattern of circular RNAs (circRNAs) across developmental stages is essential for skeletal muscle growth and functional analysis. However, there are few analyses on the potential functions of circRNAs in rabbit skeletal muscle development. Results Initially, the paraffin sections showed extremely significant differences in the diameter, number, area and density of skeletal muscle fibers of the fetus, child, adult rabbit hind legs (P < 0.01). Then, RNA-seq libraries of these three stages were constructed. A total of 481 differentially expressed circRNAs (DE-circRNAs) and 5,658 differentially expressed genes (DEGs) were identified. Subsequently, DE-circRNAs, whose host genes were DEGs or non-DEGs, were analyzed by GO respectively. In the fetus vs. child group, up-regulated DE-circRNAs (whose host genes were DEGs) were related to muscle fiber structure, and down-regulated ones were related to mitosis. The up-regulated DE-circRNAs (whose host genes were non-DEGs) were involved in enzyme activity, methylation and glycosylation, and the down-regulated ones were involved in mitosis and catabolism. In the fetus vs. adult group, the up-regulated DE-circRNAs (whose host genes were DEGs) were related to skeletal muscle basic structure, and the down-regulated ones were also associated with cell proliferation. But the up-regulated DE-circRNAs (whose host genes were non-DEGs) were connected with regulation of histone ubiquitination, chromatin and organelles. The down-regulated DE-circRNAs were connected with the catabolism processes. In addition, novel_circ_0022663 and novel_circ_0005489, which might have coding potential, and novel_circ_0004210 and novel_circ_0001669, which might have miRNA sponge capability, were screened out. Conclusions In this study, hind leg muscles of fetus, child and adult rabbits were collected for paraffin section and RNA-seq to observe the structural changes of skeletal muscle and obtain circRNA expression profiles at different stages. These data provided a catalog of circRNAs related to muscle development in New Zealand rabbits, allowing us to better understand the functional transitions in mammalian muscle development.

Multi–Omics Analysis of Key microRNA–mRNA Metabolic Regulatory Networks in Skeletal Muscle of Obese Rabbits

microRNAs (miRNAs), small non-coding RNA with a length of about 22 nucleotides, are involved in the energy metabolism of skeletal muscle cells. However, their molecular mechanism of metabolism in rabbit skeletal muscle is still unclear. In this study, 16 rabbits, 8 in the control group (CON–G) and 8 in the experimental group (HFD–G), were chosen to construct an obese model induced by a high–fat diet fed from 35 to 70 days of age. Subsequently, 54 differentially expressed miRNAs, 248 differentially expressed mRNAs, and 108 differentially expressed proteins related to the metabolism of skeletal muscle were detected and analyzed with three sequencing techniques (small RNA sequencing, transcriptome sequencing, and tandem mass tab (TMT) protein technology). It was found that 12 miRNAs and 12 core genes (e.g., CRYL1, VDAC3 and APIP) were significantly different in skeletal muscle from rabbits in the two groups. The network analysis showed that seven miRNA-mRNA pairs were involved in metabolism. Importantly, two miRNAs (miR-92a-3p and miR-30a/c/d-5p) regulated three transcription factors (MYBL2, STAT1 and IKZF1) that may be essential for lipid metabolism. These results enhance our understanding of molecular mechanisms associated with rabbit skeletal muscle metabolism and provide a basis for future studies in the metabolic diseases of human obesity.

Untargeted Metabolomic Characteristics of Skeletal Muscle Dysfunction in Rabbits Induced by a High Fat Diet

Background: Type 2 diabetes and metabolic syndrome caused by a high fat diet (HFD) have become public health problems around the world. These diseases are characterized by disrupted mitochondrial oxidation and insulin resistance in skeletal muscle, but the mechanism is not clear. Therefore, this study aims to reveal how a high-fat diet induces skeletal muscle metabolism disorder.Methods：Sixteen weaned rabbits were randomly divided into two groups, one fed with a standard normal diet (SND) and another one fed a HFD for five weeks. Skeletal muscle tissue samples were extracted from each rabbit at the end of the 5-week trial. An untargeted metabolomics profiling was performed using ultraperformance liquid chromatography combined with mass spectrometry (UHPLC-MS/MS).Results: The HFD significantly altered the expression levels of phospholipids, LCACs, histidine, carnosine and tetrahydrocorticosterone in skeletal muscle. Principal component analysis (PCA) and least square discriminant analysis (PLS-DA) indicated that rabbit skeletal muscle metabolism in the HFD group was significantly up-regulated compared with that of the SND group. Among the 43 skeletal muscle metabolites in the HFD group, phospholipids, LCACs, histidine, carnosine and tetrahydrocorticosterone were identified as biomarkers for skeletal muscle metabolic diseases, and may also serve as potential physiological targets for related diseases in the future.Conclusion: The untargeted metabolomics analysis revealed that a HFD altered the rabbit skeletal muscle metabolism of phospholipids, carnitine, amino acids, and steroids. Notably, phospholipids, LCACs, histidine, carnosine and tetrahydrocorticosterone blocked the oxidative ability of mitochondria, and disturbed the oxidative ability of glucose and the fatty acid-glucose cycle in rabbit skeletal muscle.

Calsequestrin: a well-known but curious protein in skeletal muscle

Calsequestrin (CASQ) was discovered in rabbit skeletal muscle tissues in 1971 and has been considered simply a passive Ca2+-buffering protein in the sarcoplasmic reticulum (SR) that provides Ca2+ ions for various Ca2+ signals. For the past three decades, physiologists, biochemists, and structural biologists have examined the roles of the skeletal muscle type of CASQ (CASQ1) in skeletal muscle and revealed that CASQ1 has various important functions as (1) a major Ca2+-buffering protein to maintain the SR with a suitable amount of Ca2+ at each moment, (2) a dynamic Ca2+ sensor in the SR that regulates Ca2+ release from the SR to the cytosol, (3) a structural regulator for the proper formation of terminal cisternae, (4) a reverse-directional regulator of extracellular Ca2+ entries, and (5) a cause of human skeletal muscle diseases. This review is focused on understanding these functions of CASQ1 in the physiological or pathophysiological status of skeletal muscle.

Sarcolipin Exhibits Abundant RNA Transcription and Minimal Protein Expression in Horse Gluteal Muscle

Ca2+ regulation in equine muscle is important for horse performance, yet little is known about this species-specific regulation. We reported recently that horse encode unique gene and protein sequences for the sarcoplasmic reticulum (SR) Ca2+-transporting ATPase (SERCA) and the regulatory subunit sarcolipin (SLN). Here we quantified gene transcription and protein expression of SERCA and its inhibitory peptides in horse gluteus, as compared to commonly-studied rabbit skeletal muscle. RNA sequencing and protein immunoblotting determined that horse gluteus expresses the ATP2A1 gene (SERCA1) as the predominant SR Ca2+-ATPase isoform and the SLN gene as the most-abundant SERCA inhibitory peptide, as also found in rabbit skeletal muscle. Equine muscle expresses an insignificant level of phospholamban (PLN), another key SERCA inhibitory peptide expressed commonly in a variety of mammalian striated muscles. Surprisingly in horse, the RNA transcript ratio of SLN-to-ATP2A1 is an order of magnitude higher than in rabbit, while the corresponding protein expression ratio is an order of magnitude lower than in rabbit. Thus, SLN is not efficiently translated or maintained as a stable protein in horse muscle, suggesting a non-coding role for supra-abundant SLN mRNA. We propose that the lack of SLN and PLN inhibition of SERCA activity in equine muscle is an evolutionary adaptation that potentiates Ca2+ cycling and muscle contractility in a prey species domestically selected for speed.