Identification of genes related to skeletal muscle growth and development by integrated analysis of transcriptome and proteome in myostatin-edited Meishan pigs.

Embryonic development of skeletal muscle is a complex process that is important to the growth of skeletal muscle after birth. However, the mechanisms by which skeletal muscle growth and development in embryonic phase remain unclear. We have previously produced myostatin-knockout (MKO) Meishan pigs with double-muscle (DM) phenotype via zinc finger nucleases (ZFN) technology. To further investigate the molecular mechanisms involved in skeletal muscle growth and development, in this study, we performed an integrated analysis of transcriptome and proteome in longissimus dorsi muscle from myostatin wild type (MWT) and MKO pigs on 65 days post coitus. Results showed that, compared with MWT group, there were 438 differentially expressed genes (DEGs) and 66 differentially expressed proteins (DEPs) in MKO group. These DEGs and DEPs were mainly enriched in signaling pathways that are involved in skeletal muscle growth and development, glucose metabolism and apoptosis. Furthermore, we identified two key genes, Troponin T 1 (TNNT1) and Myosin regulatory light chain 9 (MYL9), which showed significant changes in both mRNA and protein levels with the similar changing trends in MKO group. It is thus speculated that TNNT1 and MYL9 may play an important role in skeletal muscle growth and development. SIGNIFICANCE: Our study analyzed some important regulatory genes and proteins during skeletal muscle growth and development, our results provided (1) a new insight to further understanding of the molecular mechanisms by which growth and development are regulated in porcine skeletal muscle, and (2) some possible molecular makers for improvement of meat quality in the animal husbandry and diagnosis of human muscle diseases in medicine.

Li X ，Xie S ，Qian L ，Cai C ，Bi H ，Cui W ... -  《-》

An integrated analysis of mRNA and miRNA in skeletal muscle from myostatin-edited Meishan pigs.

Myostatin (MSTN) is a key muscle factor that negatively regulates skeletal muscle growth and development. Our laboratory recently produced genetically engineered Meishan pigs containing a -edited MSTN loss-of-function mutation (MSTN, MKO) that led to the hypertrophy of skeletal muscles. In this study, we performed transcriptome sequencing and miRNA sequencing in skeletal muscle samples from MKO and wildtype Meishan (MWT) pigs to investigate the effect of MSTN on expression of mRNA and miRNA. Our results indicated that, compared to MWT pigs, there were 200 genes and 4 miRNAs being significantly up-regulated, and 238 genes and 5 miRNAs being significantly down-regulated in MKO pigs. Analysis by GO and KEGG pathways revealed that differentially expressed miRNAs and their target genes of those differentially expressed miRNAs were involved in the signal pathways of skeletal muscle growth and development such as AMPK, mTOR, and TGF-beta. An integrated analysis of the correlation between miRNA-mRNA and transcriptome predicated that and were target genes for miR-499-5p, while was a target gene for miR-490-3p. Our results provide important clues to help us further investigate MSTN's regulatory mechanisms during skeletal muscle growth and development.

Xie S ，Li X ，Qian L ，Cai C ，Xiao G ，Jiang S ，Li B ，Gao T ，Cui W ... -  《-》

Targeted mutations in myostatin by zinc-finger nucleases result in double-muscled phenotype in Meishan pigs.

Qian L ，Tang M ，Yang J ，Wang Q ，Cai C ，Jiang S ，Li H ，Jiang K ，Gao P ，Ma D ，Chen Y ，An X ，Li K ，Cui W ... -  《Scientific Reports》

A comparison of prenatal muscle transcriptome and proteome profiles between pigs with divergent growth phenotypes.

The growth of pigs is an important economic trait that involves multiple genes and coordinated regulatory mechanisms. The growth rate and potential of skeletal muscles are largely decided by embryonic myofiber development. Tibetan pig (TP) that is a mini-type breed has a divergent phenotype in growth rate and adult body weight with Wujin pig (WJ) and large White pig (LW). In the current study, the transcriptome (using RNA-seq) and proteome (using the isobaric tag for relative and absolute quantification [iTRAQ]) data from the prenatal muscle tissues were analyzed to identify the genes related to postnatal growth rate and growth potential in pigs. In the RNA-seq experiment, 19 626 genes were detected in the embryonic muscle tissues, and 3626 unique differentially expressed genes (DEGs) were identified in TP in comparison to that in LW and WJ. In the iTRAQ experiment, 2474 proteins were detected, and 735 unique differentially expressed proteins (DEPs) were identified in TP in comparison to that in LW and WJ. Combining the DEGs and DEPs, 209 genes were found to be differentially expressed, consistently at both the messenger RNA and protein levels, between TP and the other two breeds; these are mainly involved in 2-oxocarboxylic acid metabolism, citrate cycle, and biosynthesis of amino acids. Of these, 20 genes that were related to myoblast differentiation and muscle fiber formation might have important roles in determining the postnatal growth rate and potential body weight in pigs. Our results provide new candidate genes and insights into the molecular mechanisms involved muscle growth traits in pigs.

Shang P ，Wang Z ，Chamba Y ，Zhang B ，Zhang H ，Wu C ... -  《-》

Identification of differentially expressed genes in longissimus dorsi muscle between Wei and Yorkshire pigs using RNA sequencing.

Intramuscular fat (IMF) content is an important trait closely related to meat quality, which is highly variable among pig breeds from diverse genetic backgrounds. High-throughput sequencing has become a powerful technique for analyzing the whole transcription profiles of organisms. In order to elucidate the molecular mechanism underlying porcine meat quality, we adopted RNA sequencing to detect transcriptome in the longissimus dorsi muscle of Wei pigs (a Chinese indigenous breed) and Yorkshire pigs (a Western lean-type breed) with different IMF content. For the Wei and Yorkshire pig libraries, over 57 and 64 million clean reads were generated by transcriptome sequencing, respectively. A total of 717 differentially expressed genes (DEGs) were identified in our study (false discovery rate < 0.05 and fold change > 2), with 323 up-regulated and 394 down-regulated genes in Wei pigs compared with Yorkshire pigs. Gene Ontology analysis showed that DEGs significantly related to skeletal muscle cell differentiation, phospholipid catabolic process, and extracellular matrix structural constituent. Pathway analysis revealed that DEGs were involved in fatty acid metabolism, steroid biosynthesis, glycerophospholipid metabolism, and protein digestion and absorption. Quantitative real time PCR confirmed the differential expression of 11 selected DEGs in both pig breeds. The results provide useful information to investigate the transcriptional profiling in skeletal muscle of different pig breeds with divergent phenotypes, and several DEGs can be taken as functional candidate genes related to lipid metabolism (ACSL1, FABP3, UCP3 and PDK4) and skeletal muscle development (ASB2, MSTN, ANKRD1 and ANKRD2).

Xu J ，Wang C ，Jin E ，Gu Y ，Li S ，Li Q ... -  《-》