Gene Expression Profiling of Skeletal Muscles

Chromatin profiling reveals TFAP4 as a critical transcriptional regulator of bovine satellite cell differentiation

BACKGROUND

Satellite cells are myogenic precursor cells in adult skeletal muscle and play a crucial role in skeletal muscle regeneration, maintenance, and growth. Like embryonic myoblasts, satellite cells have the ability to proliferate, differentiate, and fuse to form multinucleated myofibers. In this study, we aimed to identify additional transcription factors that control gene expression during bovine satellite cell proliferation and differentiation.

RESULTS

Using chromatin immunoprecipitation followed by sequencing, we identified 56,973 and 54,470 genomic regions marked with both the histone modifications H3K4me1 and H3K27ac, which were considered active enhancers, and 50,956 and 59,174 genomic regions marked with H3K27me3, which were considered repressed enhancers, in proliferating and differentiating bovine satellite cells, respectively. In addition, we identified 1,216 and 1,171 super-enhancers in proliferating and differentiating bovine satellite cells, respectively. Analyzing these enhancers showed that in proliferating bovine satellite cells, active enhancers were associated with genes stimulating cell proliferation or inhibiting myoblast differentiation whereas repressed enhancers were associated with genes essential for myoblast differentiation, and that in differentiating satellite cells, active enhancers were associated with genes essential for myoblast differentiation or muscle contraction whereas repressed enhancers were associated with genes stimulating cell proliferation or inhibiting myoblast differentiation. Active enhancers in proliferating bovine satellite cells were enriched with binding sites for many transcription factors such as MYF5 and the AP-1 family transcription factors; active enhancers in differentiating bovine satellite cells were enriched with binding sites for many transcription factors such as MYOG and TFAP4; and repressed enhancers in both proliferating and differentiating bovine satellite cells were enriched with binding sites for NF-kB, ZEB-1, and several other transcription factors. The role of TFAP4 in satellite cell or myoblast differentiation was previously unknown, and through gene knockdown and overexpression, we experimentally validated a critical role for TFAP4 in the differentiation and fusion of bovine satellite cells into myofibers.

CONCLUSIONS

Satellite cell proliferation and differentiation are controlled by many transcription factors such as AP-1, TFAP4, NF-kB, and ZEB-1 whose roles in these processes were previously unknown in addition to those transcription factors such as MYF5 and MYOG whose roles in these processes are widely known.

Thigh muscle metabolic response is linked to feed efficiency and meat characteristics in slow-growing chicken

The Korat chicken (KR) is a slow-growing Thai chicken breed with relatively poor feed efficiency (FE) but very tasty meat with high protein and low fat contents, and a unique texture. To enhance the competitiveness of KR, its FE should be improved. However, selecting for FE has an unknown effect on meat characteristics. Thus, understanding the genetic basis underlying FE traits and meat characteristics is needed. In this study, 75 male KR birds were raised up to 10 wk of age. For each bird, the feed conversion ratio (FCR), residual feed intake (RFI), and physicochemical properties, flavor precursors, and biological compounds in the thigh meat were evaluated. At 10 wk of age, thigh muscle samples from 6 birds (3 with high FCR and 3 with low FCR values) were selected, and their proteomes were investigated using a label-free proteomic method. Weighted gene coexpression network analysis (WGCNA) was used to screen the key protein modules and pathways. The WGCNA results revealed that FE and meat characteristics significantly correlated with the same protein module. However, the correlation was unfavorable; improving FE may result in a decrease in meat quality through the alteration in biological processes including glycolysis/gluconeogenesis, metabolic pathway, carbon metabolism, biosynthesis of amino acids, pyruvate metabolism, and protein processing in the endoplasmic reticulum. The hub proteins of the significant module (TNNT1, TNNT3, TNNI2, TNNC2, MYLPF, MYH10, GADPH, PGK1, LDHA, and GPI) were also identified to be associated with energy metabolism, and muscle growth and development. Given that the same proteins and pathways are present in FE and meat characteristics but in opposite directions, selection practices for KR should simultaneously consider both trait groups to maintain the high meat quality of KR while improving FE.

Transcriptome-based analysis of early post-mortem formation of pale, soft, and exudative (PSE) pork

Pale, soft, and exudative (PSE) meat can cause consumer dissatisfaction and economic losses. This study determined meat quality, glycolytic enzyme activity, and differential gene expression in the longissimus lumborum (LL) and semimembranosus (SM) of normal and PSE pork carcasses. The SM did not result in PSE meat. Hexokinase, lactate dehydrogenase, and pyruvate kinase activities were lower in the SM of PSE carcasses than in the normal carcasses. Functional enrichment analysis revealed that immune, inflammatory, and muscle fibre genes were significantly enriched in PSE pork. More specifically, PPP1R3G and MSS51 may be key genes regulating pork quality in the SM. Meanwhile, the differential expression of PLVAB, ADIPOQ, LEP, MYH4, MYH7, MYL3, MYL6B, FOS, ATF3, and HSPA6 may induce PSE formation in the LL. These results may provide insights into PSE pork formation mechanisms and reveal candidate genes for improving meat quality after validation.

Systematic identification of aberrant non-coding RNAs and their mediated modules in rotator cuff tears

Background: Rotator cuff tears (RCT) is the most common cause of shoulder dysfunction, however, its molecular mechanisms remain unclear. Non-coding RNAs(ncRNAs), such as long ncRNA (lncRNA), microRNA (miRNA) and circular RNA (circRNA), are involved in a variety of diseases, but little is known about their roles in RCT. Therefore, the purpose of this study is to identify dysregulated ncRNAs and understand how they influence RCT.

Methods: We performed RNA sequencing and miRNA sequencing on five pairs of torn supraspinatus muscles and matched unharmed subscapularis muscles to identify RNAs dysregulated in RCT patients. To better comprehend the fundamental biological processes, we carried out enrichment analysis of these dysregulated mRNAs or the co-expressed genes of dysregulated ncRNAs. According to the competing endogenous RNA (ceRNA) theory, we finally established ceRNA networks to explore the relationship among dysregulated RNAs in RCT.

Results: A total of 151 mRNAs, 38 miRNAs, 20 lncRNAs and 90 circRNAs were differentially expressed between torn supraspinatus muscles and matched unharmed subscapularis muscles, respectively. We found that these dysregulated mRNAs, the target mRNAs of these dysregulated miRNAs or the co-expressed mRNAs of these dysregulated ncRNAs were enriched in muscle structure development, actin-mediated cell contraction and actin binding. Then we constructed and analyzed the ceRNA network and found that the largest module in the ceRNA network was associated with vasculature development. Based on the topological properties of the largest module, we identified several important ncRNAs including hsa_circ_0000722, hsa-miR-129-5p and hsa-miR-30c-5p, whose interacting mRNAs related to muscle diseases, fat and inflammation.

Conclusion: This study presented a systematic dissection of the expression profile of mRNAs and ncRNAs in RCT patients and revealed some important ncRNAs which may contribute to the development of RCT. Such results could provide new insights for further research on RCT.