Genome-wide identification and characterization of the ubiquitin-specific protease (USP) gene family in cattle: primary analysis of muscle-specific USP genes and their influence on myogenesis

The ubiquitin-proteasome system(UPS) is a critical biological pathway that regulates protein function and plays a pivotal role in muscle formation. Nevertheless, the current comprehension of the ubiquitin-specific protease (USP) family, an important component of the UPS, in relation to bovine myoblast development remains relatively limited. This study aims to characterize the bovine USPs and conduct a preliminary analysis of their function, to provide valuable insights for enhancing beef yield and quality. A comprehensive genome-wide analysis was conducted to explore the genetic characteristics of the USP family, which is categorized into 13 unique categories. The genetic homology of the USP family between cattle and other related species was discovered through collinearity analysis. Notably, cattle muscle tissue exhibits high expression levels of USP2, USP13, USP19, USP25, USP28, USP38, USP47, and USP53. Furthermore, the expression patterns of these genes during myogenic cell differentiation can be categorized into 4 distinct types. By designing small interfering RNA(siRNA) to interfere with the expression of USP2, USP28, USP38, and USP47 in the myogenic cell, the silencing of these genes reduced the proliferation capacity of the myogenic cell. Meanwhile, the silencing of USP2, USP28, and USP38 facilitated myogenic cell differentiation, while USP47 exerted an opposing effect. In this study, a total of 53 members of USPs were successfully identified in Bos taurus. SiRNA interference experiments revealed that USP2, USP28, USP38, and USP47 are implicated in the regulation of myogenic cell proliferation and differentiation. These findings lay the foundation for further investigation into the precise roles of USPs in governing myoblast behavior and hold promise for enhancing beef quality.