Bioscience Methods 2025, Vol.16, No.2, 83-99 http://bioscipublisher.com/index.php/bm 83 Feature Review Open Access Single-Cell Multi-Omics Analysis of Epigenetic and Transcriptional Regulatory Mechanisms of Goat Skeletal Muscle Development Xuezhong Zhang, Xiaofang Lin Tropical Animal Medicine Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding email: xiaofang.lin@hitar.org Bioscience Methods, 2025, Vol.16, No.2 doi: 10.5376/bm.2025.16.0009 Received: 21 Feb., 2025 Accepted: 31 Mar., 2025 Published: 11 Apr., 2025 Copyright © 2025 Zhang and Lin, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Zhang X.Z., and Lin X.F., 2025, Single-cell multi-omics analysis of epigenetic and transcriptional regulatory mechanisms of goat skeletal muscle development, Bioscience Methods, 16(2): 83-99 (doi: 10.5376/bm.2025.16.0009) Abstract The normal development of goat skeletal muscle is crucial for the growth performance and meat quality of meat goats. This study focuses on the application of single-cell multi-omics technology in the study of goat skeletal muscle development and explores the key mechanisms of epigenetic and transcriptional regulation. This study first outlines the stages, cell types and molecular regulators of goat skeletal muscle development, emphasizing its species-specific characteristics. It then discusses how single-cell transcriptomics can identify cell subpopulations and gene expression profiles in muscle tissue, revealing the heterogeneity and differentiation trajectory of muscle lineage cells. The role of epigenetic mechanisms such as chromatin accessibility, histone modification and DNA methylation in muscle development is then explained, and the method of integrating transcriptome and epigenomic data to construct regulatory networks is introduced. Through case studies, the representative results of single-cell multi-omics in the study of livestock and poultry skeletal muscle development, such as the discovery of key signaling pathways and transcription factors, are summarized, and the implications of these findings for future research and genetic improvement are discussed. Finally, the application prospects of single-cell multi-omics in livestock research are prospected, and possible ways to translate research results into breeding practice are discussed, as well as the challenges faced at the technical, ethical and practical levels. This study aims to provide a comprehensive and systematic insight into the molecular mechanisms of goat skeletal muscle development and provide a scientific basis for genetic breeding and meat quality improvement of goats and other livestock. Keywords Goat; Skeletal muscle development; Single-cell multi-omics; Transcriptional regulation; Epigenetic 1 Introduction Goats are important livestock species, and the growth and development of their skeletal muscles directly affects the meat production and quality of meat goats (Deng et al., 2021; He and Li, 2024). Skeletal muscle is one of the most abundant tissues in mammals, accounting for about 40% of body weight (Xiong et al., 2022). Muscle development (myogenesis) is a complex and orderly process, which can generally be divided into the generation of muscle fibers in the embryonic period and the growth of muscle fibers after birth. During embryonic development, muscles originate from somitic cells in the mesoderm, undergo proliferation, differentiation and fusion of myogenic precursor cells to form protomyotubes, and further develop into primary and secondary muscle fibers (Cao et al., 2023). After birth, muscle fibers mainly achieve hypertrophy and growth through the proliferation and differentiation of satellite cells (i.e., muscle stem cells). Continuous muscle fiber hypertrophy will be limited if there is a lack of new nuclei contributed by satellite cells. Therefore, muscle stem cells and their differentiation are crucial for muscle formation and growth, both in the embryonic period and in the growth stage. The muscle development process is strictly regulated by a variety of molecules such as the myogenic regulatory factors (MRFs) family. Among them, MyoD and Myf5 mainly determine the fate of myogenic precursors, and Myogenin and MRF4 (also known as Myf6) mediate the differentiation and fusion of myoblasts (Qiu et al., 2020; Zhou et al., 2022). The formation of muscle fiber types is regulated by specific transcription factors, such as NFATc1 and MEF2C, which contribute to the formation of slow muscle fibers, while FoxO1 promotes the formation of fast muscle fibers. Goat skeletal muscle development includes a series of precisely regulated stages in time and space, involving the coordination of multiple cell types and signal pathways.
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