Deciphering skeletal muscle development: cellular heterogeneity and molecular regulatory networks from single-cell and spatial transcriptomic perspectives

The development of skeletal muscle is a biological process of great complexity and high regulation whereby there is a spatiotemporal coordination of interactions amongst various cell and molecular events. Recent advances in scRNA-seq and ST have enabled systematic dissection of skeletal muscle dynamics at single-cell resolution, thereby revealing the underlying molecular regulatory processes. This review provides an overview of existing evidence on molecular components of cellular heterogeneity of skeletal muscle development, which synergistically stabilize transcription factor network, epigenetic regulation, and metabolic reprogramming in cell fate regulation. By systematically comparing findings across species—including humans, mice, pigs, and chickens—we highlight both evolutionarily conserved mechanisms and species-specific regulatory features. This combination of scRNA-seq, ST, and multimodal data enables us to understand the microenvironment as a spatial regulator of muscle stem cell (MuSC) behavior: the composition of the niche, intercellular communication, and mechanical cues. These discoveries not only elucidate the fundamental principles of skeletal muscle development but also provide a theoretical basis for therapeutic strategies against muscle-related diseases and for improving economically important traits in livestock breeding.