The myotendinous junction (MTJ) is a composite region enriched in extracellular matrix where muscle fibres attach to tendons; as such, it experiences high degrees of strain. Skeletal muscle fibres contain thousands of nuclei, and distinct regions of a myofibre require myonuclei that execute specialised transcriptional programmes fine-tuned to a specific function. Elucidating regional transcription patterns at the MTJ is important for understanding the physiology of this complex structure. In this study (Karlsen et al., 2023), Abigail Mackey and co-workers apply single-nucleus RNA sequencing (snRNA-seq) and spatial transcriptomics to human muscle-tendon tissue. The snRNA-seq data are available on the interactive portal Myoatlas. This approach allows both detailed profiling of various cell types present in the MTJ and classification of specialised myonuclei based on transcriptional signatures. The authors identify a novel panel of transcripts enriched in a cluster of nuclei that express both collagen XXII (COL22A1), an MTJ marker, and predominantly fast skeletal muscle-specific myosin heavy chain isoforms (MYH1 and MYH2). Combined with spatial transcriptomics and tissue immunofluorescence, the transcriptional profile of MTJ myonuclei highly correlates with transcript and protein expression patterns at the muscle-tendon interface. These findings provide a much-needed molecular characterisation of the MTJ, representing a valuable resource to better understand pathways dysregulated in conditions such as muscle strain injury and muscular dystrophy.