Multi-omics analysis deciphers tenocytes chromatin states and epigenetic regulation of tendon homeostasis

Abstract

Tenocytes are the principal effector cells responsible for tendon homeostasis and repair, whose functions are governed by precise transcription programs. However, the epigenetic basis underlying the establishment and maintenance of their cellular identity, particularly the genome-wide landscape of chromatin accessibility, histone modifications and chromatin states remains largely unexplored. We performed a multi-omics analysis of primary tenocytes, including ATAC-seq, CUT&Tag profiling of six key histone modifications (H3K4me1, H3K4me3, H3K27ac, H3K36me3, H3K9me3 and H3K27me3), and RNA-seq. By utilizing ChromHMM algorithm, we defined a comprehensive chromatin state map for tenocytes. We established a high-resolution epigenetic atlas, segmenting the tenocyte genome into 10 distinct states with well-defined biological functions. Integrative analysis revealed that active promoter states, marked by H3K4me3, H3K27ac, and open chromatin, were tightly linked to the high expression of genes essential for tendon function, including extracellular matrix components and key transcription factors. Motif analysis revealed a putative regulatory network of these genes, which was centered on ETS and Zinc-finger family transcription factors. In contrast, repressed promoter states, enriched for the Polycomb-associated mark H3K27me3, were found at genes mainly involved in alternative developmental pathways (e.g., neural, epidermal) and hormone secretion functions, suggesting an active silencing mechanism that safeguards tenocyte lineage fidelity. This study provides an integrated epigenomic landscape of tenocytes, establishing a chromatin-level blueprint for understanding their cellular identity. This resource identifies key regulatory elements controlling tendon signature gene expression and offers a valuable dataset for future investigations into the epigenetic regulation of tendon homeostasis and regeneration.