Coordinated epigenomic reprogramming and chromatin-mediated transcriptional regulation during soybean callus development

Introduction Callus formation is a fundamental developmental process involving cellular dedifferentiation and regeneration in plants. However, the epigenetic mechanisms underlying this process remain poorly understood. Methods Here, we performed integrative analyses of time-series ATAC-seq, ChIP-seq (H3K27ac and H3K27me3), and transcriptome datasets to investigate chromatin-mediated transcriptional regulation during soybean callus development. Results Genome-wide profiling identified extensive epigenetic remodeling during early callus induction, including 15,740 differentially accessible regions (DARs) associated with dynamic transcriptional changes. Distinct chromatin accessibility patterns corresponded to sequential developmental programs, including repression of explant identity, activation of hormone-responsive cell proliferation pathways, and stress-associated responses during later stages. Chromatin accessibility and H3K27ac were strongly associated with transcriptional activation during early induction, whereas de novo open chromatin regions (OCRs) were closely associated with increased expression of key developmental regulators. Motif enrichment and chromVAR analyses further identified stage-specific TF motif-associated regulatory signatures involving the ARF–LBD, ERF, E2F/DP, and BES1 families during early proliferative reprogramming, followed by WOX- and WRKY-associated signatures during callus maintenance and stress adaptation. Discussion Together, our findings suggest that soybean callus formation is accompanied by hierarchical epigenetic reprogramming involving dynamic chromatin remodeling and stage-specific TF motif-associated regulatory signatures, providing a genome-wide framework for understanding plant cellular reprogramming and improving regeneration-based crop biotechnology.