ATAC-Seq and RNA-Seq Integration Reveals Chromatin Accessibility and Transcriptional Dynamics During Fruit Color Development in Mulberry.

Fruit color, a defining characteristic in mulberry, varies markedly across cultivars, ranging from black and red to pink and white. However, the regulatory mechanisms governing pigmentation during fruit development remain poorly characterized. In this study, ATAC-seq and RNA-seq were integrated to investigate genome-wide chromatin accessibility and identify putative transcription factors involved in fruit development in Da10 (Yueshenda10, Morus atropurpurea Roxb.). Differentially accessible chromatin regions and differentially expressed genes were jointly analyzed to generate a genome-wide map of regulatory elements and transcriptional activity. This integrative approach enabled the reconstruction of a transcriptional regulatory network that facilitated the identification of candidate transcription factors and target genes associated with the biosynthesis of bioactive compounds, including sugars, flavonoids, diterpenoids, and anthocyanins. The expression levels of RNA-seq were confirmed by qRT-PCR. Motif enrichment analysis revealed seven and 23 enriched cis-elements at the S1 and S3 developmental stages, respectively. Integration with the transcriptional regulatory network established a robust framework for identifying candidate genes involved in the accumulation of key metabolites. Additionally, the dataset enables exploration of previously uncharacterized traits during turning stages of mulberry fruit development. Collectively, these findings advance our understanding of the regulatory architecture underlying fruit maturation and provide a foundation for future strategies to enhance mulberry fruit quality.