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ATAC-Seq and RNA-Seq Integration Reveals Chromatin Accessibility and Transcriptional Dynamics During Fruit Color
Yichun Zeng1,2, Yilei Wu1,2, Jie Dai1,2
1Sericulture Research Institute, Sichuan Academy of Agricultural Sciences (Institute of Special Economic Animal and Plant, Sichuan Academy of Agricultural Sciences), Nanchong 637000, China.
International Journal of Molecular Sciences
|January 10, 2026
Summary
Researchers mapped gene regulation in mulberry fruit development to understand how fruit color and quality are controlled. This study identifies key factors influencing the biosynthesis of sugars, flavonoids, and anthocyanins.
Area of Science:
- Plant Biology
- Genomics
- Biochemistry
Background:
- Fruit color in mulberry (Morus spp.) is a key trait with diverse variations.
- The molecular mechanisms controlling mulberry fruit pigmentation and development are not well understood.
Purpose of the Study:
- To investigate genome-wide chromatin accessibility and gene expression during mulberry fruit development.
- To identify transcription factors and regulatory networks controlling fruit quality traits.
Main Methods:
- Integration of ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) and RNA-seq (RNA sequencing).
- Analysis of differentially accessible chromatin regions and differentially expressed genes.
- Reconstruction of transcriptional regulatory networks and motif enrichment analysis.
Main Results:
- A genome-wide map of regulatory elements and transcriptional activity was generated.
- Candidate transcription factors and target genes involved in the biosynthesis of sugars, flavonoids, diterpenoids, and anthocyanins were identified.
- Key cis-elements regulating gene expression at different developmental stages were revealed.
Conclusions:
- The study provides a comprehensive understanding of the regulatory architecture governing mulberry fruit maturation.
- Identified regulatory networks and candidate genes offer a foundation for improving mulberry fruit quality and yield.
- The generated dataset facilitates further research into uncharacterized traits of mulberry fruit development.
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