2025/09/30 by Yaxin Deng (邓雅欣), Weihua Zhao (赵伟华), Weihua Zhao +10 · 1 voice · 2 citations
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Plant Molecular Biology Research #Plant Reproductive Biology #Plant Virus Research Studies
paper · doi:10.1093/plcell/koaf236
openalex publication_date 2025/09/30 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30
Enhancers control gene expression, orchestrating plant development, and responses to stimuli. However, the regulatory codes of enhancers that confer tissue-specific expression in plants remain largely unexplored. Using massively parallel reporter assays (MPRAs) in tomato tissues, we tested the enhancer activity of 11,180 promoter fragments derived from fruit-specific genes. We discovered 2,436 active fruit enhancer sequences, a subset of which showed differential activity between fruit and leaves, suggesting that they can drive fruit-specific gene expression in tomato. We dissected the sequence determinants of fruit enhancers using deep learning. Guided by the regulatory rules learned from our MPRA dataset, we designed synthetic enhancers and experimentally validated their ability to specifically target tomato fruit. Our study provides a comprehensive landscape of functional enhancers in tomato fruit, facilitating the de novo design of synthetic enhancers for tissue-specific gene expression in plants.