Dissecting gene regulatory networks driving grape berry ripening using comparative systems biology across non-climacteric fleshy fruits: the NAC-centered hierarchy revisited

Abstract Understanding how fruits ripen holds enormous potential for agro-industrial applications, enabling the development of healthier foods and plant-based medicines. Studying transcription factors (TFs) in non-conventional model species such as grapevine and strawberry remains challenging, yet offers strong translational value, as deciphering the regulatory mechanisms controlling ripening and the accumulation of health-beneficial compounds can support strategies to enhance fruit quality and also mitigate the impacts of climate change. Over the past decade, genome-wide studies in grapevine have applied systems biology approaches to reconstruct gene regulatory networks by integrating temporal transcriptomic and metabolomic data, revealing novel transcriptional relationships underlying berry ripening. Here, we review how these approaches have advanced grapevine research, with particular emphasis on DNA Affinity Purification followed by Sequencing (DAP-seq), a high-throughput method that maps TF binding sites using in vitro-expressed TFs and genomic DNA. DAP-seq provides a scalable and cost-effective alternative for TF characterization in grapevine, where stable genetic transformation remains difficult, enabling the rapid interrogation of large numbers of regulators. We further explore how integrating DAP-seq data with temporal transcriptomes from early- and late-ripening cultivars reveals novel regulatory targets and interconnections among known TFs controlling ripening-related processes. Within this framework, we highlight NAC60 as a high-hierarchy regulator of berry ripening, with a potential role in promoting sugar transport and signaling while modulating R2R3-MYB factors controlling specialized metabolite accumulation. Finally, comparative transcriptomic and network analyses in strawberry uncover conserved NAC-regulated ripening modules shared with grapevine, governing key physiological and metabolic transitions, including sugar transport, ABA biosynthesis, chlorophyll degradation, and flavonoid accumulation, supporting conserved regulatory principles across non-climacteric fleshy fruits.