It’s a berry story: integrating cistromics and co-expression to decode the MYB14/15 regulon in grapevine

Abstract

The R2R3-MYB transcription factors VviMYB14 and VviMYB15 are established master regulators of the stilbene biosynthetic pathwayin grapevine, directly modulating stilbene synthase (STS) genes. Despite their characterized roles, the broader regulatory network—including downstream effectors and pathway-coordinating genes—remains largely unresolved. The differential accumulation of stilbenes in early- versus late-ripening cultivars provides a unique transcriptomic window into how these MYBs govern metabolic shifts during fruit maturation.

To decode this complexity, we developed PETAL, an interactive R/Shiny web-platform that integrates DNAaffinity purification sequencing (DAP-seq) data with multi-tissue gene co-expression networks, bridging the gap between in vitro binding potential and in vivo functional relevance. A private version of PETAL was constructed utilizing grapevine DAP-seq data from 187 transcription factors (TFs) in Cabernet franc (a collaborative effort of the Universities of Padova and Verona) and the extensive Vitviz co-expressionnetwork. By applying stringent filters for binding affinity, promoter proximity, and tissue-specific expression, PETAL enabled the identification of the MYB14/15 regulon with unprecedented stringency.

Notably, the identification of C4H2 and ERF110 as direct targets suggests a dual-level control mechanism: MYB14/15 may simultaneously prime upstream phenylpropanoid flux via C4H2 while initiating a regulatory cascade through the ethylene-responsive factor ERF110 to coordinate stilbene synthesis with the broader ripening program.

Our current objective is to cement these computational predictions by evaluating them against an independent, berry-specific transcriptomic dataset. This ongoing work focuses on berry development in two varieties with contrasting phenologies: Pinot grigio (early-ripening) and Raboso piave (late-ripening). By cross-referencing PETAL-derived regulons with the expression trajectories of these varieties, we aim to determine if these regulatory modules represent a conserved core across different genetic backgrounds. Thisvalidation step, alongside ongoing dual-luciferase assays and metabolite-transcript correlations, seeks to anchor the identified nodesin the physiological reality of fruit ripening. We also announce the imminent public release of the PETAL platform on Plantaeviz.

Acknowledgements

The DAPseq data for this work is generated from joint project by the University of Padova and University of Verona, while the berrytranscriptome was constructed as part of the Agritech Project Pinoso.

The coexpression data for the PETAL app was taken from the Plantaeviz platform where PETAL will eventually be integrated.

References

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