Title：Trans-organ analysis of gene co-expression networks reveals a mobile long-distance regulator that balances shoot and root development in Arabidopsis

Jia Yuan Ye, Yasuhito Sakuraba, Meng Na Zhuo, Yousuke Torii, Namie Ohtsuki, Wen Hao Tian, Chong Wei Jin, Shao Jian Zheng，Keiichi Mochida & Shuichi Yanagisawa

Abstract

Long-distance regulation between individual organs is a fundamental process for the optimized adaptation of the plant body to diverse environments. However, systematic methods for identifying key genes for long-distance regulation are currently unavailable. Here we present a new approach, trans-organ analysis of gene co-expression networks, which offers a unique way of identifying candidates for such genes. This approach revealed that TGA7 functions as a shoot-to-root mobile bZIP transcription factor in Arabidopsis to activate photosynthetic genes directly in shoots and nitrate-uptake-related genes, both directly and via a transcriptional cascade, in roots. Analysis of grafted chimeras showed that nitrogen-deficiency-induced enhanced TGA7 expression in shoot vascular tissue promotes TGA7 protein accumulation in roots, boosting root growth and nitrate uptake. Furthermore, the loss of TGA7-mediated long-distance regulation perturbed the balance between shoot and root development under nitrogen deficiency. These findings underscore the utility of our approach for uncovering long-distance regulation in plants.

Link: https://www.nature.com/articles/s41477-025-02052-3#data-availability