# Integrated Gene Regulatory Network Analysis Reveals Coordinated Transcriptional Reprogramming in the Arabidopsis thaliana–Trichoderma atroviride Interaction

## TL;DR

This study explores how plants and fungi coordinate their gene activity during a mutualistic interaction, revealing key regulatory networks and small RNA dynamics.

## Contribution

The paper introduces integrated gene regulatory networks and sRNA analysis to uncover coordinated transcriptional reprogramming in a plant-fungus mutualism.

## Key findings

- Arabidopsis activates hypoxia, stress, and root development pathways during interaction with Trichoderma atroviride.
- Fungal transcriptional reprogramming focuses on membrane transport and primary metabolism, coordinated by key transcription factors.
- T. atroviride shows strong induction of 20–22 nt sRNAs that target host genes related to root function and immunity.

## Abstract

Mutualistic interactions between plants and beneficial fungi rely on extensive transcriptional reprogramming in both partners, yet the underlying regulatory mechanisms coordinating these responses remain incompletely understood. Here, we combined a transcriptomics analysis with a gene regulatory network (GRN) inference to dissect the interaction between Arabidopsis thaliana and the growth-promoting fungus Trichoderma atroviride. At an early but established stage of colonization (72 h post-inoculation), we identified widespread transcriptional changes in both of the organisms, including host activation of hypoxia, stress and root development-related pathways in Arabidopsis, and fungal reprogramming of membrane transport and primary metabolism. Using DNA-binding motifs and GENIE3-based regulatory inference, we reconstructed interaction-specific GRNs for each species. The subnetworks focused on the main differentially expressed biological processes and uncovered ERF-, WRKY-, NAC- and DOF-centered modules linking hypoxia responses with developmental remodeling in the plant, whereas the putative orthologs of TFs involved in developmental and stress-related TFs in fungi, such as CrzA, RME1, NsdC, PacC and RPN4, formed a regulatory core coordinating fungal transport and metabolic adjustment. In parallel, we uncovered contrasting sRNA dynamics between the partners. While the Arabidopsis sRNA changes were limited, T. atroviride exhibited a strong induction of 20–22 nt sRNAs, including a small set of high-confidence sRNA–mRNA interactions targeting host genes involved in root function and immunity. Together, our results extend previous pathway-based descriptions of the Arabidopsis–Trichoderma mutualism and provide a systems-level, testable framework for how coordinated regulatory programs in both of the partners support the interaction.