Prioritizing Metabolic Gene Regulators through Multi-Omic Network Integration in Maize

Elucidating gene regulatory networks (GRNs) is a major area of study within plant systems biology. Phenotypic traits are intricately linked to specific gene expression profiles. These expression patterns arise primarily from regulatory connections between sets of transcription factors (TFs) and their target genes. In this study, we integrated publicly available co-expression networks derived from more than 6,000 RNA-seq samples, 283 protein-DNA interaction assays, and 16 million of SNPs used to identify expression quantitative loci (eQTL), to construct TF-target networks. In total, we analyzed ∼4.6M interactions to generate four distinct types of TF-target networks: co-expression, protein-DNA interaction (PDI), trans -expression quantitative loci ( trans -eQTL), and cis -eQTL combined with PDIs. To improve the functional annotation of TFs based on its target genes, we implemented three different strategies to integrate these four types of networks. We subsequently evaluated the effectiveness of our method through loss-of function mutant and random networks. The multi-network integration allowed us to identify transcriptional regulators of hormone-, metabolic- and development-related processes. Finally, using the topological properties of the fully integrated network, we identified potentially functional redundant TF paralogs. Our findings retrieved functions previously documented for numerous TFs and revealed novel functions that are crucial for informing the design of future experiments. The approach here-described lays the foundation for the integration of multi-omic datasets in maize and other plant systems.