Abstract:
The abiotic stress response in plants is complex and tightly controlled by gene regulation. We present an abiotic stress gene
regulatory network of 200,014 interactions for 11,938 target genes by integrating four complementary reverse-engineering solutions
through average rank aggregation on an Arabidopsis thaliana microarray expression compendium. This ensemble performed the
most robustly in benchmarking and greatly expands upon the availability of interactions currently reported. Besides recovering 1182
known regulatory interactions, cis-regulatory motifs and coherent functionalities of target genes corresponded with the predicted
transcription factors. We provide a valuable resource of 572 abiotic stress modules of coregulated genes with functional and
regulatory information, from which we deduced functional relationships for 1966 uncharacterized genes and many regulators. Using
gain- and loss-of-function mutants of seven transcription factors grown under control and salt stress conditions, we experimentally
validated 141 out of 271 predictions (52% precision) for 102 selected genes and mapped 148 additional transcription factor-gene
regulatory interactions (49% recall). We identified an intricate core oxidative stress regulatory network where NAC13, NAC053,
ERF6, WRKY6, and NAC032 transcription factors interconnect and function in detoxification. Our work shows that ensemble
reverse-engineering can generate robust biological hypotheses of gene regulation in a multicellular eukaryote that can be tested by
medium-throughput experimental validation.
