Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions

Loss-of-function mutant alleles were characterized for 22 maize transcription factors to test the functional relevance of prior yeast-one-hybrid and co-expression gene regulatory network predictions. The transcriptome and phenolic metabolome of these mutants were profiled to document the functional roles of these transcription factors. A subset of the prior gene regulatory network predictions were supported but had limited overall power in predicting changes in gene expression or phenolic compounds. The limitations of testing transcription factor-target predictions with single TF knockouts are discussed. Loss-of-function mutant alleles were isolated for 22 maize transcription factors. Transcriptome profiling by RNA-seq was performed for each TF mutant allele to characterize genome-wide perturbations of expression. Enrichment tests were performed to determine if predicted target genes were enriched for differential expression.