Abstract
Target gene identification for transcription factors is a prerequisite for the systems wide understanding of organismal behaviour. NAM-ATAF1/2-CUC2 (NAC) transcription factors are amongst the largest transcription factor families in plants, yet limited data exist from unbiased approaches to resolve the DNA-binding preferences of individual members. Here, we present a TF-target gene identification workflow based on the integration of novel protein binding microarray data with gene expression and multi-species promoter sequence conservation to identify the DNA-binding specificities and the gene regulatory networks of 12 NAC transcription factors. Our data offer specific single-base resolution fingerprints for most TFs studied and indicate that NAC DNA-binding specificities might be predicted from their DNA-binding domain's sequence. The developed methodology, including the application of complementary functional genomics filters, makes it possible to translate, for each TF, protein binding microarray data into a set of high-quality target genes. With this approach, we confirm NAC target genes reported from independent in vivo analyses. We emphasize that candidate target gene sets together with the workflow associated with functional modules offer a strong resource to unravel the regulatory potential of NAC genes and that this workflow could be used to study other families of transcription factors.
Highlights
Plants use cellular strategies to survive exposure to biotic and abiotic stresses
ANAC055 and ATAF1 are closely related to ANAC019 [13,39], and ATAF1 is a control for the Protein binding microarrays (PBMs) experiments [40]
Since only the NAC domain is used in this study and since remote disordered regions may fine-tune both specificity and affinity of deoxyribonucleic acid (DNA) binding [51], full-length ANAC092 was used for the PBM experiments
Summary
Plants use cellular strategies to survive exposure to biotic and abiotic stresses. Salt, high temperature and microbial infections are amongst the most frequent abiotic and biotic stresses encountered by plants [1,2,3,4] Expression of genes that function in stress sensing and tolerance are regulated upon stress exposure by specific transcription factors (TFs) [1,2]. Nac mutant plants have been shown to display loss of secondary wall thickening, perturbed resistance towards microbial attack as well as delayed senescence [1,5,6,10], though functional redundancy often has hampered characterization of individual NAC members
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