Abstract
AUXIN RESPONSE FACTORS (ARFs) are plant-specific transcription factors (TFs) that couple perception of the hormone auxin to gene expression programs essential to all land plants. As with many large TF families, a key question is whether individual members determine developmental specificity by binding distinct target genes. We use DAP-seq to generate genome-wide in vitro TF:DNA interaction maps for fourteen maize ARFs from the evolutionarily conserved A and B clades. Comparative analysis reveal a high degree of binding site overlap for ARFs of the same clade, but largely distinct clade A and B binding. Many sites are however co-occupied by ARFs from both clades, suggesting transcriptional coordination for many genes. Among these, we investigate known QTLs and use machine learning to predict the impact of cis-regulatory variation. Overall, large-scale comparative analysis of ARF binding suggests that auxin response specificity may be determined by factors other than individual ARF binding site selection.
Highlights
AUXIN RESPONSE FACTORS (ARFs) are plant-specific transcription factors (TFs) that couple perception of the hormone auxin to gene expression programs essential to all land plants
According to the canonical auxin signaling model, when auxin levels are low Aux/IAAs physically interact with particular ARFs preventing expression of their target genes; in conditions of high auxin auxin promotes binding between Aux/IAAs and SCFTIR1/AFB E3 ligases which results in degradation of the transcriptionally repressive Aux/ IAAs and allows certain ARFs to activate downstream target genes[1]
TF family expansion is a common feature in many organisms and assessing DNA-binding specificity among different family members will broadly inform our understanding of genetic redundancy and diversification
Summary
AUXIN RESPONSE FACTORS (ARFs) are plant-specific transcription factors (TFs) that couple perception of the hormone auxin to gene expression programs essential to all land plants. According to the canonical auxin signaling model, when auxin levels are low Aux/IAAs physically interact with particular ARFs preventing expression of their target genes; in conditions of high auxin auxin promotes binding between Aux/IAAs and SCFTIR1/AFB E3 ligases which results in degradation of the transcriptionally repressive Aux/ IAAs and allows certain ARFs to activate downstream target genes[1] Due to their pivotal position in the auxin signaling pathway and expansion in all higher plant species, ARFs are strong candidates for triggering tissue-type and cell type-specific transcriptional changes[2,3,4]. We report genome-wide in vitro DNA binding site maps for fourteen maize ARFs. Overall, our data reveal both specific and redundant aspects of ARF binding that provide a framework for understanding hormone-dependent regulation in species with expanded TF family repertoires. These datasets represent a valuable resource for use in molecular-assisted breeding and genome editing approaches in maize
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