The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family

Mary Galli, Arjun Khakhar, Zefu Lu, Zongliang Chen, Sidharth Sen, Trupti Joshi, Jennifer L. Nemhauser, Robert J. Schmitz and Andrea Gallavotti ()
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Mary Galli: Rutgers University
Arjun Khakhar: University of Washington
Zefu Lu: The University of Georgia
Zongliang Chen: Rutgers University
Sidharth Sen: University of Missouri
Trupti Joshi: University of Missouri
Jennifer L. Nemhauser: University of Washington
Robert J. Schmitz: The University of Georgia
Andrea Gallavotti: Rutgers University

Nature Communications, 2018, vol. 9, issue 1, 1-14

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41467-018-06977-6

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