The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family

• Published in: Nature communications Vol. 9; no. 1; pp. 4526 - 14
• Main Authors: Galli, Mary, Khakhar, Arjun, Lu, Zefu, Chen, Zongliang, Sen, Sidharth, Joshi, Trupti, Nemhauser, Jennifer L., Schmitz, Robert J., Gallavotti, Andrea
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 30.10.2018; Nature Publishing Group; Nature Portfolio
• Subjects: 38; 45; 45/23; 45/91; 631/337/572/2102; 631/449/1741/1576; 631/449/2675; Binding sites; Comparative analysis; Corn; Deoxyribonucleic acid; DNA; DNA - metabolism; Gene expression; Gene Expression Regulation, Plant; Gene mapping; Genes; Genomes; Humanities and Social Sciences; Learning algorithms; Machine learning; multidisciplinary; Quantitative Trait Loci; Science; Science (multidisciplinary); Site selection; Transcription factors; Transcription Factors - metabolism; Zea mays - genetics; Zea mays - metabolism
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-018-06977-6

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. AUXIN RESPONSE FACTORS (ARFs) are a family of plant-specific transcriptional factors involved in auxin signaling. Here, the authors adapt DAP-seq technology to show the binding landscape of 14 maize ARFs and reveal class-specific binding properties and transcriptional coordination by ARFs from different classes.