The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family

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 bindi...

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Published inNature 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
LanguageEnglish
Published London Nature Publishing Group UK 30.10.2018
Nature Publishing Group
Nature Portfolio
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ISSN2041-1723
2041-1723
DOI10.1038/s41467-018-06977-6

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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. 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.
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ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-018-06977-6