Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA.
Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA.
Nat Commun. 2018 Oct 30;9(1):4526. 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.
生长素响应因子（ARFs）是植物特有的转录因子（TFs），它们将激素生长素的感知与所有陆地植物所必需的基因表达程序联系起来。与许多大型 TF 家族一样，一个关键问题是，单个成员是否通过结合不同的靶基因来决定发育特异性。我们使用 DAP-seq 为来自进化上保守的 A 和 B 类群的十四种玉米 ARF 生成全基因组体外 TF：DNA 相互作用图谱。比较分析显示，相同类群的 ARF 具有高度的结合位点重叠，但 A 类群和 B 类群的结合位点则大不相同。然而，许多位点被来自两个类群的 ARF 共同占据，这表明许多基因的转录协调。在这些基因中，我们研究了已知的 QTL，并使用机器学习来预测顺式调控变异的影响。总的来说，对 ARF 结合的大规模比较分析表明，生长素反应的特异性可能不是由单个 ARF 结合位点选择以外的因素决定的。
