Auxin is a key hormone performing a wealth of functions throughout the life cycle of plants. It acts largely by regulating genes at the transcriptional level through a family of transcription factors called auxin response factors (ARFs). Even though all ARF monomers analyzed so far bind a similar DNA sequence, there is evidence that ARFs differ in their target genomic regions and regulated genes. Here, we report the use of position weight matrices (PWMs) to model ARF DNA binding specificity based on published DNA affinity purification sequencing (DAP-seq) data. We found that the genome binding of two ARFs (ARF2 and ARF5/Monopteros [MP]) differ largely because these two factors have different preferred ARF binding site (ARFbs) arrangements (orientation and spacing). We illustrated why PWMs are more versatile to reliably identify ARFbs than the widely used consensus sequences and demonstrated their power with biochemical experiments in the identification of the regulatory regions of IAA19, an well-characterized auxin-responsive gene. Finally, we combined gene regulation by auxin with ARF-bound regions and identified specific ARFbs configurations that are over-represented in auxin-upregulated genes, thus deciphering the ARFbs syntax functional for regulation. Our study provides a general method to exploit the potential of genome-wide DNA binding assays and to decode gene regulation.

生长素是在植物的整个生命周期中执行多种功能的关键激素。它主要通过称为生长素反应因子（ARF）的转录因子家族在转录水平上调控基因来发挥作用。即使到目前为止分析的所有ARF单体都结合了相似的DNA序列，但有证据表明ARF在其目标基因组区域和受调控的基因方面有所不同。在这里，我们报告基于公开的DNA亲和纯化测序（DAP-seq）数据，使用位置权重矩阵（PWM）来建模ARF DNA结合特异性。我们发现两个ARF（ARF2和ARF5 / Monopteros [MP]）的基因组结合差异很大，因为这两个因素具有不同的首选ARF结合位点（ARFbs）排列（方向和间距）。IAA19，一个特征明确的生长素应答基因。最后，我们结合了生长素与ARF结合区域的基因调控，并鉴定了在生长素上调的基因中过分表达的特定ARFbs构型，从而破译了ARFbs的调控语法。我们的研究提供了一种一般方法，可利用全基因组DNA结合测定的潜力并解码基因调控。