Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West 168(th) Street, HHSC 1104, New York, NY 10032, USA.
Cell. 2011 Dec 9;147(6):1270-82. doi: 10.1016/j.cell.2011.10.053.
Members of transcription factor families typically have similar DNA binding specificities yet execute unique functions in vivo. Transcription factors often bind DNA as multiprotein complexes, raising the possibility that complex formation might modify their DNA binding specificities. To test this hypothesis, we developed an experimental and computational platform, SELEX-seq, that can be used to determine the relative affinities to any DNA sequence for any transcription factor complex. Applying this method to all eight Drosophila Hox proteins, we show that they obtain novel recognition properties when they bind DNA with the dimeric cofactor Extradenticle-Homothorax (Exd). Exd-Hox specificities group into three main classes that obey Hox gene collinearity rules and DNA structure predictions suggest that anterior and posterior Hox proteins prefer DNA sequences with distinct minor groove topographies. Together, these data suggest that emergent DNA recognition properties revealed by interactions with cofactors contribute to transcription factor specificities in vivo.
转录因子家族的成员通常具有相似的 DNA 结合特异性，但在体内执行独特的功能。转录因子通常作为多蛋白复合物结合 DNA，这增加了复合物形成可能改变其 DNA 结合特异性的可能性。为了检验这一假设，我们开发了一种实验和计算平台 SELEX-seq，可用于确定任何转录因子复合物与任何 DNA 序列的相对亲和力。将该方法应用于所有 8 种果蝇 Hox 蛋白，我们表明当它们与二聚体辅助因子 Extradenticle-Homothorax (Exd) 结合 DNA 时，它们获得了新的识别特性。Exd-Hox 的特异性分为三大类，符合 Hox 基因共线性规则，并且 DNA 结构预测表明前侧和后侧 Hox 蛋白更喜欢具有不同小沟形貌的 DNA 序列。这些数据表明，与辅助因子相互作用所揭示的新兴 DNA 识别特性有助于体内转录因子的特异性。
