先锋转录因子 (TF) 结合并打开封闭的染色质，促进参与基因激活或抑制的其他调控因子的参与。先锋转录因子缺乏化学探针，这阻碍了它们在细胞中的机制研究。在这里，我们报告了亲电化合物的化学蛋白质组学发现，这些化合物能够立体选择性地、位点特异性地结合先锋 TF 叉头盒蛋白 A1 (FOXA1) 的叉头 DNA 结合域内的半胱氨酸 (C258)。我们发现这些共价配体以 DNA 依赖性方式与 FOXA1 发生反应，并迅速重塑其在前列腺癌细胞中的先驱活性，这反映在 FOXA1 结合在基因组中的重新分布以及染色质可及性的定向相关变化。基序分析支持一种机制，即配体通过加强与预测接近 C258 的次优序列的相互作用来放松 FOXA1 的典型 DNA 结合偏好。我们的研究结果揭示了 FOXA1 具有惊人的可塑性，可通过小分子控制其开创性功能。版权所有 © 2024 Elsevier Inc. 保留所有权利。

Pioneer transcription factors (TFs) bind to and open closed chromatin, facilitating engagement by other regulatory factors involved in gene activation or repression. Chemical probes are lacking for pioneer TFs, which has hindered their mechanistic investigation in cells. Here, we report the chemical proteomic discovery of electrophilic compounds that stereoselectively and site-specifically bind the pioneer TF forkhead box protein A1 (FOXA1) at a cysteine (C258) within the forkhead DNA-binding domain. We show that these covalent ligands react with FOXA1 in a DNA-dependent manner and rapidly remodel its pioneer activity in prostate cancer cells reflected in redistribution of FOXA1 binding across the genome and directionally correlated changes in chromatin accessibility. Motif analysis supports a mechanism where the ligands relax the canonical DNA-binding preference of FOXA1 by strengthening interactions with suboptimal sequences in predicted proximity to C258. Our findings reveal a striking plasticity underpinning the pioneering function of FOXA1 that can be controlled by small molecules.Copyright © 2024 Elsevier Inc. All rights reserved.