FoxP3 is an essential transcription factor (TF) for immunologic homeostasis, but how it utilizes the common forkhead DNA-binding domain (DBD) to perform its unique function remains poorly understood. We here demonstrated that unlike other known forkhead TFs, FoxP3 formed a head-to-head dimer using a unique linker (Runx1-binding region [RBR]) preceding the forkhead domain. Head-to-head dimerization conferred distinct DNA-binding specificity and created a docking site for the cofactor Runx1. RBR was also important for proper folding of the forkhead domain, as truncation of RBR induced domain-swap dimerization of forkhead, which was previously considered the physiological form of FoxP3. Rather, swap-dimerization impaired FoxP3 function, as demonstrated with the disease-causing mutation R337Q, whereas a swap-suppressive mutation largely rescued R337Q-mediated functional impairment. Altogether, our findings suggest that FoxP3 can fold into two distinct dimerization states: head-to-head dimerization representing functional specialization of an ancient DBD and swap dimerization associated with impaired functions.

FoxP3 是免疫稳态的重要转录因子 (TF)，但它如何利用常见的叉头 DNA 结合域 (DBD) 来执行其独特的功能仍然知之甚少。我们在这里证明，与其他已知的叉头 TF 不同，FoxP3 在叉头域之前使用独特的链接器（Runx1 结合区域 [RBR]）形成了头对头二聚体。头对头二聚化赋予了独特的 DNA 结合特异性，并为辅因子 Runx1 创建了一个停靠位点。RBR 对于叉头结构域的正确折叠也很重要，因为 RBR 的截断会诱导叉头的结构域交换二聚化，这在以前被认为是 FoxP3 的生理形式。相反，交换二聚化损害了 FoxP3 功能，正如致病突变 R337Q 所证明的那样，而交换抑制突变在很大程度上挽救了 R337Q 介导的功能障碍。总而言之，我们的研究结果表明 FoxP3 可以折叠成两种不同的二聚化状态：代表古代 DBD 功能特化的头对头二聚化和与受损功能相关的交换二聚化。