FOXP3 is a transcription factor that is essential for the development of regulatory T cells, a branch of T cells that suppress excessive inflammation and autoimmunity^1,2,3,4,5. However, the molecular mechanisms of FOXP3 remain unclear. Here we here show that FOXP3 uses the forkhead domain—a DNA-binding domain that is commonly thought to function as a monomer or dimer—to form a higher-order multimer after binding to T_nG repeat microsatellites. The cryo-electron microscopy structure of FOXP3 in a complex with T₃G repeats reveals a ladder-like architecture, whereby two double-stranded DNA molecules form the two ‘side rails’ bridged by five pairs of FOXP3 molecules, with each pair forming a ‘rung’. Each FOXP3 subunit occupies TGTTTGT within the repeats in a manner that is indistinguishable from that of FOXP3 bound to the forkhead consensus motif (TGTTTAC). Mutations in the intra-rung interface impair T_nG repeat recognition, DNA bridging and the cellular functions of FOXP3, all without affecting binding to the forkhead consensus motif. FOXP3 can tolerate variable inter-rung spacings, explaining its broad specificity for T_nG-repeat-like sequences in vivo and in vitro. Both FOXP3 orthologues and paralogues show similar T_nG repeat recognition and DNA bridging. These findings therefore reveal a mode of DNA recognition that involves transcription factor homomultimerization and DNA bridging, and further implicates microsatellites in transcriptional regulation and diseases.

FOXP3 是一种转录因子，对于调节性 T 细胞的发育至关重要，调节性 T 细胞是抑制过度炎症和自身免疫的 T 细胞分支^1,2,3,4,5 。然而，FOXP3 的分子机制仍不清楚。在这里，我们展示了 FOXP3 使用叉头结构域（一种通常被认为充当单体或二聚体的 DNA 结合结构域）在与 T _n G 重复微卫星结合后形成更高阶的多聚体。具有 T ₃ G 重复序列的复合物中 FOXP3 的冷冻电子显微镜结构揭示了一种梯状结构，其中两个双链 DNA 分子形成由五对 FOXP3 分子桥接的两个“侧轨”，每对形成一个“横档”。每个 FOXP3 亚基在重复序列中占据 TGTTTGT，其方式与 FOXP3 结合叉头共有基序 (TGTTTAC) 的方式无法区分。梯级内界面的突变会损害 FOXP3 的 T _n G 重复识别、DNA 桥接和细胞功能，但不会影响与叉头共有基序的结合。 FOXP3 可以耐受可变的梯级间距，这解释了其在体内和体外对 T _n G 重复序列的广泛特异性。 FOXP3 直系同源物和旁系同源物都显示出相似的 T _n G 重复识别和 DNA 桥接。因此，这些发现揭示了一种涉及转录因子同源多聚化和DNA桥接的DNA识别模式，并进一步暗示微卫星在转录调控和疾病中的作用。