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bioRxiv · 10.1101/2023.07.12.548762

Ladder-like multimerization of FoxP3 enables microsatellite recognition and DNA bridging

Zhang, W.·Leng, F.·Wang, X.·Ramirez, R. N.·Park, J.·Benoist, C.·Hur, S.
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Abstract

FoxP3 is a transcription factor (TF) essential for development of regulatory T cells (Tregs), a branch of T cells that suppress excessive inflammation and autoimmunity1-5. Molecular mechanisms of FoxP3, however, remain elusive. We here show that FoxP3 utilizes the Forkhead domain--a DNA binding domain (DBD) that is commonly thought to function as a monomer or dimer--to form a higher-order multimer upon binding to TnG repeat microsatellites. A cryo-electron microscopy structure of FoxP3 in complex with T3G repeats reveals a ladder-like architecture, where 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 the manner indistinguishable from that of FoxP3 bound to the Forkhead consensus motif (FKHM; TGTTTAC). Mutations in the "intra-rung" interface impair TnG repeat recognition, DNA bridging and cellular functions of FoxP3, all without affecting FKHM binding. FoxP3 can tolerate variable "inter-rung" spacings, explaining its broad specificity for TnG repeat-like sequences in vivo and in vitro. Both FoxP3 orthologs and paralogs show similar TnG repeat recognition and DNA bridging. These findings thus reveal a new mode of DNA recognition that involves TF homo-multimerization and DNA bridging, and further implicates microsatellites in transcriptional regulation and diseases.

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Zhang, W., Leng, F., Wang, X., Ramirez, R. N., Park, J., Benoist, C., Hur, S.. 2023-07-12. Ladder-like multimerization of FoxP3 enables microsatellite recognition and DNA bridging. https://doi.org/10.1101/2023.07.12.548762

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