FoxP3 forms a head-to-head dimer in vivo and stabilizes its multimerization on adjacent microsatellites

Area of Science:

• Molecular Biology
• Immunology
• Epigenetics

Background:

• FoxP3 is the master regulator of regulatory T cells (Tregs).
• FoxP3 utilizes distinct DNA-binding modes: multimerization on TnG repeats and head-to-head (H-H) dimerization on inverted repeat forkhead motifs (IR-FKHM).
• In vivo evidence for FoxP3 H-H dimerization was previously lacking.

Purpose of the Study:

• To identify novel DNA motifs driving FoxP3 H-H dimerization.
• To perform a genome-wide analysis of FoxP3 binding modes in Tregs.
• To understand the interplay between FoxP3's DNA-binding modes and chromatin architecture.

Main Methods:

• Unbiased pull-down sequencing to identify FoxP3-binding motifs.
• Genome-wide analysis of FoxP3 binding in Tregs.
• Comparative analysis of FoxP3 orthologs.

Main Results:

• Discovery of relaxed motifs that promote FoxP3 H-H dimerization.
• Demonstration that FoxP3 binds genomic DNA as both H-H dimers and multimers in Tregs.
• Evidence that H-H dimerization can initiate and stabilize multimerization on adjacent TnG repeats, particularly suboptimal ones.
• Identification of H-H dimerization as a FoxP3-specific trait, absent in other FoxP members, due to its divergent accessory loop.

Conclusions:

• FoxP3 employs a dual-mode DNA-binding strategy (H-H dimerization and multimerization) in vivo.
• This dual-mode binding expands FoxP3's sequence recognition and enhances its function in chromatin looping.
• H-H dimerization is a unique feature of FoxP3 orthologs, contributing to its specialized regulatory role.