Molecule of the Month: FOXP3

The immune system walks a fine line. It must defend the body against an enormous variety of foreign invaders, from pathogenic bacteria to viruses. At the same time, this system must exercise restraint, avoiding attacks on the body’s own cells and molecules, a process known as self-tolerance. Essential to this immunological balance are cells known as regulatory T cells, or Tregs. Tregs act as guardians of the immune system by suppressing white blood cells that are self-reactive and modulating the immune response of a wide variety of other immune cells. Without Tregs, the immune system can attack its own tissues and organs, leading to disease and chronic inflammation. For their discoveries regarding Tregs, Mary Brunkow, Fred Ramsdell and Shimon Sakaguchi were awarded the Nobel Prize in Physiology or Medicine in 2025.

The development and function of Tregs is controlled by the transcription factor Forkhead box protein P3 (FOXP3), an important transcriptional regulator that is estimated to control the expression of numerous genes.

FOXP3 is a member of a family of transcription factors that share a protein motif called a forkhead box domain. The forkhead box has been shown to bind to DNA in a manner that is structurally similar to the linker histone H5. As shown in the illustration on the right, FOXP3's forkhead box domain has been shown to bind to DNA in different ways: as a head-to-head pair (PDB 7TDW, 7TDX), as well as a domain-swapped dimer that is able to bridge two strands of DNA (PDB 3QRF). Additional domains of FOXP3 (not shown in the illustration) include a zinc finger domain and a leucine zipper domain, and are important for oligomerization and binding a wide variety of regulatory partners.

Biochemical studies have shown that FOXP3 can interact with diverse binding partners to form a large complex of hundreds of factors. These factors include additional transcription factors and proteins involved in epigenetic remodeling, such as methyltransferases and deacetylases. The composition of FOXP3 complexes has been shown to be dynamic, changing in response to signaling and environmental cues.

Recent structural studies are shedding light on how large FOXP3-containing complexes may form. Multiple copies of FOXP3 can bind to repeating segments of DNA known as microsatellite DNA, forming long polymers. FOXP3 polymers can then associate with one another in a variety of ways through their forkhead domains to form highly stable higher-order multimers that bring together multiple strands of DNA (as shown on the left, PDB 9D2L) . Researchers hypothesize that these large and flexible FOXP3-mediated DNA bridges play an important role in stabilizing chromatin loops at thousands of genetic sites scattered across the genome, thereby shaping transcription in a global manner in Treg cells.

Loss or dysfunction of FOXP3 causes a disease known as IPEX syndrome (Immune dysregulation, Polyendocrinopathy, Enteropathy, X-linked). IPEX is a devastating and often fatal disease, manifesting as a constellation of autoimmune disorders affecting organs throughout the body. Over 70 FOXP3 mutations can cause IPEX. Many of these mutations are found in the forkhead box domain and impact FOXP3's stability and binding to DNA and/or protein partners.