Toward a mechanistic understanding of DNA binding by forkhead transcription factors and its perturbation by pathogenic mutations

Abstract

Forkhead box (FOX) proteins are an evolutionarily conserved family of transcription factors that play numerous regulatory roles in eukaryotes during developmental and adult life. Dysfunction of FOX proteins has been implicated in a variety of human diseases, including cancer, neurodevelopment disorders and genetic diseases. The FOX family members share a highly conserved DNA-binding domain (DBD), which is essential for DNA recognition, binding and function. Since the first FOX structure was resolved in 1993, >30 FOX structures have been reported to date. It is clear now that the structure and DNA recognition mechanisms vary among FOX members; however, a systematic review on this aspect is lacking. In this manuscript, we present an overview of the mechanisms by which FOX transcription factors bind DNA, including protein structures, DNA binding properties and disease-causing mutations. This review should enable a better understanding of FOX family transcription factors for basic researchers and clinicians.

FoxP3 can fold into two distinct dimerization states with divergent functional implications for T cell homeostasis

“…H-H dimerization is required for DNA binding and this is mediated by the unique RBR linker region. This requirement for H-H dimerization distinguishes FoxP3 from other forkhead TFs characterized to date, including FoxP1/2/4, which can bind DNA as individual DBDs (Dai et al, 2021). As a result, FoxP3 reads DNA sequence spanning ∼18 bp, rather than 7 bp as monomeric forkhead does.…”

“…First, both FoxP3 ∆N' and FoxP3 ∆N" form the winged-helix, non-swap conformation, rather than the swap dimer (Figure 1E, Figure S2C). As with other forkhead TFs with the winged-helix fold (Dai et al, 2021), FoxP3 inserts the signature helix 3 (H3) into the major groove forming a sequence-specific interaction with DNA, while the wing 1 region forms additional contact with the DNA phosphate backbone. The potential source of the discrepancy between our structure versus the previous swap dimer structure and the functional implications of the new structure will be discussed in detail in Figure 2.…”

“…One of the largest families of DBDs in eukaryotes is the forkhead DBD, which commonly displays a winged-helix fold and recognizes the consensus sequence known as forkhead motif (FKHM) – TGTTTAC (Dai et al, 2021). There are about 50 forkhead TFs in human, which play important roles in key biological processes, from development to reproduction, to aging and to immunity (Benayoun et al, 2011; Hannenhalli and Kaestner, 2009).…”

“…One of the largest families of DBDs in eukaryotes is the forkhead DBD, which commonly displays a winged-helix fold and recognizes the consensus sequence known as forkhead motif (FKHM) -TGTTTAC (Dai et al, 2021).There are about 50 forkhead TFs in human, which play important roles in key biological processes, from development to reproduction, to aging and to immunity (Benayoun et al, 2011;Hannenhalli and Kaestner, 2009). Some forkhead TFs function as pioneering TFs that can directly recognize DNA sequence within the condensed chromatin and open its structure with the help of chromatin modifiers (Drouin, 2014), while others utilize pre-existing chromatin landscape without dramatically altering its structure .…”

Paving Therapeutic Avenues for FOXG1 Syndrome: Untangling Genotypes and Phenotypes from a Molecular Perspective

“…The high degree of evolutionary conservation of the FKHD among different species already hinted towards its critical role for FOXG1 functions. It is thus expected that mutations affecting the DNA-binding domain of FOXG1 or the DNA-binding regulatory region within the N-terminal protein domain are poorly tolerated and lead to severely dysfunctional FOXG1 variants [5], [21], [22]. Puzzling though was the finding that the mutation hotspots of c.256dupC and c.460dupG associated with great variability of features and severities.…”