A role for pH dynamics regulating transcription factor DNA-binding selectivity

Intracellular pH (pHi) dynamics regulates diverse cell processes such as proliferation, dysplasia, and differentiation, often mediated by the protonation state of a functionally critical histidine residue in endogenous pH sensing proteins. How pHi dynamics can directly regulate gene expression or whether transcription factors can function as pH sensors has received limited attention. We tested the prediction that transcription factors with a histidine in their DNA-binding domain (DBD) that forms hydrogen bonds with nucleotides can have pH-regulated activity, which is relevant to more than 85 transcription factors in distinct families, including FOX, KLF, SOX, and MITF/Myc. Focusing on FOX family transcription factors, we use unbiased SELEX-seq to identify pH-dependent DNA-binding motif preferences and confirm pH-regulated binding affinities for FOXC2, FOXM1, and FOXN1 to a canonical FkhP DNA motif that are greater at pH 7.0 compared with pH 7.5 and for FOXN1 to a preferred FHL motif at higher pHi in cells. For FOXC2, we also find that greater activity for an FkhP motif at lower pH is dependent on a conserved histidine (His122) in the DBD. ChIP-seq and RNA-seq with FOXC2 also reveal pH-dependent differences in enriched promoter motifs. Our findings identify pH-regulated transcription factor-DNA binding selectivity with relevance to how pHi dynamics can regulate gene expression for myriad cell behaviours.