Target search dynamics of Sox transcription factors.

Abstract

Transcription factors (TFs) are central players in regulating gene expression through their ability to bind sequence-specific sites. Nonetheless, how TFs search the genome to locate their binding sites is unclear. The facilitated diffusion theory proposes that TFs combine 1D-sliding on DNA and 3D-diffusion in the nucleus, and that local nonspecific interactions mediated by electrostatic forces drive the search efficiency beyond the one that would be reached by free diffusion alone. While such models are descriptive of the situation in prokaryotes, how eukaryotic TFs search the chromatinized genome is poorly understood. Furthermore, the relevance of regions outside DNA-binding domains (DBDs) for the search process remains unknown. Herein, we hypothesize that positive charges in DBD flanking regions accelerate TF target search through nonspecific interactions with DNA. A comparative study between Sox2 and Sox17 can demonstrate how electric charges within intrinsically disordered regions (IDRs) affect the target search process. These Sox-TF recognize the same motifs but have opposite charge distributions at their DBD C-terminus. Single-molecule imaging techniques allow for investigating the search efficiency. our results show that Sox2 exhibited a two-fold higher pseudo-on-rate than Sox17 and a Sox2 variant having an acidic stretch of Sox17. This is consistent with in vitro measurements, directly reporting a two-fold higher on-rate for wild-type Sox2 compared to the negatively-charged Sox2 variant. Moreover, the Sox2 variant showed a decreased ability to bind target sites within compact chromatin. Since Sox2 is known as a pioneer factor, quantifying their interactions with synthetically-chromatinized DNA will elucidate search mechanisms of pioneer TFs. In this regard, we foresee that more positively-charged IDRs stabilize the specific binding of TFs to nucleosomal DNA and help them to invade chromatin. Altogether, this work will dissect how the charge distribution of DBD flanking regions modulates TF target search on chromatin.