Chromatin sequesters pioneer transcription factor Sox2 from exerting force on DNA

Abstract

Formation of biomolecular condensates constitutes an emerging mechanism for transcriptional regulation. Recent studies suggest that the co-condensation between transcription factors (TFs) and DNA can generate mechanical forces driving genome rearrangements. However, the reported forces generated by such protein-DNA co-condensation are typically below one piconewton (pN), questioning its physiological significance. Moreover, the force-generating capacity of these condensates in the chromatin context remains unknown. Using single-molecule biophysical techniques, we show that Sox2, a nucleosome-binding pioneer TF, forms co-condensates with DNA, thereby exerting considerable mechanical tension on DNA strands both in cis and trans. Sox2 can generate forces up to 7 pN—similar in magnitude to other cellular forces. Sox2:DNA condensates are highly stable, withstanding disruptive forces high enough to melt DNA. We find that the disordered domains of Sox2 are required for maximum force generation but not condensate formation per se. Finally, we show that nucleosomes dramatically attenuate the mechanical stress exerted by Sox2 via sequestering it from coalescing on bare DNA. Our findings reveal that TF-mediated DNA condensation can exert significant mechanical stress which can nonetheless be alleviated by the chromatin organization, suggesting a new function of eukaryotic chromatin in protecting the genome from potentially deleterious nuclear forces.

Structure and DNA bridging activity of the essential Rec114–Mei4 trimer interface

“…By extension, we infer that the more complex condensates containing RM complexes and other proteins in vivo also both respond to and impose force on chromatin. There is a growing appreciation of the importance of capillary forces imposed by biomolecular condensates (Gouveia et al, 2022), including forces on DNA from nucleoprotein assemblies such as those made by transcription factors (Quail et al, 2021;Renger et al, 2021;Nguyen et al, 2022).…”