Gene expression emerges from a dynamic interplay between transcription factors (TFs) and RNA polymerases operating on crowded DNA templates. In this seminar, I will present two complementary single-molecule studies using optical tweezers to probe this interplay. First, we show that intrinsically disordered regions (IDRs) of the yeast transcription factor Msn2 drive an efficient target-search mechanism by promoting non-specific DNA binding and one-dimensional diffusion toward specific motifs. Promoter-derived sequences enhance both binding and scanning kinetics, demonstrating that Msn2–DNA interactions alone can confer promoter selectivity beyond canonical motifs. Second, we examine what occurs when an elongating RNA polymerase encounters a DNA-bound TF within gene bodies. We find that polymerase progression is transiently delayed but progressively destabilizes the bound factor. CpG methylation increases TF dissociation, attenuating its barrier effect on elongation and providing a mechanistic rationale for gene-body methylation. Together, these studies highlight how dynamic protein–DNA interactions shape transcription from target recognition to elongation.FOR THE LATEST UPDATES AND CONTENT ON SOFT MATTER AND BIOLOGICAL PHYSICS AT THE WEIZMANN, VISIT OUR WEBSITE: https://www.bio
