Choreography of chromatin regulation captured on the molecular level

Understanding how regulatory factors interact with chromatin, modulated by epigenetic modifications, requires tools to establish defined chromatin states and to capture dynamic processes at molecular resolution. Our single-molecule platform, combined with chemical biology approaches, enables direct observation of the action of chromatin-modifying complexes, transcription factors (TFs) or chromatin remodelers. By integrating single-molecule imaging in vitro and in cells, chemical and structural biology, and multicolor FRET, we resolve the mechanistic steps through which chromatin regulators navigate and modulate the nucleosome landscape. This allowed us, to directly observe the function of PRC1, a repressive complex, in cooperatively deposit H2A ubiquitylation within chromatin in real-time in a concerted reaction, resulting in structural changes altering gene expression [1]. Conversely, in the area of transcription regulation, we are investigating how TFs invade compact chromatin to activate gene expression. We show that intrinsically disordered regions (IDRs) flanking the DNA-binding domains are critical for efficient chromatin engagement. In particular positively charged regions of the TF Sox2 enhance its search process, by increasing both target site recognition and promoting nonspecific nucleosome interactions that reinforce its pioneer activity in chromatin [2]. When bound, pioneer TFs establish an open chromatin state. Using multicolor FRET, we resolve mechanistic steps of chromatin invasion and collaboration with remodeler complexes to displace nucleosomes.

Together, these studies reveal how the interplay between disordered TF regions, chromatin remodelers, and histone modifications governs the dynamic regulation of genome accessibility. Our findings establish a mechanistic framework for chromatin engagement by regulatory factors and demonstrate the power of single-molecule methods to resolve the molecular choreography underlying gene activation and repression.