Phase-Separated Transcriptional Condensates Accelerate Target-Search Process Revealed by Live-Cell Single-Molecule Imaging

Compartmentalization by liquid-liquid phase separation is implicated in transcription. It remains unclear whether and how transcriptional condensates accelerate the search of transcriptional regulatory factors for their target sites. Furthermore, the molecular mechanisms by which regulatory factors nucleate on chromatin to assemble transcriptional condensates remain incompletely understood. The CBX-PRC1 complexes compartmentalize key developmental regulators for repression through phase-separated condensates driven by the chromobox 2 (CBX2) protein. Here, by using live-cell single-molecule imaging, we show that CBX2 nucleates on chromatin independently of H3K27me3 and CBX-PRC1. The interactions between CBX2 and DNA are essential for nucleating CBX-PRC1 on chromatin to assemble condensates. The assembled condensates shorten 3D diffusion time and reduce trials for finding specific sites through revisiting the same or adjacent sites repetitively, thereby accelerating CBX2 in searching for target sites. Overall, our data suggest a generic mechanism by which transcriptional regulatory factors nucleate to assemble condensates that accelerate their target-search process.