Real-time visualization of reconstituted transcription reveals RNAPII activation mechanisms at single promoters

RNA polymerase II (RNAPII) is regulated by sequence-specific transcription factors (TFs) and the pre-initiation complex (PIC): TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and Mediator. TFs, Mediator, and RNAPII contain intrinsically disordered regions (IDRs) and form phase-separated condensates, but how IDRs control RNAPII function remains poorly understood. Using purified PIC factors, we developed a real-time in vitro fluorescence transcription (RIFT) assay for second-by-second visualization of transcription at hundreds of promoters simultaneously. Our results establish IDRs as essential for rapid RNAPII activation, without condensate formation. For example, HSF1 condensates and single molecules function identically, whereas MED1-IDR can functionally replace HSF1 but activates RNAPII with slower kinetics. Through their IDRs, Mediator and TFs rapidly and synergistically activate RNAPII bursting and re-initiation, and surprisingly, Mediator drives TF-promoter recruitment without TF-DNA binding. Importantly, RIFT directly addresses questions largely intractable with cell-based methods, yielding mechanistic insights about condensates, IDRs, enhancer-promoter communication, and RNAPII bursting that complement live-cell imaging data.