Transcription machinery clustering by Integrator synchronizes histone gene expression

Numerous components of the transcription machinery, including RNA polymerase II (Pol II), accumulate in high-concentration clusters at promoters. Whether these clusters assemble on demand during transcription or constitute regulatory units remains unclear. Examining the Drosophila histone locus--where histone genes are transcribed exclusively during S phase--we unexpectedly found large clusters containing non-chromatin-bound Pol II and elongation factors outside S phase. When transcription is activated during S phase, P-TEFb drives accelerated turnover of cluster components. Dispersion of clusters through depletion of the Integrator complex endonuclease module causes histone transcription to have a diminished S-phase peak and instead occur ectopically throughout the cell cycle. We propose that clusters act as gatekeeping hubs by maintaining a poised machinery pool, thereby restricting gene activation to defined temporal windows.