Textbooks tell us that an RNA polymerase tracks like a locomotive down the template.
We think this is wrong; instead we think the active enzyme is immobilized in a larger structure we call a transcription factory, and works by reeling in its template as it extrudes the transcript. Then, active polymerases are one of the critical molecular ties that organize the genome into loops (a review), and promoter-factory distance determines how frequently a gene is transcribed (a review).
This YouTube movie shows how we think an immobilized RNA polymerase might work. This movie contains audio; the the text below also describes what happens.
|Alternative description of movie.
When genes strung along a template are transcribed, active polymerases aggregate into clusters to loop intervening DNA. We call a cluster a transcription 'factory' as it contains several polymerizing complexes and transcription units. Each factory is then surrounded by a 'cloud' of loops.
Only one loop with two transcription units is shown attached to a factory:
• on the left, through one unit and an engaged polymerase (transcription has just initiated, and the transcript is just beginning to emerge),
• on the right, through a cluster of transcription factors (for the sake of convenience, this attachment is shown – incorrectly – to be stable, but it is repeatedly broken and remade).
Another polymerase and a tetrameric '200S' particle are shown docked on the surface of the factory.
Clustering ensures there is a high local concentration of polymerases in the factory, so few (if any) transcripts are made elsewhere.
When the movie starts:
• the polymerase (left) reels in its template, as it extrudes its transcript (which is packaged into the 200S particle),
• the other promoter diffuses through the nucleoplasm and collides with a polymerase in the factory, transcription begins, and the transcript is incorporated into the 200S particle,
• on termination, transcription units and polymerases detach and the 200S particle diffuses away (Iborra et al., 1998; 2000).
Go to a higher-power view of one polymerizing complex in a factory.