The DNA replication process recognizes transcription regulatory elements as punctuation marks at the start and end of genes, according to new research by Ekaterina V. Mirkin, Sergei M. Mirkin (University of Illinois, Chicago), and colleagues.
Because transcription and replication often occur concurrently and share a template, they occasionally collide. Sergei Mirkin and colleagues previously saw that the Escherichia coli replication fork slowed considerably during collisions with the moving RNA polymerase. The group now shows that replication also slows down upon colliding with a motionless RNA polymerase.
The stall occurs either just before or just after the coding frame, depending on the direction of the collision. Replication forks coming from the gene's tail end paused at the promoter. When the transcription cassette was flipped to coorient transcription and replication, the fork paused at the terminator instead.
The fork's pause signals are the transcription initiation and termination complexes, depending on the direction. “This polarity,” says Mirkin, “assures the replication fork pauses immediately after it passes the coding region, no matter which direction it came from.”
Mirkin suggests that these pauses might be a window of opportunity to correct mistakes in the newly replicated DNA. “Imagine a mark for the replication fork that says, ‘Look, you just finished copying a very important part of the text. Now slow down and check your work.’”