The study focused on the ensyme responsible for transcription, RNA polymerase II. During transcription, numbers of RNA polymerase II molecules assemble on DNA and then synthesize RNA by sequentially recruiting complementary RNA nucleotides.
3 phases of Transcription
To visualize the transcription process, the researchers used living mammalian cells, each of which contained 200 copies of an artificial gene that they had inserted into one of the cell’s chromosomes. Then, by attaching fluorescent tags to RNA polymerase II, they were able to closely monitor all three phases of the transcription process:
- binding of the enzyme molecules to DNA,
- initiation (when the enzyme links the first few RNA nucleotides together) and
- elongation (construction of the rest of the RNA molecule).
As they observed the RNA polymerase II molecules attaching to DNA and making new RNA, they saw many cases where enzyme molecules attached — and then promptly fell off.
Transcription is inefficient
During the first two phases the transcription process is really inefficient. It turns out that only one percent of polymerases that bind to the gene actually remain on to help in synthesizing an RNA molecule.
Transcription may be inefficient for a reason. All the factors needed for transcription have to come together at the right time and the right place, so there’s a lot of falling off and adding on of polymerases until everything is precisely coordinated.
The researchers observed that
- the binding phase of transcription lasted six seconds and
- initiation phase lasted 54 seconds.
- the elongation phase lasted 517 seconds (about eight minutes).
The “lead” polymerase on the growing polymerase II enzyme sometimes “paused” for long periods, retarding transcription in the same way that a Sunday driver on a narrow road slows down all traffic behind him.
But in the absence of pausing, elongation proceeded much faster — about 70 nucleotides synthesized per second — than has previously been reported.
These two phenomena — pausing and rapid RNA synthesis during elongation — may be crucial for regulating gene expression. Once the ‘paused’ polymerase starts up again, in a very short time you could synthesize a new batch of messenger RNA molecules that might suddenly be needed for making large amounts of a particular protein.