Figure 1: An illustration showing RNA polymerase II (silver structure) transcribing DNA (yellow and orange helix) into messenger RNA. RIKEN researchers have conducted a structural study of the elongation complex of RNA polymerase II during promoter-proximal pausing of transcription. © 2025 RIKEN Center for Biosystems Dynamics Research
A detailed picture of what happens when DNA transcription is paused early in the process, has been obtained by structural biologists at RIKEN1. This could help inform the development of new therapies.
When the molecular machinery in our cells gets to work transcribing the genetic information encoded in DNA into messenger RNA (mRNA), it pauses shortly after starting.
Known as promoter-proximal pausing, this interruption in the transcription activity of RNA polymerase II-the enzyme responsible for transcribing DNA into mRNA (Fig. 1)-plays a critical role in ensuring accurate transcription and in regulating developmental genes.
In particular, it allows the state of RNA polymerase II known as the elongation complex to transform into a structure that allows for efficient transcription. Promoter-proximal pausing is important for various normal biological processes and also in disorders, notes Shun-ichi Sekine of the RIKEN Center for Biosystems Dynamics Research (Current affiliation: RIKEN Center for Integrative Medical Sciences).
"Promoter-proximal pausing has been implicated in the differentiation of stem cells, embryonic development and stress responses," he says. "It also plays a role in diseases such as cancer and viral infections."
While it has been much studied, the mechanics of how it occurs is still little understood.
Now, Sekine and co-workers have used the powerful imaging technique of cryo-electron microscopy to look at promoter-proximal pausing on an atomic level.
To obtain structural clues to how the process works, the team looked at the elongation complex of RNA polymerase II that had stalled on a nucleosomal DNA.
They discovered that RNA polymerase II binds in two distinct ways to the negative elongation factor-one of the three regulatory factors involved in promoter-proximal pausing. One of these binding modes had been reported earlier, but the other one was previously unknown. With the second mode, the negative elongation factor cooperates with the nucleosome to strictly limit further progression of transcription.
The type of binding seems to determine the outcome of the pause, with one type leading to early termination of transcription, whereas the other continues in the paused state until it receives a signal to proceed.
"While this discovery of a second binding mode was unexpected, it explains previous observations and resolves discrepancies," notes Masahiro Naganuma, also of the RIKEN Center for Biosystems Dynamics Research (Current affiliation: RIKEN Center for Integrative Medical Sciences).
The discovery could have practical implications. "Our findings may contribute to a better understanding of diseases caused by dysregulated transcription," says Sekine. "And they could eventually support the development of novel therapeutic strategies."
Sekine and team now intend to explore the detailed mechanism of how transcription resumes after pausing through both structural and biochemical approaches.
