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Elemental Mechanism Driving “Transcriptional Pausing”--Which Controls Gene Expression in All Living Organisms--Revealed by Work at UW-Madison; Study Also Reveals New Understanding of RNA Polymerase

A study published online on January 8, 2019 in eLife, and led by University of Wisconsin–Madison Professor of Biochemistry and Bacteriology Robert Landick, PhD, and his research team, reveals, for the first time, the elemental mechanism behind transcriptional pausing, a phenomenon that underlies the control of gene expression in all living organisms. The work also provides new understanding of the enzyme RNA polymerase, an important drug target for treating conditions such as Clostridium difficile infections and tuberculosis. The findings could ultimately improve our understanding of how certain drugs work against the enzyme and aid in actively targeting it. Gene expression is the process by which DNA is translated into all the proteins and other molecules living organisms need. Although it is a process that all introductory biology students learn about very early, scientists are still a long ways from fully understanding it. The process occurs in two steps. Transcription is the first, where RNA polymerase reads the information on a strand of DNA, which is then copied into a new molecule of messenger RNA (mRNA). In the second stage, the mRNA moves on to be processed (“translated”) into proteins by ribosomes. To help control gene expression levels, “transcriptional pausing” by RNA polymerase can occur between the two stages, providing a kind of “roadblock” where transcription may be terminated or modulated by the cell if need be. “A sequence that causes pausing of RNA polymerases in all organisms, from bacteria to mammals, halts the enzyme in a paused state from which longer-lived pauses can arise,” explains Dr. Landick. “As the fundamental mechanism of this elemental pause is not well defined, we decided to explore this using a variety of biochemical and biophysical approaches.”

The team’s analyses first revealed that the elemental pause process involves several biological players, which, together, create a barrier to prevent escape from paused states. The process also causes a modest conformational shift that makes RNA polymerase “stumble” when feeding DNA into its reaction center, temporarily stopping it from making RNA.

“We also found that transcriptional pausing makes RNA polymerase loosen its grip and backtrack on the DNA while paused,” says Dr. Landick. “Together, these results provide a framework to understand how the process is controlled by certain conditions and regulators within cells.”

He adds that these insights could aid future efforts to design synthetic genes, for example to direct the pausing behavior of RNA polymerase in a way that yields desired outputs from genes. It could also help our understanding of how certain drugs, known as RNA polymerase inhibitors, target the enzyme.

“For now, we would like to try and generate structures of paused transcription complexes obtained at a series of time intervals,” Dr. Landick concludes. “This would allow us to see exactly how parts of the enzyme move as it enters and leaves the paused state.”

This BioQuick posting is based on an article by UW-Madison biochemistry science writer Kaine Korzekwa, the Marketing Specialist for the UW-Madison Department of Biochemistry. Korzekwa’s article, in turn, was adapted from a press release by Emily Packer, Senior Press Officer for eLife. This latter release was posted on Eureka Alert. Links to both layman’s summaries of the research, the one by Korzekwa and the one by Packer, are provided below.

The eLife article is titled “The Elemental Mechanism of Transcriptional Pausing,” and was originally published on bioRxiv (


The image here is an illustration of the transcriptional pause process, which helps control gene expression in cells. (Credit: Robert Landick).

[UW summary] [eLife release] [eLife abstract]