This article has been reviewed according to Science X's editorial process and policies. Editors have highlighted the following attributes while ensuring the content's credibility: All living things have a fleet of tiny copy machines that turn instructions from DNA into RNA molecules responsible for helping build proteins that keep organisms alive. One of those nanoscale machines, called eukaryotic RNA polymerase II, performs a crucial early step required by nearly every biological process.
It makes messages, copying and carrying instructions from the cell nucleus to make proteins. Until recently, scientists had only witnessed eukaryotic RNA polymerase II at work in carefully assembled test tubes, stripped of the chaotic realities of life inside a cell. Now, a team led by Penn State researchers has captured a glimpse of this molecular machinery as it operates inside living organisms.
They reported their findings in the journal Nature Communications. "This is the first time we're seeing this process as it actually happens; the way it acts when no one is watching," said Katsuhiko Murakami, the Stanley Person Professor of Molecular Biology and director of the Huck Center for Structural Biology at Penn State and co-corresponding author on the study. "Previously, we had to use highly purified samples under ideal lab conditions to visualize their structures, which is not how life really works.
Now, we must completely change our thinking because what we're seeing is not anything we have seen before." Using fruit fly embryos, the team developed a method to extract intact "transcription complexes," the clusters of RNA polymerase II and DNA involved in reading and copying genes. They then used cryo-electron microscopy (cryo-EM), a powerful imaging technique that freezes molecules in place and visualizes them at near-atomic detail, to map what they found. What emerged was a far more dynamic and surprising picture of the copy machine process, called gene transcription, than they had expected.
Murakami explained that the project began in 2021 when David Gilmour, emeritus professor of biochemistry and molecular biology at Penn State, showed him purified RNA polymerase II extracted from a fruit fly embryo. "It wasn't clean, but it sparked an idea," Gilmour said. "We could use cryo-EM to analyze native transcription complexes from it.
After years of hard work, we've now captured these complexes in a near-native state, and what we found was actually pretty surprising." Prior to this study, RNA polymerase II was thought to be made up of 12 subunits that come together to form a complete unit, so most researchers assumed they all looked the same in cells, Gilmour said. But the team's results showed that's not always the case. Some of them have all 12 subunits, as expected, but others are missing two subunits, leaving them with only 10 subunits.
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