How RNAP accomplishes this feat is largely unknown. A snapshot of RNAP in the act of opening that bubble would provide a wealth of information, but the process happens too quickly for current technology to easily capture visualizations of these structures. Now, a new study in Nature Structural & Molecular Biology describes E. coli RNAP in the act of opening the transcription bubble.

The findings, captured within 500 milliseconds of RNAP mixing with DNA, shed light on fundamental mechanisms of transcription, and answer long-standing questions about the initiation mechanism and the importance of its various steps. “This is the first time anybody has been able to capture transient transcription complexes as they form in real time,” says first author Ruth Saecker, a research specialist in Seth Darst’s laboratory at Rockefeller. “Understanding this process is crucial, as it is a major regulatory step in gene expression.”

An unprecedented view

Darst was the first to describe the structure of bacterial RNAP, and teasing out its finer points has remained a major focus of his lab. While decades of work have established that RNAP binding to a specific sequence of DNA triggers a series of steps that open the bubble, how RNAP separates the strands and positions one strand in its active site remains hotly debated.

Early work in the field suggested that bubble opening acts as a critical slowdown in the process, dictating how quickly RNAP can move onto RNA synthesis. Later results in the field challenged that view, and multiple theories emerged about the nature of this rate-limiting step. “We knew from other biological techniques that, when RNAP first encounters DNA, it makes a bunch of intermediate complexes that are highly regulated,” says coauthor Andreas Mueller, a postdoctoral fellow in the lab. “But this part of the process can happen in less than a second, and we were unable to capture structures on such a short timescale.”

To better understand these intermediate complexes, the team collaborated with colleagues at the New York Structural Biology Center, who developed a robotic, inkjet-based system that could rapidly prepare biological samples for cryo-electron microscopy analysis. Through this partnership, the team captured complexes forming in the first 100 to 500 milliseconds of RNAP meeting DNA, yielding images of four distinct intermediate complexes in enough detail to enable analysis.

For the first time, a clear picture of the structural changes and intermediates that form during the initial stages of RNA polymerase binding to DNA snapped into focus. “The technology was extremely important to this experiment,” Saecker says. “Without the ability to mix DNA and RNAP quickly and capture an image of it in real-time, these results don’t exist.”

Getting into position

Upon examining these images, the team managed to outline a sequence of events showing how RNAP interacts with the DNA strands as they separate, at previously unseen levels of detail. As the DNA unwinds, RNAP gradually grips one of the DNA strands to prevent the double helix from coming back together. Each new interaction causes RNAP to change shape, enabling more protein-DNA connections to form. This includes pushing out one part of a protein that blocks DNA from entering RNAP’s active site. A stable transcription bubble is thus formed.

The team proposes that the rate-limiting step in transcription may be the positioning of the DNA template strand within the active site of the RNAP enzyme. This step involves overcoming significant energy barriers and rearranging several components. Future research will aim to confirm this new hypothesis and explore other steps in transcription.

“We only looked at the very earliest steps in this study,” Mueller says. “Next, we’re hoping to look at other complexes, later time points, and additional steps in the transcription cycle.”

Beyond resolving conflicting theories about how DNA strands are captured, these results highlight the value of the new method, which can capture molecular events happening within milliseconds in real-time. This technology will enable many more studies of this kind, helping scientists visualize dynamic interactions in biological systems.

“If we want to understand one of the most fundamental processes in life, something that all cells do, we need to understand how its progress and speed are regulated,” says Darst. “Once we know that, we’ll have a much clearer picture of how transcription begins.”

Young adults who have higher levels of inflammation, which is associated with obesity, physical inactivity, chronic illness, stress and smoking, may experience reduced cognitive function in midlife, a new study out of UC San Francisco has found.

Researchers previously linked higher inflammation in older adults to dementia, but this is one of the first studies to connect inflammation in early adulthood with lower cognitive abilities in midlife.

“We know from long-term studies that brain changes leading to Alzheimer’s disease and other dementias may take decades to develop,” said first author Amber Bahorik, PhD, of the UCSF Department of Psychiatry and Behavioral Sciences and the Weill Institute for Neurosciences. “We wanted to see if health and lifestyle habits in early adulthood may play a part in cognitive skills in midlife, which in turn may influence the likelihood of dementia in later life.”

In their study, publishing in Neurology on July 3, researchers found that only 10% of those with low inflammation performed poorly on testing of processing speed and memory, compared to 21% and 19%, respectively, of those with either moderate or higher levels of inflammation.

When researchers adjusted for factors like age, physical activity and total cholesterol, disparities remained in processing speed; and the researchers also found differences in executive functioning, which includes working memory, problem solving and impulse control.

The study followed 2,364 adults in the CARDIA study, which aims to identify the factors in young adulthood that lead to cardiovascular disease two-to-three decades later.

Participants were 18 to 30 years old when they entered the study and were tested four times over an 18-year period for the inflammatory marker C-reactive protein (CRP). They took the cognitive tests five years after their last CRP measurement, by which time most participants were in their forties and fifties.

About half the participants were female; a little under half were Black, and the rest were white. Some 45% had lower stable inflammation, while 16% had moderate or increasing inflammation; 39% had higher levels.

A link between inflammation and health risks

The researchers also linked higher levels of inflammation with physical inactivity, higher BMI and current smoking.

“Inflammation plays a significant role in cognitive aging and may begin in early adulthood,” said senior author Kristine Yaffe, MD, a professor of psychiatry and behavioral sciences, neurology, and epidemiology and biostatistics at UCSF. “There is likely a direct and indirect effect of inflammation on cognition.”

Yaffe is a member of the first team of experts to determine that 30% of dementia risk is preventable. Her recent research has looked at the association in midlife between fragmented sleep and lower cognition and the effects of personalized health and lifestyle changes in preventing memory loss in higher-risk older adults.

“Fortunately, there are ways to reduce inflammation — such as by increasing physical activity and quitting smoking — that might be promising paths for prevention,” Yaffe said.

Lunar swirls have defied easy explanation, but recent modeling and spacecraft data shed light on the twisty mystery. The data shows that rocks in the swirls are magnetized, and these rocks deflect or redirect solar wind particles that constantly bombard the Moon. Nearby rocks take the hit instead. Over time, neighboring rocks become darkened by chemical reactions caused by the collisions, while the swirls remain light colored.

But how did the rocks in lunar swirls get magnetized? The Moon does not have a magnetic field today. No astronaut or rover has yet visited a lunar swirl to investigate.

“Impacts could cause these types of magnetic anomalies,” said Michael J. Krawczynski, an associate professor of earth, environmental and planetary sciences in Arts & Sciences at Washington University in St. Louis. He notes that meteorites regularly deliver iron-rich material to areas on the Moon’s surface. “But there are some swirls where we’re just not sure how an impact could create that shape and that size of thing.”

Krawczynski believes it’s more likely that something else has locally magnetized the swirls.

“Another theory is that you have lavas underground, cooling slowly in a magnetic field and creating the magnetic anomaly,” said Krawczynski, who designed experiments to test this explanation. His results are published in the Journal of Geophysical Research: Planets.

Krawczynski and study first author Yuanyuan Liang, who recently earned her PhD in earth, environmental and planetary sciences in Arts & Sciences, measured the effects of different combinations of atmospheric chemistry and magmatic cooling rates on a mineral called ilmenite to see if they could produce a magnetizing effect.

“Earth rocks are very easily magnetized because they often have tiny bits of magnetite in them, which is a magnetic mineral,” Krawczynski said. “A lot of the terrestrial studies that have focused on things with magnetite are not applicable to the Moon, where you don’t have this hyper-magnetic mineral.”

But ilmenite, which is abundant on the Moon, can also react and form particles of iron metal, which can be magnetized under the right conditions, Krawczynski and his team found.

“The smaller grains that we were working with seemed to create stronger magnetic fields because the surface area to volume ratio is larger for the smaller grains compared to the larger grains,” Liang said. “With more exposed surface area, it is easier for the smaller grains to undergo the reduction reaction.”

“Our analog experiments showed that at lunar conditions, we could create the magnetizable material that we needed. So, it’s plausible that these swirls are caused by subsurface magma,” said Krawczynski, who is a faculty fellow in the university’s McDonnell Center for the Space Sciences.

Determining the origin of lunar swirls is considered key in understanding what processes have shaped the lunar surface, the history of a magnetic field on the Moon and even how the surfaces of planets and moons generally affect the space environment surrounding them.

This study will help interpret data acquired by future missions to the Moon, especially those that explore magnetic anomalies on the lunar surface. NASA intends to send a rover to the lunar swirl area known as Reiner Gamma in 2025 as part of the Lunar Vertex mission.

“If you’re going to make magnetic anomalies by the methods that we describe, then the underground magma needs to have high titanium,” Krawczynski said. “We have seen hints of this reaction creating iron metal in lunar meteorites and in lunar samples from Apollo. But all of those samples are surface lava flows, and our study shows cooling underground should significantly enhance these metal-forming reactions.”

For now, his experimental approach is the best way to test predictions about how unseen lava may be driving the magnetic effects of the mysterious lunar swirls.

“If we could just drill down, we could see if this reaction was happening,” Krawczynski said. “That would be great, but it’s not possible yet. Right now, we’re stuck with the surface.”