Computer modeling shows that close encounters between distant DNA regions cause bursts of genetic activity

Researchers at Kyushu University have revealed how the spatial distance between specific regions of DNA is linked to bursts of genetic activity. Using advanced cellular imaging and computer modeling techniques, researchers have shown that the folding and movement of DNA, as well as the accumulation of certain proteins, changes depending on whether a gene is active or inactive .

The study, published December 6 in Scientific advancesprovides insight into the complex world of gene expression and could lead to new therapeutic techniques for diseases caused by inappropriate regulation of gene expression.

Gene expression is a fundamental process that occurs within cells, with two main phases: transcription, where DNA is copied into RNA, and translation, where RNA is used to make proteins. For each cell to perform its specific functions in the body or to respond to changing conditions, the right amount of protein must be produced at the right time, which means that genes must be carefully turned on and off.

Previously, gene transcription was thought to occur in a continuous, fluid process. But thanks to better technology for looking at individual cells, scientists now know that transcription occurs in short, unpredictable bursts.

“A gene will turn on randomly for a few minutes and large amounts of RNA will be produced. Then the gene will suddenly turn off,” explains Professor Hiroshi Ochiai, from the Medical Institute of Bioregulation at the University of Kyushu and lead author of the study. “This happens in almost all genes and in all living things, from plants to animals to bacteria.”

This erratic and dynamic nature of transcription, known as transcriptional bursting, is a key mechanism for controlling gene activity in individual cells. This is one reason why cells from the same tissue or culture environment exhibit variability in their gene expression levels, which is crucial for processes such as early embryonic development and the evolution of cancer. However, the exact mechanisms behind the burst remain unknown.

In this study, the researchers decided to examine the role of DNA sequences known as enhancers and promoters, and the impact of their spatial distance on transcriptional bursting. The promoter is usually located right next to the gene and is where the protein that carries out transcription attaches to the DNA. Enhancers, on the other hand, are often found several hundred thousand bases away from the gene, but as DNA strands move and fold, enhancers can still end up near genes in 3D space, thus amplifying gene activity.

“We think activators play a crucial role in why transcription occurs in bursts of activity, but so far the research is unclear,” says Ochiai.

To test this idea, Ochiai and his team used an advanced imaging technique called seq-DNA/RNA-IF-FISH, which labels specific DNA, RNA, and proteins with fluorescent probes.

This three-layer technique allowed researchers to simultaneously capture the location of specific DNA, RNA, and proteins in 3D space within individual mouse embryonic stem cells. Using this information, the team was able to determine whether certain genes were turned on or off, see how promoters and enhancers interacted during periods of activity, and where proteins accumulated, with an unprecedented level of detail.

As an example, the researchers focused on a gene called Nanog, a 770,000 base length of DNA on chromosome 6, which has one promoter and three enhancer regions and is known to undergo a transcriptional burst in cells. mouse embryonic strains in culture.

The researchers found that in cells imaged where Nanog RNA was present (meaning the gene was active), the most distant enhancer was located in close spatial proximity to the Nanog gene. In contrast, when Nanog was inactive, imaging showed that the same enhancer region was physically further away.

Additionally, the scientists also found that proteins involved in transcription regulation also accumulated in the area around enhancers and promoters when Nanog was active.

To better understand the mechanism, Ochiai and his team used computer modeling to simulate how different parts of DNA interact and move inside the cell, both when the Nanog gene is active and inactive. .

They developed their model using data from their imaging experiments to create a “map” of how often different regions of DNA interact with each other and how the DNA folds in space. Using this map, the model then simulated how the DNA chain might move randomly.

The model predicts that when in the active state, each enhancer region interacts with promoters for more than twice as long as when the gene is inactive.

The model showed that these longer interaction periods occurred because of “friction” around the DNA. Due to the accumulation of proteins and RNA when Nanog was active, the fluid became more viscous and resulted in slow movement of the modeled DNA strand. Therefore, the gene was able to remain active for longer periods. In contrast, simulated DNA moved faster when Nanog was inactive, meaning the promoter and enhancers did not have time to interact.

“The modeling suggests that the bursting is stabilized through these reinforcing loops,” concludes Ochiai. “Of course, this is just a simulation. The next step is to prove that this mechanism also occurs in cells.”