Scientists Unravel the Mystery of Gene Expression Bursting

Researchers at Kyushu University have discovered a connection between bursts of gene activity and the spatial distance between particular DNA regions. Using sophisticated cell imaging methods and computer modeling, the researchers demonstrated how the presence or absence of a gene affects DNA folding, movement, and protein accumulation.

The study, published in Science Advances, provided insight into the complex realm of gene expression and may result in novel treatment approaches for illnesses caused by incorrect gene expression regulation.

Transcription, which converts DNA into RNA, and translation, which uses RNA to create proteins, are the two primary stages of gene expression, a basic process that takes place inside cells.

Genes must be carefully turned on and off for each cell to produce the proper quantity of a protein at the appropriate time, which is necessary for each cell to perform its unique tasks in the body or to react to changing circumstances.

It was previously believed that gene transcription happens continuously and smoothly. However, thanks to improved technology that allows them to view individual cells, scientists now know that transcription happens in brief, erratic bursts.

A gene will randomly switch on for a few minutes and large amounts of RNA will be produced. Then, the gene will suddenly switch off again. It happens in nearly all genes, and in all living things, from plants to animals, to bacteria.”

Hiroshi Ochiai, Professor and Study Senior Author, Kyushu University

One important mechanism for regulating gene activity in individual cells is transcriptional bursting, which is the unpredictable and dynamic nature of transcription. It is one of the reasons why cells in the same tissue or culture environment exhibit different levels of gene expression, which is important for processes like the evolution of cancer and early embryonic development. The precise mechanisms underlying bursting are still unknown.

This study investigated the function of enhancers and promoters, two types of DNA sequences, and the effects of their spatial separation on transcriptional bursting.

The protein that performs transcription binds to the DNA at the promoter, which is typically found directly adjacent to the gene. However, because DNA strands can move and fold, enhancers can still end up near genes in three dimensions, increasing gene activity even though they are typically hundreds of thousands of bases away from the gene.

We believe that enhancers play a crucial role in why transcription occurs in bursts of activity, but so far, the research is unclear.”

Hiroshi Ochiai, Professor and Study Senior Author, Kyushu University

Ochiai and his colleagues tested this theory using seq-DNA/RNA-IF-FISH, a sophisticated imaging method that uses fluorescent probes to label DNA, RNA, and proteins. Thanks to this triple-layered technique, the researchers were able to concurrently record the locations of particular proteins, RNA, and DNA in three dimensions within individual mouse embryonic stem cells.

With that information, the team could see, in unprecedented detail, where the proteins were accumulating, how the promoters and enhancers were interacting during bursts of activity, and whether specific genes were on or off.

For instance, the researchers concentrated on a gene called Nanog, which is located on chromosome 6 and is 770,000 bases long. It has three enhancer regions and a promoter, and it is known to experience transcriptional bursting in mouse embryonic stem cells that are cultured.

The researchers discovered that the most distant enhancer was situated in close spatial proximity to the Nanog gene in imaged cells that contained Nanog RNA, indicating that the gene was active. The imaging, however, revealed that the same enhancer region was physically farther away when Nanog was not in use.

Furthermore, when Nanog was active, the researchers discovered that proteins that control transcription also gathered near enhancers and promoters.

Ochiai and his colleagues employed computer modeling to better understand the mechanism by describing the movement and interaction of the various DNA segments within the cell, both in the active and inactive states of the Nanog gene.

They created their model by creating a “map” of the frequency of interactions between various DNA regions and the spatial folding of DNA using data from their imaging experiments. The model then used this map to simulate the random movement of the DNA chain.

According to the model, each enhancer region interacted with the promoters for over twice as long when the gene was active as it did when it was dormant.

The model demonstrated that “friction” around the DNA was the cause of these extended periods of interaction. When Nanog was active, proteins and RNA accumulated, making the fluid more viscous and slowing the movement of the modeled DNA strand. As a result, the gene could remain active for extended periods.

On the other hand, when Nanog was inactive, the simulated DNA moved more quickly, which prevented the promoter and enhancers from interacting.

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

Hiroshi Ochiai, Professor and Study Senior Author, Kyushu University