Researchers from Kyushu University have provided new insights into DNA movement, spatial organization, and gene activity. Their recent study in Science Advances examines how interactions between DNA enhancers and promoters contribute to transcriptional bursts—a phenomenon where genes rapidly switch between active and inactive states. Using cutting-edge imaging and computational techniques, the team provides new perspectives on the dynamic regulation of gene expression, a process critical for cellular function and disease development.
Understanding Gene Expression and Transcriptional Bursts
Gene expression involves transcription (DNA to RNA) and translation (RNA to proteins). While earlier models suggested that transcription occurs smoothly, recent observations reveal that it operates in unpredictable, intermittent 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,” explained Hiroshi Ochiai, senior author of the study and a professor at Kyushu University’s Medical Institute of Bioregulation. This erratic behavior, known as transcriptional bursting, is observed across all living organisms and plays a key role in processes like embryonic development and cancer progression. However, the underlying mechanisms behind these bursts have remained unclear.
Exploring DNA Interactions in 3D Space
Ochiai's team focused on DNA sequences called promoters and enhancers. Promoters, located adjacent to genes, serve as docking sites for transcription machinery, while enhancers, often located far from genes, influence gene activity by folding into close proximity in 3D space. “We believe that enhancers play a crucial role in why transcription occurs in bursts of activity, but so far, the research is unclear,” noted Ochiai.
Using a sophisticated imaging technique called seq-DNA/RNA-IF-FISH, the researchers labeled DNA, RNA, and proteins with fluorescent markers. This method allowed them to visualize the 3D positions of these molecules in single mouse embryonic stem cells and identify their relationships during gene activity.
One gene of interest was Nanog, a regulator of stem cell pluripotency. The researchers observed that when Nanog was active, its distant enhancer regions were positioned closer to the gene. In contrast, when the gene was inactive, these enhancers were spatially separated. Additionally, proteins regulating transcription accumulated near both the promoter and enhancers during gene activation.
Modeling DNA Dynamics and Gene Activity
To further probe these interactions, the team developed computational models simulating DNA movement and folding within cells. Using imaging data as a framework, the model predicted how enhancers and promoters interact during transcriptional bursts.
The simulations revealed that active enhancers and promoters remained in contact for more than twice as long compared to their inactive states. This extended interaction was attributed to changes in the local environment. Accumulation of RNA and proteins during transcription increased viscosity, slowing DNA movement and allowing sustained interactions. When Nanog was inactive, the DNA moved more freely, reducing the likelihood of enhancer-promoter contact.
“The modeling suggests that bursting is stabilized due to these reinforcing loops,” stated Ochiai. “Of course, this is just a simulation. The next step is to prove this mechanism also occurs in cells.”
Publication Details
Hiroaki Ohishi et al., Transcription-coupled changes in genomic region proximities during transcriptional bursting. Sci. Adv.10, eadn0020(2024). DOI: 10.1126/sciadv.adn0020