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The human genome can be compared to a complex ball of yarn, intricately composed of 3 billion molecular units that are sequentially arranged and tightly coiled. Within this structure lie genes—specific DNA segments that are transcribed into proteins, which act as tiny molecular machines within our cells. The three-dimensional configuration of this genetic yarn influences which genes are expressed, and when disruptions occur in this process, diseases can manifest. Until recently, however, scientists struggled to visualize the interactions between different DNA regions across both time and spatial dimensions.
A research team at Stanford University, led by Stanley Qi, an associate professor of bioengineering, and W.E. Moerner, a professor of chemistry, has developed an innovative tool that illuminates any region of the genome in living cells. This groundbreaking advancement allows researchers to observe how different genomic areas communicate dynamically with one another.
This tool, as detailed in a recent publication in the journal Cell, promises to deepen our understanding of gene regulation in both healthy and diseased cells, including cancer. Traditionally, researchers could only capture still images of DNA interactions at specific moments in preserved cells, akin to a series of photographs. The new technology transforms this approach, adding a temporal dimension and enabling real-time observation of genomic changes.
“Our work turns Instagram into YouTube,” remarked Qi. “It provides a direct glimpse into cellular dynamics over time.”
Notably, the focus has shifted to previously dismissed regions of DNA that lie outside the 2% that is known to encode proteins. This 98% of the genome, often labeled as ‘junk DNA’, is now recognized as containing vital elements that play roles in regulating gene expression.
“These regions are akin to the software that drives the DNA program,” Qi explained.
By producing real-time visualizations of these overlooked genomic segments, scientists can gain valuable insights into biological processes. Furthermore, tracking how these regulatory areas evolve in healthy versus diseased cells could uncover mechanisms behind aberrant gene expression linked to various illnesses.
Fluorescent Mailmen
The foundational step in creating this tool involved discovering a method to track specific genomic areas amidst the vast complications of the DNA structure. The researchers utilized a modified version of CRISPR technology.
This adaptation employs an engineered protein known as dCas9, paired with a complementary RNA molecule that directs the complex to a targeted site within the genome. Acting like a mailman, the dCas9-RNA assembly attaches to the designated DNA address, bringing along a fluorescent dye that becomes visible under a microscope.
To amplify their fluorescent signal, the researchers deployed multiple molecular mailmen to the same genomic location, thus illuminating the “street” of any gene under investigation. In standard light microscopy, such activity would appear as a blurry mass due to the tiny scale of DNA movements, which are millions of times smaller than a human hair.
The Qi lab collaborated with Moerner’s team, known for pioneering techniques able to detect light from individual fluorescent molecules, a contribution that earned Moerner the Nobel Prize in Chemistry in 2014.
While super-resolution microscopy has become commonplace, many existing methods still struggle to capture three-dimensional molecular movement simultaneously. Typically, studies highlight lateral movements but miss crucial vertical dynamics. To address this shortcoming, Moerner’s team introduced an optical technique allowing simultaneous measurement of DNA position in three dimensions.
“By incorporating a specialized optical component, we could reconfigure a single light signal into two, enabling depth information to be encoded in the angle between these signals,” Moerner elaborated.
These light signals correspond to the fluorescent mailmen targeting the DNA, with the angle providing essential spatial information that reveals the complete picture of DNA architecture in real time.
Visualizing DNA Movement During Transcription
The team subsequently tested their molecular mailmen to monitor the so-called “software” regions—previously classified as junk DNA—that regulate the transcription process, which precedes protein synthesis. Their findings indicated that during transcription, these regulatory regions remained closer together and exhibited less movement, suggesting they communicate in a coordinated manner. Understanding the specific language of this interaction, its molecular participants, and whether this behavior is consistent across all genes, are avenues for future exploration.
“Transcription is a core biological process, and we now have a nanoscale view that few have previously been able to achieve,” explained Ashwin Balaji, a graduate student in Moerner’s lab.
The tool’s capacity to be administered into living cells enables observation of primary cells—those isolated directly from their tissue of origin—providing insights into physiological processes.
“The ability to visualize different DNA sites in primary cells, such as neurons and immune cells, is particularly exciting as it has not been achieved before,” said Yanyu Zhu, a postdoctoral researcher in Qi’s group.
In the future, this technology may be applied to patient samples, including tumor biopsies, enhancing our understanding of non-coding regulatory DNA regions and their contributions to various diseases.
“We are striving to unlock the mysteries behind the 98% of DNA once labeled as junk,” Qi remarked. “While we no longer consider it ‘junk’ due to its recognized significance, there remains a vast amount of information about its functions that we have yet to uncover, especially regarding its role in diseases.”
To facilitate further research, the Stanford team has made their design and analysis algorithms freely available. This initiative has benefited from collaborative efforts involving a third lab at Stanford led by Andrew Spakowitz, underscoring the power of interdisciplinary cooperation.
“Collaborations like these are incredibly potent as they allow us to achieve far more than any individual group could accomplish,” Moerner stated. “The diverse skills each team brings creates a stimulating and exciting environment for innovation.”
More information:
Yanyu Zhu et al, High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH, Cell (2025). DOI: 10.1016/j.cell.2025.03.032
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Stanford University
Source
phys.org