real-time organization of DNA

June 30, 2023

(Nanowerk News) Doing cutting-edge science requires thinking outside the box and bringing together multiple disciplines. Sometimes this even means being in the right place at the right time. For David Brückner, postdoctoral researcher and NOMIS fellow at ISTA, all of the above came into play when he attended a lecture on campus by Professor Thomas Gregor of Princeton University. Inspired by the talk, Brückner reached out with an idea: to physically interpret the specific data set that Gregor presented.

Now, the results of their collaboration are published in Science (“Stochastic motion and transcription dynamics of distal DNA locus pairs in condensed chromosomes”). They highlighted the stochastic (random) movement of two specific gene elements on a chromosome, which must touch for the gene to become active in 3D space. Physical proximity is necessary for gene activity. Video shows 3 nuclei (black circle with green border). Target genes are not activated in the upper and lower nuclei, as a clear physical separation between enhancer (blue dots) and promoter (green dots) is observed. In the nuclei of the intervening cells, the target genes are active (red dots), because the blue and green spots overlap. (Image: Hongtao Chen, Princeton University)

How does DNA get into the cell nucleus

Living organisms like humans are built on genes stored in DNA—our molecular blueprint. DNA is a polymer, a large molecule made of smaller individual parts (monomers). It is located in the nucleus of every cell. “Depending on the organism, DNA polymers can be several meters long, but the size of the nucleus is on the order of microns,” explained Brückner. To fit into a small nucleus, DNA is condensed by being rolled up as if on a reel and then compressed into the well-known shape of chromosomes, which we all encounter in biology textbooks.

“Despite being very dense, chromosomes are not static; they wiggle all the time,” the physicist continued. This dynamic is very important. Every time a particular gene has to be activated, two regions on the polymer called the “enhancer” and the “promoter” have to come into contact and bind with each other. Only when this happens do cellular machinery read out gene information and form RNA molecules, which eventually give rise to proteins that are essential for all the processes a living organism needs.

Depending on the organism, enhancer and promoter can be very far from each other on the chromosome. “With the method used before, you can get a static view of the spacing between these elements, but not how the system evolves over time,” explained Brückner. Intrigued by this missing information, scientists set out to dynamically see how these elements are arranged and how they move in 3D space in real time.

Visualizing gene regions

To achieve this goal, experimental scientists from Princeton devised a method to track these two DNA elements over a period of time in a fly embryo. Through genetic manipulation, DNA elements are labeled fluorescently, with enhancer regions glowing green and promoters blue. Using direct imaging (live-cell time-lapse microscopy), scientists can visualize fluorescent spots in fly embryos to see how they move to find one another.

Once the two dots are close together, the gene is activated and an additional red light is turned on because the RNA is also tagged with a red fluorophore. Brückner excitedly added, “We get a visual readout when the enhancer and promoter make contact. That gives us a lot of information about their trajectory. A look into the nucleus of a fly embryo A look into the nucleus of a fly embryo. The enhancer (blue) and promoter (green) must be in physical proximity for gene activity (red) to occur. Tracking the movement of these elements in real-time reveals that the DNA is tightly packed and therefore close together, but exhibits rapid movement, allowing the elements to come into contact quickly. (Image: David Brückner, ISTA)

DNA is dense and shows fast movement

The challenge then is how to analyze this very large stochastic motion data set. His background in theoretical physics allowed Brückner to extract statistics to understand the typical behavior of systems. He applied two simplified and different physical models to slice the data.

One of them is the Rouse model. It is assumed that each polymer monomer is an elastic spring. This predicts a loose structure and fast diffusion — random motion, where the occasional gene regions bump into one another. Another model is called a “fractal globule”. This predicts a very compact structure and therefore slow diffusion. “Surprisingly, we found in the data that the system is described by a combination of these two models — the very dense structure that you would expect from the fractal globule model, and the diffusion described by statistics from the Rouse model,” Brückner explains.

Due to the combination of dense packing and fast movement, the binding of these two gene regions is much less dependent on their distance along the chromosome than previously thought. “If such a system is always in a fluid and dynamic state, long-distance communication is much better than we think,” added Brückner.

This study brings together the worlds of biology and physics. For physicists, this is exciting, because scientists test the dynamics of complex biological systems with long-standing physical theories; and for biologists, it provides insight into chromosome characteristics, which might help understand gene interactions and gene activation in greater detail.

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