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Gene expression is controlled, in part, by the interactions between genes and regulatory elements located along the genome. Those interactions depend on the ability of chromatin — a mix of DNA and proteins — to move around within a crowded space.
In a new study, MIT researchers have measured chromatin movement at timescales ranging from hundreds of microseconds to hours, allowing them to rigorously quantify those dynamics for the first time.
Their analysis revealed that chromatin can exist in two different categories: In one, chromatin moves in a constrained way that allows it to primarily contact only neighboring regions of the genome; in the other, chromatin moves more freely and contacts regions that are farther away, but only over longer timescales.
The findings offer insight into how gene expression is regulated, as well as how chromatin segments come together for other processes such as DNA repair, the researchers say.
“Because we were able to look at chromatin dynamics for the first time at these very fast timescales, and also for the first time across the full dynamic range, we were able to observe chromatin motion over a range that just wasn’t possible before,” says Anders Sejr Hansen, an associate professor of biological engineering at MIT and the senior author of the new study, which appears today in Nature Structural and Molecular Biology.
The paper’s lead authors are MIT postdoc Matteo Mazzocca, Domenic Narducci PhD ’25, and Simon Grosse-Holz PhD ’23. Jessica Matthias, chief commercial officer of Abberior Instruments, and Tatiana Karpova, manager of the National Cancer Institute Optical Microscopy Core, are also authors of the paper.
Constrained movement
In textbooks, chromatin is often depicted as a static structure within the cell nucleus, but in reality, it is constantly moving. Those movements are necessary for genes to interact with DNA regulatory sequences such as enhancers, which can be as far as 1 million base pairs away. They also ensure that when DNA breaks occur, the two ends of DNA can encounter each other to be repaired.
“Chromatin dynamics are foundational to all processes in the nucleus, and especially processes that involve two things finding each other. That’s important in DNA repair, gene regulation, recombination, or moving a particular gene to the right compartment of the nucleus,” Hansen says.
The movement of any particular location on the genome, or locus, is constrained by the fact that DNA is a polymer. After moving in any direction, a locus will be pulled back by the DNA on either side of it.
“Chromosomes are polymers. They’re held together by many nucleotides of DNA. Being part of DNA is a little bit like running while holding hands with other people. If a hundred people are holding hands and you, in the middle of the chain, try to run in one direction, you’ll get pulled back,” Hansen says.
This type of behavior is known as subdiffusive movement. Previous studies have yielded conflicting reports on how subdiffusive chromatin is, mainly because the studies were not able to track the movement over a long enough period of time to obtain statistically robust measurements. Because the movements are so small, on the order of nanometers, data needs to be obtained over long dynamic ranges — from milliseconds to hours.
In those earlier studies, researchers used imaging techniques that can track the position of a single molecule over time by comparing images frame by frame. These are useful but can only be used over a small dynamic range because of the limitations of conventional microscopy.
To generate more statistically robust data, the MIT team used MINFLUX — a super-resolution light microscopy technique that can track the movement of tiny objects such as proteins over longer periods of time. This technique was recently developed by Stefan Hell of the Max Planck Institute, a Nobel laureate for his work in super resolution microscopy. In this study, the MIT team became the first to apply this technique to chromatin in living cells.
“MINFLUX allowed us to get around the limitations of conventional microscopy, letting us measure chromatin movement faster and for a longer period of time than ever before,” Narducci says. “To our knowledge, it’s the first time this technique has been used this way.”
Using MINFLUX, the researchers were able to study cells over timescales that covered four orders of magnitude — from 200 microseconds to 10 seconds. And by combining MINFLUX with two traditional imaging techniques, they could track chromatin movement over seven orders of magnitude across time, from hundreds of microseconds to several hours.
“Region of influence”
These studies, performed across several different mouse and human cell types, allowed the researchers to identify two distinct classes of chromatin dynamics. In both classes, over short and intermediate timescales (up to 200 seconds), any given locus tends to move only within about 200 nanometers. This suggests that the subdiffusive pull is stronger than had been previously thought.
“One of the main takeaways is that you have this region of influence where a genomic locus has access to other genomic loci, and this is roughly a couple hundred nanometers large,” Grosse-Holz says. “If loci are much closer together than a couple hundred nanometers, they’re effectively in contact all the time. You get a cutoff at a couple hundred nanometers where everything within that region around a given locus can see that locus, and everything outside cannot.”
This constant contact is likely beneficial for DNA repair, as the broken strands remain in close proximity to each other. The findings also suggest that for genes and regulatory elements that are within about 100,000 base pairs, they don’t need any extra help to find each other — they will do so routinely through their normal movement.
“If they are closer than 100,000 bases, and most regulatory elements are, then those elements are going to find their target gene within a few milliseconds or a few minutes,” Mazzocca says. “These are timescales that are completely consistent with transcription.”
In the other class of chromatin dynamics that the researchers identified, chromatin is able to move over a wider range, but only at longer timescales (a few minutes to hours). This class of chromatin appeared in some types of cells but not others, for reasons that are not yet understood.
“It would be reasonable to assume that the behavior would be more or less the same in all cell types, but that’s not at all what we found,” Hansen says. “It’s very different in different cell types, with no obvious way of categorizing things.”
He adds that the strength of the subdiffusive pull that the researchers found in this study can’t be explained with existing models that have been developed to study chromatin dynamics — the Rouse model and the fractal globule model. This suggests that the models may need to incorporate factors that were previously left out, such as the interactions between chromatin and the crowded nucleoplasm it sits within.
“These findings are significant for two key reasons,” says Luca Giorgetti, a group leader at the Friedrich Miescher Institute for Biomedical Research in Switzerland, who was not involved in the study. “First, they rigorously confirm longstanding but anecdotal observations that chromatin motion is strongly subdiffusive. Second, they demonstrate that this behavior is consistent across multiple cell types and persists across all measured timescales.”
The research was funded, in part, by the National Institutes of Health, a National Science Foundation CAREER Award, a Pew-Stewart Scholar for Cancer Research Award, and the Bridge Project, a partnership between the Koch Institute for Integrative Cancer Research at MIT and the Dana-Farber/Harvard Cancer Center.
