Stirred, not shaken — Scientists uncover how transcription drives motion within the genome

A team of scientists has discovered surprising connections among gene activity, genome packing, and genome-wide motions, revealing aspects of the genome’s organization that directly affect gene regulation and expression.

The findings, reported in the journal Nature Communications, bolster our understanding of the mechanics behind transcription-dependent motions of single genes—the dysfunction of which may lead to neurological and cardiovascular disorders as well as to cancer.

“The genome is ‘stirred’ by transcription-driven motions of single genes,” explains Alexandra Zidovska, a professor of physics at New York University and the senior author of the study. “Genes move differently, depending on whether they are being read or not, leading to complex, turbulent-like motions of the human genome. Understanding the mechanics behind transcription-dependent motions of single genes in the nucleus might be critical for understanding the human genome in health and disease.”

The human genome consists of two meters (six and a half feet) of DNA, which is packed inside the cell in a nucleus barely 10 micrometers in diameter—or 100,000 times smaller than the length of the genome’s DNA. The DNA molecule encodes information for all cellular processes and functions, with genes serving as units of information. Different genes are read, and their information is processed at different times. When a gene is being read, there is molecular machinery that accesses it and transcribes its information into an mRNA molecule, a process known as transcription. 

It had previously been discovered, by Zidovska and her colleagues, that the genome undergoes a lot of “stirring,” or movement, leading to its reorganization and repositioning in the nucleus. 

However, the origin of these motions is little understood. Scientists have hypothesized that molecular motors fueled by adenosine triphosphate (ATP) molecules, which provide energy for many biological processes, are the drivers. These active motors are thought to apply forces on DNA, which can lead to a motion of DNA and the nucleoplasm—its surrounding fluid. But the larger physical machinations behind it remain elusive.

With this in mind, Zidovska and her colleagues focused on RNA polymerase II—responsible for the transcription and one of the most abundant molecular motors in the cell nucleus. When a gene is active, i.e. actively transcribed, the responsible molecular machinery applies forces on DNA during its processing.

The Nature Communications study investigated how a motion of a single actively transcribed gene affects the motions of the genome around it in live human cells. To do so, the authors employed CRISPR technology to fluorescently label single genes, two-color high-resolution live cell microscopy to visualize motion of these labeled genes, and displacement correlation spectroscopy (DCS) to simultaneously map flows of the genome across the nucleus. The high-resolution imaging data were then processed through a physical and mathematical analysis, uncovering a never-before-seen physical picture of how genes move inside the cell. 

In their study, the researchers initially examined the motions of the genes—when they are inactive—then “switched” these genes on and observed how their motion changes once “active.” At the same time, the authors used DCS to map flows of the surrounding genome, monitoring how the genome flows across the nucleus before and after gene activation.

Overall, the authors found that active genes contribute to the stirring motion of the genome. Through simultaneous mapping of single-gene and genome-wide motions, they reveal that the compaction of the genome affects how the gene is contributing. Specifically, a motion-correlation analysis indicated that a single active gene drives the genome’s motions in low-compaction regions, but a high-compaction genome drives gene motion regardless of its activity state. 

“By revealing these unexpected connections among gene activity, genome compaction, and genome-wide motions, these findings uncover aspects of the genome’s spatiotemporal organization that directly impact gene regulation and expression,” says Zidovska.

The work also adds to our understanding of physics.

“This research provides new insights into the physics of active and living systems,” she observes. “By revealing an emergent behavior of active living systems, such as the human genome, it teaches us new physics.”

The paper’s other authors were Fang-Yi Chu and Alexis S. Clavijo, NYU doctoral students, and Suho Lee, an NYU postdoctoral researcher. 

This research was supported by grants from the National Institutes of Health (R00-GM104152 and R01-GM145924), the National Science Foundation (CAREER PHY-1554880, PHY-2210541, and CMMI-1762506), and a New York University Whitehead Fellowship for Junior Faculty in Biomedical and Biological Sciences.

Video:
This video depicts single gene motion within the surrounding genomic flows (Caption: motion of a single gene (white dot) is marked by its trajectory (colored curve) within the flows of the surrounding genome (arrows). Credit: Image courtesy of Alexandra Zidovska, Department of Physics, NYU).

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