Some scientists that speak of poking and prodding DNA mean it literally—that is, they are talking about physically nudging chromatin to assess DNA’s physical nature. And they would add, just as literally, that such work demands a light touch.
At Princeton University, scientists have been nudging DNA by using light-inducible biomolecular condensates to generate capillary forces at targeted DNA loci. These condensates are part of a platform called VECTOR, which stands for viscoelastic chromatin tethering and organization.
VECTOR was introduced in the journal Cell, in an article titled, “Condensate interfacial forces reposition DNA loci and probe chromatin viscoelasticity.” According to the Princeton team, VECTOR quantifies capillary forces at the interfaces that form between biomolecular condensates and cellular structures.
“VECTOR can be utilized to programmably reposition genomic loci on a timescale of seconds to minutes, quantitatively revealing local heterogeneity in the viscoelastic material properties of chromatin,” the article’s authors explained. “These synthetic condensates are built from components that naturally form liquid-like structures in living cells, highlighting the potential role for native condensates to generate forces and do work to reorganize the genome and impact chromatin architecture.”
With VECTOR, scientists can, with the flick of a light, rearrange life’s information materials, bending DNA strands back on themselves to reveal the material nature of the genome. For example, VECTOR can be used to determine how much force is required to move parts of a chromosome around and how well it snaps back to its original position. In the current study, VECTOR helped the Princeton team see that chromosome acts like an elastic material in some ways, and like a fluid in others.
“What’s happening here is truly incredible,” said Cliff Brangwynne, PhD, professor of chemical and biological engineering. “Basically we’ve turned droplets into little fingers that pluck on the genomic strings within living cells.”
The key to the new method lies in the researchers’ ability to generate tiny liquid-like droplets within a cell’s nucleus. The droplets form like oil in water and grow larger when exposed to a specific wavelength of blue light. Because the droplets are initiated at a programmable protein—a modified version of the protein used in the gene-editing tool known as CRISPR—they can also attach the droplet to DNA in precise locations, targeting genes of interest.
With their ability to control this process using light, the team found a way to grow two droplets stuck to different sequences, merge the two droplets together, and finally shrink the resulting droplet, pulling the genes together as the droplet recedes. The entire process takes about 10 minutes.
Physically repositioning DNA in this way represents a completely new direction for engineering cells to improve health and could lead to new treatments for disease, according to the researchers. For example, they showed that they could pull two distant genes toward each other until the genes touch. Established theory predicts this could lead to greater control over gene expression or gene regulation.
Since DNA is both a carrier of information and a physical molecule, the cell needs to unfurl the tightly coiled parts of the DNA to copy its information and make proteins. The areas along the genome that are more likely to be expressed are less rigid physically and easier to open up. The areas that are silenced are physically more coiled and compact and therefore harder for the cell to open up and read. Like an instruction manual that opens more easily to some pages than others.
The research team, including postdoctoral scholar Amy R. Strom, PhD, and recently graduated PhD student Yoonji Kim, opted to use blobs of liquid known as condensates to do the work of bending the DNA strands and moving them around. Although some cellular components are like soap bubbles, with a distinct membrane keeping the insides separated from the outside, condensates are liquid-like droplets that fuse together more like raindrops, with no membrane holding them together. After forming and carrying out a cellular function, they can break apart and disperse again.
To study chromatin in more detail, Strom and Kim (the Cell paper’s lead authors) built upon previous research from the Brangwynne lab that engineered condensates from biological molecules in the cell using laser light to create and fuse droplets together. In this new work, they utilized an additional component that attaches the condensate to specific locations on the DNA strands and directs their movement quickly and precisely via surface tension-mediated forces also known as capillary forces, which Princeton researchers had suggested could be ubiquitous in living cells. Previously, moving DNA like this relied on random interactions over a period of hours or even days.
“We haven’t been able to have this precise control over nuclear organization on such quick timescales before,” Brangwynne said.
Now that they can move the strands around in this controlled way, they can start to look at whether the genes in their new positions are expressed differently. This is potentially important for furthering our understanding of the physical mechanisms and material science of gene expression.
Strom said that scientists have looked at the stiffness of the nucleus by poking at it from the outside and taking a measurement of the whole nucleus. Scientists can also look at one gene and see if it is turned on or off. But the space in between is not well understood.
“We can use this technology to build a map of what’s going on in there and better understand when things are disorganized like in cancer,” Strom noted.
This new tool is poised to help researchers understand gene expression better, but it is not intended to edit the DNA. “Our tool does not actually cleave the DNA sequences like CRISPR does,” Kim remarked.
“CRISPR is really good for diseases that are related to the need to cut and actually change the DNA sequence,” Strom pointed out. This technology could work for a different class of diseases, especially those related to protein imbalances such as cancer. “If we can control the amount of expression by repositioning the gene,” Strom suggested, “there is a potential future for something like our tool.”
