When a gene turns on, it creates structural ripples along DNA that can activate or suppress neighboring genes, MIT researchers find.
Image Credit: Scientific Frontline
Scientific Frontline: Extended "At a Glance" Summary: Gene Syntax and DNA Folding
The Core Concept: When a gene is transcribed, it creates physical ripples along the DNA strand that can either activate or suppress neighboring genes. The physical ordering and arrangement of these genes, known as "gene syntax," directly dictates how their structural interactions couple their expression.
Key Distinction/Mechanism: While traditional synthetic gene circuits rely primarily on biochemical components (like repressor or activator molecules) to control output, this approach utilizes the biophysical manipulation of the DNA polymer itself. Transcription unwinds the DNA helix, making the strand looser upstream (easier for RNA polymerase to attach) and more tightly wound downstream (forming twisted structures called plectonemes that hinder binding).
Origin/History: The foundational concept was proposed through computational modeling in 2022 by MIT researchers Katie Galloway and Christopher Johnstone. In April 2026, the team published a breakthrough study in Science confirming these predicted phenomena in human cells.
Major Frameworks/Components:
- Tandem Arrangement: One gene sequentially follows another; turning on the upstream gene suppresses the downstream gene due to tight DNA winding.
- Divergent Arrangement: Neighboring genes are transcribed in opposite directions, which synergistically amplifies the expression of both genes.
- Convergent Arrangement: Neighboring genes are transcribed toward one another, which can be utilized for alternating pulses.
- Supercoiling-Mediated Feedback: The physical tangling (plectonemes) up to 2,000 base pairs away that mechanically limits or boosts enzyme access to the genetic code.
- STRAIGHT-IN Dual System: A novel genome engineering tool developed with Leiden University Medical Center to efficiently insert dual-gene circuits into the exact same DNA strand.
Branch of Science: Synthetic Biology, Biophysics, Genetics, and Chemical Engineering.
Future Application: The framework will be used to design advanced dynamic synthetic circuits—like toggle switches, cellular oscillators, and pulse generators. Real-world applications include maximizing the production of therapeutic antibodies (such as those for yellow fever), optimizing gene therapies, and precisely reprogramming adult cells into new tissue types.
Why It Matters: Understanding gene syntax adds a crucial physical dimension to genetic engineering. It allows scientists to seamlessly program dynamic behaviors and maximize or alternate outputs without relying solely on complex biochemical additions, fundamentally changing how synthetic biology circuits are built.
When a gene is turned on in a cell, it creates a ripple effect along the DNA strand, changing the physical structure of the strand. A new study by MIT researchers shows that these ripples can stimulate or suppress neighboring genes.
These effects, which result from the winding or unwinding of neighboring DNA, are determined by the order of genes along a strand of DNA. Genes upstream of the active gene are usually turned up, while those downstream are inhibited.
The new findings offer guidance that could make it easier to control the output of synthetic gene circuits. By altering the relative ordering and arrangement of genes, or “gene syntax,” researchers could create circuits that synergize to maximize their output, or that alternate the output of two different genes.
“This is really exciting because we can coordinate gene expression in ways that just weren’t possible before,” says Katie Galloway, an assistant professor of chemical engineering at MIT. “Syntax will be really useful for dynamic circuits. Now we have the ability to select not only the biochemistry of circuits, but also the physical design to support dynamics.”
Galloway is the senior author of the study, which appears today in Science. MIT postdoc Christopher Johnstone PhD ’26 is the paper’s lead author. Other authors include MIT graduate student Kasey Love, members of the lab of Brandon DeKosky, an MIT associate professor of chemical engineering, and researchers from Peter Zandsta’s lab at the University of British Columbia and the labs of Christine Mummery and Richard Davis at Leiden University Medical Center in the Netherlands.
Gene syntax
When a gene is copied into messenger RNA, or “transcribed,” the double-stranded DNA helix must be unwound so that an enzyme called RNA polymerase can access the DNA and start copying it. That unwinding leads to physical changes in the structure of DNA strand.
Upstream of the gene, DNA becomes looser, while downstream, it becomes more tightly wound. These changes affect RNA polymerase’s ability to access the DNA: Upstream of an active gene, it’s easier for the enzyme to attach; downstream, it’s more difficult.
In a study published in 2022, Galloway and Johnstone performed computational modeling that explored how these biophysical changes might influence gene expression. They studied three different arrangements, or types of syntax: tandem, divergent, and convergent.
Most synthetic gene circuits are designed in a tandem arrangement, with one gene followed by another downstream. In a divergent arrangement, neighboring genes are transcribed in opposite directions (away from each other), and in convergent syntax, they are transcribed toward each other.
The modeling suggested that the divergent arrangement was most likely to produce circuits where both genes are expressed at a high level. Tandem arrangements were predicted to result in the downstream gene being suppressed by the upstream gene.In the new study, the researchers wanted to see if they could observe these predicted phenomena in human cells.
“Normally, we think about gene circuits and pieces of DNA as these lines that we draw, but they’re polymers that have physical characteristics,” Galloway says. “The thing that we were trying to solve in this paper was: When you put two genes on the same piece of DNA, how does their physical interaction become coupled?”
The researchers engineered circuits that each contained two genes, in either a tandem, divergent, or convergent configuration, into human cell lines and human induced pluripotent stem cells.
The results confirmed what their modeling had predicted: In divergent circuits, expression of both genes was amplified. In tandem circuits, turning on the upstream gene suppressed the expression of the downstream gene.
These effects produced as much as a 25-fold increase or decrease in gene expression, and they could be seen at distances of up to 2,000 base pairs between genes.
Using a high-resolution genome mapping technique called Region Capture Micro-C, the researchers were also able to analyze how the DNA structure changed when nearby genes were being transcribed.
As predicted, they found that the DNA regions downstream from an active gene formed tightly twisted structures known as plectonemes, similar to the tangles seen in a twisted telephone cord. These structures make it harder for RNA polymerase to bind to DNA.
To engineer these cells, the researchers used a new system they developed with the LUMC team called STRAIGHT-IN Dual, which allows them to efficiently insert two genes into the same DNA strand at both alleles. This system is being reported in a second paper published today, in Nature Biomedical Engineering.
Precise control
The new findings could help guide the design of synthetic gene circuits, which are usually designed to be controlled by biochemical interactions with activator or repressor molecules. Now, circuit designers can also perform biophysical manipulations to enhance or repress genes expression.
“Everyone thinks about the components they need, and the biochemical properties they need to build a circuit,” Galloway says. “Now, we have added the physical construction of those components, which is going to change how those biochemical units are interpreted.”
As a demonstration of one potential application, the researchers built synthetic circuits containing the genes for two segments of a novel antibody discovered by the Dekosky lab, used to treat yellow fever, and incorporated them into human cells. As they expected, the divergent syntax produced larger quantities of the yellow fever antibody.
Galloway’s lab has also used this approach to optimize the output of synthetic gene circuits they previously reported that could be used to deliver gene therapy or to reprogram adult cells into other cell types.
This strategy could also be used to build a variety of other types of dynamic synthetic circuits, such as toggle switches, oscillators, or pulse generators, for any application that requires precise control over gene expression.
“If you want coordinated expression, a divergent circuit is great. If you want something that’s either/or, you can imagine using a convergent or tandem circuit, so when one turns on, the other turns off, and you can alternate pulses,” Galloway says. “Now that we understand the syntax, I think this will pave the way for us to program dynamic behaviors.”
Funding: The research was funded, in part, by the National Institutes of Health, the National Institute for General Medical Sciences, a National Science Foundation CAREER Award, the Pershing Square Foundation, the Air Force Research Laboratory, and the Koch Institute Support (core) Grant from the National Cancer Institute.
Published in journal:
- Science
- Nature Biomedical Engineering
Title:
- Gene syntax defines supercoiling-mediated transcriptional feedback
- STRAIGHT-IN Dual: a platform for dual single-copy integrations of DNA payloads and gene circuits into human induced pluripotent stem cells
Authors:
- Christopher P. Johnstone, Kasey S. Love, Sneha R. Kabaria, Ross D. Jones, Albert Blanch-Asensio, Deon S. Ploessl, Emma L. Peterman, Rachel Lee, Jiyoung Yun, Conrad G. Oakes, Christine L. Mummery, Richard P. Davis, Brandon J. Dekosky, Peter W. Zandstra, Kate E. Galloway
- Albert Blanch-Asensio, Deon S. Ploessl, Benjamin B. Johnson, Sara Cascione, Myrthe R. M. Berndsen, Nathan B. Wang, Valeria V. Orlova, Anna Alemany, Christine L. Mummery, Kate E. Galloway & Richard P. Davis
Source/Credit: Massachusetts Institute of Technology | Anne Trafton
Reference Number: sybi043026_01