Researchers have discovered that a gene linked to congenital heart disease acts as an engineer of the heart cell’s DNA. Losing just one copy of TBX5 can disintegrate the genome’s carefully folded 3D structure, disabling genes needed to build a healthy heart.
The effects can vary from cell to cell, which may help explain why people with the same mutation develop different heart defects. The same hidden mechanism can also play a role in other birth defects.
According to Science Daily, congenital heart disease is the most common birth defect, affecting about 1 in 100 babies born each year. This condition can have many causes, including changes involving TBX5, a gene that plays a crucial role in building the heart. In some cases, a child will have only one working copy of TBX5 instead of two healthy copies inherited from the parents.
For many years, researchers have been trying to understand why loss of function of just one copy can have such a significant impact on heart development, even when the second copy is still working.
Researchers at the Gladstone Institutes now report that TBX5 has another important role beyond controlling gene activity. It helps organize DNA into the three-dimensional physical structure that heart cells need to function properly. In a new study published in the journal Science, scientists found that losing a single copy of TBX5 can disrupt this regulation, changing the number of other genes used within heart cells.
The findings offer a new way to think about a long-standing question in genetics: why missing one copy of certain genes, a condition called haploinsufficiency, can cause serious problems during development.
“TBX5 is just one example of a broader class of genes that cause birth defects when just one copy is missing,” says Benoit Bruno, MD, director of the Gladstone Cardiovascular Institute and one of the study’s senior authors. “What’s exciting about our findings is that they suggest that many different birth defects may occur for the same reason: the cell’s 3D instruction manual is simply folded the wrong way.”
“We developed and used different computational models to analyze results from thousands of individual cells,” says Katie Pollard, director of the Gladstone Institute for Data Science and Biotechnology and the study’s other lead author. “This allowed us to finally see how loss of this protein leads to the collapse of the heart’s DNA structure at every level.”
How does DNA folding help cells function?
Packaging DNA into a cell is a remarkable achievement. It’s like pressing a miles-long instruction manual into the head of a pin. But DNA is not randomly packaged. Each type of cell folds its genetic material into a distinct three-dimensional arrangement, allowing a heart cell to access a different set of instructions than a brain cell.
This 3D structure is arranged in multiple layers. It includes large parts (such as separate volumes of evidence), domains (such as paragraphs), and chromatin loops (such as folding a page so that two far apart sentences touch). These loops allow distant genetic switches called enhancers to make physical contact with specific genes. These contacts help cells activate the instructions they need.
Scientists already knew that TBX5 is one of the master regulators of heart development. The protein helps activate many genes necessary for the development and function of heart cells. Previous work in Bruno’s lab showed that loss of one copy of TBX5 affects the levels of hundreds of other heart-specific genes. What remains unclear is how exactly this happened.
So the researchers set out to determine whether physical folding of DNA affects how heart cells behave, and whether TBX5 helps control this process.
Mapping the 3D genome of the heart
To investigate this, the team combined several advanced methods that allowed them to examine how individual cells responded to different amounts of TBX5. They directed human stem cells to become heart muscle cells. Some cells were healthy, some lacked one copy of TBX5, and others lacked both copies.
The scientists then used high-resolution 3D mapping to examine the DNA loops in extremely fine detail.
Because the experiment produced millions of data points from thousands of individual cells, the researchers relied on computational models to analyze the massive data sets.
“Using custom computational methods we developed, we were able to see for the first time how loss of TBX5 leads to the complete collapse of the heart’s 3D DNA organization,” says Xuzhen Kuang, Ph.D., first author of the study and a former bioinformatics fellow in the Pollard lab, as reported by Science Daily.
“Surprisingly, we discovered that this breakdown occurs at every level of genome organization — segments, domains, and chromatin loops.”
TBX5 acts as an engineer of the heart’s DNA
As healthy stem cells developed into heart muscle cells, researchers saw major changes in genome organization. Large portions of DNA switch between active and inactive states as cells mature.
TBX5 has emerged as a central regulator of these structural changes.
The researchers found that TBX5 acts like a GPS for a molecular motor called cohesin. TBX5 helps direct cohesin to the correct locations on DNA, creating chromatin loops that bring genes together with their enhancers.
When TBX5 levels drop too low, these rings do not form properly. DNA becomes incorrectly folded, and important genes involved in heart development may fail to work when they are needed.
“What’s amazing is how dramatically the amount of TBX5 matters,” says Zoe Grant, Ph.D., first author of the study and a postdoctoral researcher in Bruno’s lab. “The more TBX5 you removed, the greater the disruption across every level of genome organization we looked at.”
The results showed that reducing TBX5 to half its normal amount is enough to disrupt DNA folding and directly contribute to the occurrence of heart defects.
The researchers also discovered that individual heart cells do not all respond in exactly the same way to loss of TBX5. Clear differences have emerged between the two main types of heart cells, atrial and ventricular cells. Variation is also observed between individual cells of the same type.
“This may help explain why people with the same mutation develop different heart defects,” Grant says.
Broader mechanism of developmental disease
Although the findings provide new insight into congenital heart disease, researchers believe the same basic mechanism could be involved in other developmental disorders.
“We think we have discovered a new mechanism for the disease,” Bruno says. “We have shown that even a slight deficiency in a single protein can cause the DNA blueprint to fold incorrectly and lead to disease. Therefore, many birth defects currently attributed to genetic mutations may actually be caused by three-dimensional misfolding of DNA.”
The findings suggest that certain genetic mutations may cause disease not only by changing individual genetic instructions, but also by disturbing the physical arrangement of the genome itself.
Next, the team plans to determine when TBX5 first begins regulating the genome during early heart development. The researchers also want to know whether other proteins associated with birth defects shape DNA in similar ways.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)
