Researchers say a faulty gene copy can make the heart’s DNA fold wrong way

Washington DC [US], August 13 (ANI): Researchers have discovered that a gene linked to congenital heart disease acts like an architect for the heart cell's DNA. Losing just one copy of TBX5 can cause the genome's carefully folded 3D structure to unravel, disrupting the 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 could also play a role in other birth defects.
According to the Science Daily website, Congenital heart disease is the most common birth defect, affecting about 1 in 100 babies born each year. The condition can have many causes, including changes involving TBX5, a gene that plays a critical role in building the heart. In some cases, a child has only one working copy of TBX5 rather than two healthy copies inherited from the parents.
For years, researchers have been trying to understand why losing the function of just one copy can have such a major effect on heart development, even when the second copy still works.
Researchers at Gladstone Institutes now report that TBX5 has another important role beyond controlling gene activity. It helps organise DNA into the physical three-dimensional structure that heart cells need to work properly. In a new study published in Science, the scientists found that losing even one copy of TBX5 can disrupt this organisation, changing how many other genes are used inside heart cells.
The findings offer a new way to think about a long-standing question in genetics: why losing one copy of certain genes, a condition called haploinsufficiency, can cause severe problems during development.
"TBX5 is just one example of a broader class of genes that cause birth defects when only one copy is lost," says Benoit Bruneau, PhD, director of the Gladstone Institute of Cardiovascular Disease and a senior author of the study. "What's exciting about our findings is they suggest many different birth defects might happen for the same reason: the cell's 3D instruction manual simply gets folded the wrong way."
"We developed and used different computational models to analyze results from thousands of individual cells," says Katie Pollard, PhD, director of the Gladstone Institute of Data Science and Biotechnology and the other senior author of the study. "That allowed us to finally see how losing this one protein causes the heart's DNA structure to break down on every level."
How DNA Folding Helps Cells Work
Packing DNA into a cell is a remarkable feat. It is similar to squeezing a miles-long instruction manual into the head of a pin. But DNA is not packed randomly. 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 compartments (like separate binders of the manual), domains (like paragraphs), and chromatin loops (like folding a page so two distant sentences touch). These loops allow distant genetic switches called enhancers to make physical contact with specific genes. Those contacts help cells activate the instructions they need.
Scientists already knew that TBX5 is one of the major regulators of heart development. The protein helps activate many of the genes required for heart cells to develop and function. Earlier work from Bruneau's lab showed that losing one copy of TBX5 affects the levels of hundreds of other heart-specific genes. What remained unclear was exactly how that happened.
The researchers therefore set out to determine whether the physical folding of DNA influences how heart cells behave, and whether TBX5 helps control that process.
Mapping the Heart's 3D Genome
To investigate, the team combined several advanced methods that allowed them to examine how individual cells respond to different amounts of TBX5. They guided human stem cells into becoming 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 DNA loops at extremely fine detail.
Because the experiment produced millions of data points from thousands of individual cells, the researchers relied on computational models to analyse the enormous datasets.
"Using the custom computational approaches we developed, we were able to see for the first time how the loss of TBX5 triggers the total collapse of the heart's 3D DNA organisation," says Shuzhen Kuang, PhD, a first author of the study and former bioinformatics fellow in Pollard's lab as quoted by Science Daily website.
"Surprisingly, we discovered this collapse happens at every level of genome organisation -- compartments, domains, and chromatin loops."
TBX5 Acts as an Architect for Heart DNA
As healthy stem cells developed into heart muscle cells, the researchers saw major changes in the organization of the genome. Large sections of DNA switched between active and inactive states as the cells matured.
TBX5 emerged as a central organiser of these structural changes.
The researchers found that TBX5 works like a GPS for a molecular motor called cohesin. TBX5 helps direct cohesin to the correct locations on DNA, where it creates chromatin loops that bring genes together with their enhancers.

When TBX5 levels fall too low, these loops do not form properly. DNA becomes incorrectly folded, and important genes involved in heart development may fail to switch on when they are needed.
"What was striking was how the amount of TBX5 matters immensely," says Zoe Grant, PhD, a first author of the study and a postdoctoral researcher in Bruneau's lab. "The more TBX5 you removed, the worse the disruption across every level of genome organisation we looked at."
The results showed that reducing TBX5 to half its normal amount is enough to disrupt DNA folding and directly contribute to heart defects.
The researchers also discovered that individual heart cells do not all respond in exactly the same way to the loss of TBX5. Clear differences appeared between two major types of heart cells, atrial and ventricular cells. Variation was also seen among individual cells of the same type.
"This could help explain why people with the same mutation can have different heart defects," Grant says.
A Broader Mechanism for Developmental Disease
Although the findings provide new insight into congenital heart disease, the researchers believe the same basic mechanism could be involved in other developmental disorders.
"We believe we've uncovered a new mechanism of disease," says Bruneau. "We showed that even a small decrease in a single protein can cause the DNA blueprint to fold incorrectly and lead to disease. So, many birth defects currently attributed to genetic mutations may actually be caused by the 3D misfolding of DNA."
The findings suggest that some 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 organising the genome during early heart development. The researchers also want to learn whether other proteins associated with birth defects shape DNA in similar ways. (ANI)