One faulty gene copy can make the heart’s DNA fold the wrong way

Congenital heart disease, the most common birth defect, impacts roughly one in every 100 infants. This condition can stem from various causes, including alterations related to TBX5, a gene essential for heart development. In certain instances, children possess only one functional TBX5 gene copy, inherited from their parents. For years, researchers have sought to comprehend why the absence of just one TBX5 copy can significantly impact heart development, even when the second copy remains functional.

Scientists at the Gladstone Institutes have recently discovered that TBX5 plays an additional role beyond regulating gene activity. This gene aids in organizing DNA into a three-dimensional structure vital for heart cells' proper functioning. A study published in Science reveals that losing one copy of TB5 can disrupt this organization, affecting the activation of other genes within heart cells.

This discovery offers a fresh perspective on a longstanding question in genetics: why losing one copy of specific genes, a phenomenon known as haploinsufficiency, can lead to severe developmental issues. Benoit Bruneau, PhD, director of the Gladstone Institute of Cardiovascular Disease and a senior author, explains that their findings suggest many birth defects may result from the same reason: the cell's DNA instruction manual being folded incorrectly.

Katie Pollard, PhD, director of the Gladstone Institute of Data Science and Biotechnology and another senior author, adds that their research utilized various computational models to analyze data from thousands of individual cells, enabling them to observe how losing this single protein impacts the heart's DNA structure at multiple levels.

DNA packaging into cells is a complex process, akin to compressing a miles-long instruction manual into a pinhead. However, DNA is not packed randomly; it folds into distinct three-dimensional structures, allowing heart cells to access different sets of instructions than brain cells. This three-dimensional arrangement involves large compartments, domains, and chromatin loops, which enable distant genetic switches called enhancers to interact with specific genes, facilitating cell activation of necessary instructions.

TBX5, a major regulator of heart development, helps activate numerous genes required for heart cell development and function. Earlier studies showed that losing one copy of TBX5 affects the levels of hundreds of heart-specific genes. The researchers aimed to determine whether the physical folding of DNA influences heart cell behavior and whether TBX5 controls this process.

By combining advanced methods to examine how individual cells respond to varying TBX5 levels, they guided human stem cells into becoming heart muscle cells, some healthy, some with one copy of TBX5 missing, and others with both copies absent. They then used high-resolution 3D mapping to examine DNA loops at a fine level of detail.

The experiment yielded millions of data points from thousands of individual cells, necessitating the use of computational models to analyze the vast datasets. The researchers discovered that TBX5 acts like a GPS for a molecular motor called cohesin, directing it to the correct locations on DNA to form chromatin loops that bring genes together with their enhancers.

When TBX5 levels fall too low, these loops fail to form correctly, causing DNA to fold incorrectly, and critical heart development genes may fail to activate. The study found that even a reduction to half of TBX5's normal amount can disrupt DNA folding and contribute to heart defects. Additionally, they observed that not all heart cells respond identically to TBX5 loss, with clear differences between atrial and ventricular cells and among individual cells of the same type.

This variation may help explain why individuals with the same genetic mutation can exhibit different heart defects. Bruneau notes that their findings provide new insight into congenital heart disease and suggest that the same mechanism could be involved in other developmental disorders.