Scientists at Case Western Reserve University have developed advanced tools to better understand the 3D structure of DNA, offering new hope for genetic research.
Researchers at Case Western Reserve University have developed advanced tools to better understand the 3D structure of DNA.
DNA isn’t just a sequence of genetic code; it’s a complex, three-dimensional structure intricately folded within each cell. Therefore, the methods for studying DNA must be equally sophisticated, capable of deciphering not only the genetic code but also its spatial arrangement.
The researchers compared various computational tools used to study how DNA folds and interacts within human and mouse cells, potentially unlocking a deeper understanding of genetic instructions under different conditions.
Their findings, published in the journal Nature Communications, could lead to advancements in understanding disease development and cellular transformation.
“The 3D structure of DNA affects how genes interact with each other, just like the layout of a house affects how people move through it,” Fulai Jin, a professor in the Department of Genetics and Genome Sciences at the Case Western School of Medicine, said in a news release. “Understanding this structure is crucial for figuring out how diseases develop and how we might treat them.”
A major challenge the team addressed was the inconsistency in results produced by existing DNA analysis tools. Jin likened it to having multiple translators who cannot agree on the meaning of a foreign text.
Joining Jin in this groundbreaking research were Jing Li, the Arthur L. Parker Professor in the Department of Computer and Data Sciences at the Case School of Engineering, and Yan Li, an associate professor and vice chair of research in the genetics and genome sciences department.
The team rigorously tested 13 software tools on 10 datasets from mice and humans, concluding that different tools are better suited for different types of data.
They also found that preprocessing data intelligently can significantly improve the outcomes. Notably, artificial intelligence programs excelled in handling lower-quality and complex datasets.
“We’re essentially helping scientists find or build better microscopes to see how DNA works inside individual cells,” Jin added. “This could lead to a better understanding of genetic diseases and potentially new treatment strategies.”
This innovation could provide insights into which genes are activated or deactivated in diseased cells, elucidate why certain treatments are effective for some patients but not others, and track cellular changes during early development.
Further, the researchers developed a software package that allows other scientists to identify the most effective method for analyzing their specific research needs — much like how a GPS app finds the best route for your journey.
“Instead of researchers having to guess which tool might work best, our software can test multiple approaches and recommend the optimal one,” added Jin.
These sophisticated tools are freely accessible globally through GitHub, an open-source platform. This broad availability promises to accelerate discoveries across various fields of biomedical research, according to Jin.
“This is a significant step toward making sense of the massive genetic data from modern sequencing — and toward understanding how our genetic blueprint truly works,” Jin concluded.
Source: Case Western Reserve University