Exploring the shape of DNA? This tool makes it easier
Los Alamos web browser helps scientists see chromatin structures in many dimensions
DNA is a shapeshifter. Although we often encounter images of DNA as a double helix, or wrapped up as chromosomes ready for mitosis, DNA is not static. To help Los Alamos National Laboratory study the mechanisms of how DNA changes shape as an early signature of biothreats, scientists developed a tool they call 4D Genome Workflow and Browser.
Their paper in BMC Bioinformatics explains how it’s now easier for any scientist to visualize DNA data in 3D and 4D for improved biological interpretation.
Why this matters: DNA winds around proteins to form chromatin, which has distinctive shapes, including chromosomes. Scientists have assumed that chromatin is a spaghetti-like jumble of double helix and proteins; recently, they have determined that the spaghetti has architecture that moves, on demand, to unwind or rebound specific sections, exposing genes that need to be expressed or repressed.
- Environmental changes can impact gene expression through a process called epigenetics.
- Emerging evidence suggests that epigenetic regulation is closely linked to 3D chromatin structure, and that changes over time (4D) to drive key biological processes in development, disease and environmental response.
What they did: Using unique algorithms and experiments, the Los Alamos team gathered data on interactions between pieces of chromatin and combined it with a physics modeling framework to transform and filter the data to generate 3D and 4D visualizations.
- They developed a user-friendly workflow and web browser to help other scientists visualize chromatin structures for their own research and data sharing.
Funding: Laboratory Directed Research and Development, the National Science Foundation, and the U.S. Department of Energy, Office of Science, through the Biological and Environmental Research program.
LA-UR-26-21283
