Fast AI method calculates 3D genomic structures
Feb. 03, 2025.
2 mins. read.
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MIT chemists have found a new way to predict 3D genomic structures using AI, which is much faster than old methods.
Every cell in your body has the same genetic sequence, but only uses some of those genes. This makes brain cells different from skin cells. The three-dimensional structure of the genetic material decides which genes are accessible. MIT chemists have found a new way to predict these 3D structures using artificial intelligence (AI), which is much faster than old methods.
This new technique, called ChromoGen, can predict thousands of structures very quickly. It helps scientists see how the 3D DNA shape affects cell function. “We aim to predict the 3D structure from the DNA sequence,” says research leader Bin Zhang in an MIT press release.
The chemists have described the methods and results of this study in a paper published in Science Advances.
Within the cell’s nucleus, DNA wraps around proteins called histones, forming chromatin. This chromatin has layers of organization, allowing it to fit into a tiny space. Epigenetic modifications, like tags on DNA, influence how chromatin folds and which genes get turned on or off. Standard techniques map these structures by linking nearby DNA pieces, but they are slow.
ChromoGen uses deep learning to read DNA and predict how it might twist and turn in cells. It combines two parts: one reads the DNA, and the other uses AI to simulate the 3D shape based on vast amounts of previous data from experiments
Minutes rather than weeks
The model is fast, predicting structures in minutes rather than weeks. ChromoGen can predict many structures in just 20 minutes using one GPU, a type of computer chip. They tested ChromoGen on over 2,000 DNA sequences and found its predictions matched real data.
ChromoGen can even predict structures in cell types it wasn’t trained on, helping to compare how chromatin differs across cells and what that means for gene activity. It could also explore how DNA mutations change chromatin structure, possibly linking to diseases.
This research opens up new paths for studying cell biology without the slow pace of traditional methods.
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