Unlocking the Secrets of the 3D Genome
From Sequence to Structure
Every cell in your body has the same genetic sequence, yet each cell expresses only a subset of those genes. This is because of the three-dimensional structure of the genetic material, which controls the accessibility of each gene. MIT researchers have now developed a new way to determine those 3D genome structures using generative artificial intelligence.
How it Works
The researchers used a deep learning model to analyze the information encoded in the underlying DNA sequence and chromatin accessibility data. The model was trained on more than 11 million chromatin conformations generated from experiments using a variant of Hi-C on 16 cells from a line of human B lymphocytes.
Rapid Analysis
The model can generate predictions on a much faster timescale than experimental techniques. "Whereas you might spend six months running experiments to get a few dozen structures in a given cell type, you can generate a thousand structures in a particular region with our model in 20 minutes on just one GPU," said Greg Schuette, a graduate student and lead author of the paper.
Accuracy and Applications
The researchers found that the model can make accurate predictions for data from cell types other than the one it was trained on. This suggests that the model could be useful for analyzing how chromatin structures differ between cell types and how those differences affect their function.
Conclusion
The development of ChromoGen, a generative AI model, has revolutionized the field of 3D genome structure prediction. This technology has the potential to transform our understanding of how the 3D organization of the genome affects individual cells’ gene expression patterns and functions. With its ability to generate accurate predictions in just minutes, ChromoGen is set to accelerate research in this field and uncover new insights into the mysteries of the 3D genome.
FAQs
- What is the 3D genome structure?
The 3D genome structure refers to the complex, three-dimensional organization of the genetic material in the cell’s nucleus. - How does the 3D genome structure affect gene expression?
The 3D genome structure controls the accessibility of each gene, determining which genes are expressed in different cell types or at different times within a given cell. - What is ChromoGen?
ChromoGen is a generative AI model developed by MIT researchers to predict 3D genome structures from DNA sequences. - How does ChromoGen work?
ChromoGen uses a deep learning model to analyze the information encoded in the underlying DNA sequence and chromatin accessibility data, and then generates a range of possible 3D structures for each sequence. - What are the potential applications of ChromoGen?
ChromoGen could be used to study how chromatin structures differ between cell types, how those differences affect their function, and how mutations in a particular DNA sequence change the chromatin conformation, which could shed light on how such mutations may cause disease.
