Generative AI to quickly calculate 3D genomic structures

Idea Proposed

Illustration of the procedure followed by ChromoGen when making de novo predictions of chromatin organization using sequence data.

A new approach, which takes minutes rather than days, predicts how a specific DNA sequence will arrange itself in the cell nucleus.

ChromoGen, a generative model based on state-of-the-art artificial intelligence techniques that efficiently predicts three-dimensional, single-cell chromatin conformations de novo with both region and cell type specificity. These generated conformations accurately reproduce experimental results at both the single-cell and population levels.

Moreover, ChromoGen successfully transfers to cell types excluded from the training data using just DNA sequence and widely available DNase-seq data, thus providing access to chromatin structures in myriad cell types.

Implementation

The implementation of this method can be found on this paper.

Made by MIT Chemistry

This method/model is made by MIT Chemists Visit here

The researchers have made all of their data and the model available to others who wish to use it.

The research was funded by the National Institutes of Health.

Sources & citation

Greg Schuette et al. ,ChromoGen: Diffusion model predicts single-cell chromatin conformations.Sci. Adv.11,eadr8265(2025).DOI:10.1126/sciadv.adr8265