

Researchers recently created a transformer-based foundation model for the DNA methylome called MethylGPT, which was uploaded to the bioRxiv preprint* service.
Through methyl-binding proteins and modifications to chromatin accessibility, DNA methylation is a form of epigenetic alteration that controls gene expression. Through the inhibition of transposable elements, it also contributes to genomic stability. Studies have shown that different methylation signatures across disease states enable molecular diagnoses, and DNA methylation possesses characteristics of an excellent biomarker.
However, various analytic problems prevent the application of DNA methylation-based diagnostics. Current methods rely on simple statistical and linear models, which are insufficient for collecting complicated, non-linear data. They also do not take into consideration context-specific effects like higher-order interactions or regulatory networks. As a result, a unified analytical framework capable of modeling complicated, nonlinear patterns in a variety of tissues and cell types is urgently required.
Recent breakthroughs in foundation models and transformer structures have transformed the analysis of complex biological sequences. Foundation models have also been developed for several omics layers, including AlphaFold3 and ESM-3 for proteomics and Evo and Enformer for genomics. The success of the foundation models suggests that DNA methylation analyses could be altered using a similar technique.
The study and findings
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