CpGFuse: a holistic approach for accurate identification of methylation states of DNA CpG sites

Anomalous DNA methylation has wide-ranging implications, spanning from neurological disorders to cancer and cardiovascular complications. Current methods for single-cell DNA methylation analysis face limitations in coverage, leading to information loss and hampering our understanding of disease associations. The primary goal of this study is the imputation of CpG site methylation states in a given cell by leveraging the CpG states of other cells of the same type. To address this, we introduce CpGFuse, a novel methodology that combines information from diverse genomic features. Leveraging two benchmark datasets, we employed a careful preprocessing approach and conducted a comprehensive ablation study to assess the individual and collective contributions of DNA sequence, intercellular, and intracellular features. Our proposed model, CpGFuse, employs a convolutional neural network with an attention mechanism, surpassing existing models across HCCs and HepG2 datasets. The results highlight the effectiveness of our approach in enhancing accuracy and providing a robust tool for CpG site prediction in genomics. CpGFuse’s success underscores the importance of integrating multiple genomic features for accurate identification of methylation states of CpG site.