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Tangqi Fang, Xiao Wang, Zhiping Xiao, Shengqi Hang, Ghulam Murtaza, Junwei Yang, Hanwen Xu, Anupama Jha, William Noble, Sheng Wang
Understanding how genomic sequences shape three-dimensional (3D) genome architecture is funda-mental to interpreting diverse biological processes. Although previous studies have shown that sequence information can predict 3D genome architecture, they fall short in capturing cell type-specific structures because they are trained solely on sequence inputs. The widely available Hi-C data, which contain rich structural information across biosamples, can provide complementary features to sequence data for study-ing cell type-specific architectures. Recently, DNA foundation models have demonstrated encouraging performance in capturing long-range genomic dependencies, holding promise for modeling chromatin interactions. However, the extremely high computational cost of running these models limits their applicability to Hi-C analysis, which requires genome-wide sequence embeddings. Here, we present Evo2HiC, a multimodal foundation model that jointly models genomic sequences and structures to study cell type-specific chromatin structure. The key idea of Evo2HiC is to distill a large-scale DNA foundation model, Evo 2 (7B), into a compact encoder, while guiding the distillation with Hi-C data to preserve genomic features critical for 3D genome analysis. The model supports two types of encoders, one that operates directly on DNA sequences, and a second that additionally takes as input corresponding Hi-C data. Using the DNA-only encoder and predicting Hi-C contact matrices, Evo2HiC improved Spearman correlation by 10.9% over Orca. Moreover, by jointly embedding Hi-C and sequence information Evo2HiC achieved the best overall Pearson correlation when predicting five representative epigenomic assays. Interpretation analysis of Evo2HiC revealed its ability to identify cell type-specific sequence motifs that explain changes in epigenomic signals. Finally, we demonstrated the cross-species generalizability of Evo2HiC on 177 species from the DNA Zoo dataset for Hi-C resolution enhancement. In summary, Evo2HiC is a foundation model that integrates genome sequences and 3D chromatin structure information, substantially reduces computational cost while maintaining state-of-the-art accuracy on predicting various epigenomic signals and genome architecture, enables the identification of cell type-specific motifs, and demonstrates robust generalizability across species.
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