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However, current experimental techniques for detecting the 3D structure of the genome are costly and limited to the biological conditions. Here, we described \u201cChrombusXMBD,\u201d a graph convolution model capable of predicting chromatin interactions ab initio based on available chromatin features. Using dynamic edge convolution with multihead attention mechanism, Chrombus encodes the 2D-chromatin features into a learnable embedding space, thereby generating a genome-wide 3D-contactmap. In validation, Chrombus effectively recapitulated the topological associated domains, expression quantitative trait loci, and promoter\/enhancer interactions. Especially, Chrombus outperforms existing algorithms in predicting chromatin interactions over 1\u20132\u00a0Mb, increasing prediction correlation by 11.8%\u201348.7%, and predicts long-range interactions over 2\u00a0Mb (Pearson\u2019s coefficient 0.243\u20130.582). Chrombus also exhibits strong generalizability across human and mouse-derived cell lines. Additionally, the parameters of Chrombus inform the biological mechanisms underlying cistrome. Our model provides a new, generalizable analytical tool for understanding the complex dynamics of chromatin interactions and the landscape of cis-regulation of gene expression.<\/jats:p>","DOI":"10.1093\/bib\/bbaf183","type":"journal-article","created":{"date-parts":[[2025,5,2]],"date-time":"2025-05-02T19:23:12Z","timestamp":1746213792000},"source":"Crossref","is-referenced-by-count":0,"title":["Chrombus-XMBD: a graph convolution model predicting 3D-genome from chromatin features"],"prefix":"10.1093","volume":"26","author":[{"given":"Yuanyuan","family":"Zeng","sequence":"first","affiliation":[{"name":"Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]},{"name":"National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]}]},{"given":"Zhiyu","family":"You","sequence":"additional","affiliation":[{"name":"National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]}]},{"given":"Jiayang","family":"Guo","sequence":"additional","affiliation":[{"name":"National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]}]},{"given":"Jialin","family":"Zhao","sequence":"additional","affiliation":[{"name":"National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]}]},{"given":"Ying","family":"Zhou","sequence":"additional","affiliation":[{"name":"National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]}]},{"given":"Jialiang","family":"Huang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]}]},{"given":"Xiaowen","family":"Lyu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]}]},{"given":"Longbiao","family":"Chen","sequence":"additional","affiliation":[{"name":"Fujian Key Laboratory of Sensing and Computing for Smart Cities (SCSC), School of Informatics, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]}]},{"given":"Qiyuan","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]},{"name":"National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University , Xiamen, Fujian 361102 ,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,5,2]]},"reference":[{"key":"2025052702080604800_ref1","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1038\/s41580-019-0132-4","article-title":"The role of 3D genome organization in development and cell differentiation","volume":"20","author":"Zheng","year":"2019","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2025052702080604800_ref2","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/j.bbagrm.2008.07.002","article-title":"Chromatin loops in gene regulation","volume":"1789","author":"Kadauke","year":"2009","journal-title":"Biochim Biophys 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