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While single-cell Hi-C experiments allow for chromosome conformation profiling across many cells, they are still expensive and not widely available for most labs. Here, we propose an alternate approach, scENCORE, to computationally reconstruct chromatin compartments from the more affordable and widely accessible single-cell epigenetic data. First, scENCORE constructs a long-range epigenetic correlation graph to mimic chromatin interaction frequencies, where nodes and edges represent genome bins and their correlations. Then, it learns the node embeddings to cluster genome regions into A\/B compartments and aligns different graphs to quantify chromatin conformation changes across conditions. Benchmarking using cell-type-matched Hi-C experiments demonstrates that scENCORE can robustly reconstruct A\/B compartments in a cell-type-specific manner. Furthermore, our chromatin confirmation switching studies highlight substantial compartment-switching events that may introduce substantial regulatory and transcriptional changes in psychiatric disease. In summary, scENCORE allows accurate and cost-effective A\/B compartment reconstruction to delineate higher-order chromatin structure heterogeneity in complex tissues.<\/jats:p>","DOI":"10.1093\/bib\/bbae096","type":"journal-article","created":{"date-parts":[[2024,3,17]],"date-time":"2024-03-17T10:08:03Z","timestamp":1710670083000},"source":"Crossref","is-referenced-by-count":5,"title":["scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4696-0042","authenticated-orcid":false,"given":"Ziheng","family":"Duan","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of California, Irvine , 92697 CA , USA"}]},{"given":"Siwei","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of California, Irvine , 92697 CA , USA"}]},{"given":"Shushrruth","family":"Sai Srinivasan","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of California, Irvine , 92697 CA , USA"}]},{"given":"Ahyeon","family":"Hwang","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of California, Irvine , 92697 CA , USA"}]},{"given":"Che Yu","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of California, Irvine , 92697 CA , USA"}]},{"given":"Feng","family":"Yue","sequence":"additional","affiliation":[{"name":"Department of Pathology, Northwestern University , 60611 IL , USA"}]},{"given":"Mark","family":"Gerstein","sequence":"additional","affiliation":[{"name":"Molecular Biophysics & Biochemistry, Yale , 06519 CT , USA"}]},{"given":"Yu","family":"Luan","sequence":"additional","affiliation":[{"name":"Department of Cell Systems and Anatomy, UT Health San Antonio , 78229 TX , USA"}]},{"given":"Matthew","family":"Girgenti","sequence":"additional","affiliation":[{"name":"Department of Psychiatry , School of Medicine, , 06519 CT , USA"},{"name":"Yale , School of Medicine, , 06519 CT , USA"},{"name":"Clinical Neurosciences Division , National Center for PTSD, , 06477 CT , USA"},{"name":"U.S. Department of Veterans Affairs , National Center for PTSD, , 06477 CT , USA"}]},{"given":"Jing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of California, Irvine , 92697 CA , USA"}]}],"member":"286","published-online":{"date-parts":[[2024,3,16]]},"reference":[{"issue":"11","key":"2024031710074100200_ref1","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/nrg.2016.112","article-title":"Organization and function of the 3D genome","volume":"17","author":"Bonev","year":"2016","journal-title":"Nat Rev 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