{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T08:49:45Z","timestamp":1791449385132,"version":"4.3.3"},"reference-count":145,"publisher":"eLife Sciences Publications, Ltd","license":[{"start":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T00:00:00Z","timestamp":1781568000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"},{"start":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T00:00:00Z","timestamp":1781568000000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"},{"start":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T00:00:00Z","timestamp":1781568000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"name":"National Cancer Institute","award":["ZIABC010309-24"],"award-info":[{"award-number":["ZIABC010309-24"]}]},{"award":["ZIABC010309-24"],"award-info":[{"award-number":["ZIABC010309-24"]}],"id":[{"id":"https:\/\/ror.org\/02t771148","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Northern New England Clinical Translation Network","award":["GM115516"],"award-info":[{"award-number":["GM115516"]}]},{"name":"National Cancer Institute","award":["P01CA240685"],"award-info":[{"award-number":["P01CA240685"]}]},{"award":["P01CA240685"],"award-info":[{"award-number":["P01CA240685"]}],"id":[{"id":"https:\/\/ror.org\/02t771148","id-type":"ROR","asserted-by":"publisher"}]},{"name":"National Cancer Institute","award":["1F32CA220935-01A1"],"award-info":[{"award-number":["1F32CA220935-01A1"]}]},{"award":["1F32CA220935-01A1"],"award-info":[{"award-number":["1F32CA220935-01A1"]}],"id":[{"id":"https:\/\/ror.org\/02t771148","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Charlotte Perelman and Arthur Jason Perelman Fund for Cancer Research"}],"content-domain":{"domain":["elifesciences.org"],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>Cancer progression involves extensive alterations in epigenetic and gene expression programs, but the accompanying changes in higher-order genome organization remain less well understood. Using high-resolution Micro-C mapping in the MCF10 cell model of breast cancer, we profiled chromatin compartments, topologically associated domains, and chromatin loops. We find large-scale compartmental shifts occur predominantly in early stages of cancer development, with more fine-scale structural changes in topologically associating domains and loops accumulating during the later transition to metastasis. Relating these chromatin features to gene expression and enhancer-associated histone marks revealed that many differentially expressed genes are physically connected to distal regulatory elements. While enhancer\u2013promoter contact frequency and distal enhancer activity correlated with gene expression, strong changes in chromatin looping were relatively infrequent during progression, suggesting that alterations in chromatin contacts are not globally necessary, but may facilitate gene regulation at a subset of genes. These results elucidate the connection between gene regulation and genome remodeling in a cell-based cancer progression model.<\/jats:p>","DOI":"10.7554\/elife.108135","type":"journal-article","created":{"date-parts":[[2025,9,10]],"date-time":"2025-09-10T15:30:45Z","timestamp":1757518245000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.108135","source":"Crossref","is-referenced-by-count":2,"title":["Genome reorganization and its functional impact during breast cancer progression"],"prefix":"10.7554","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1466-8258","authenticated-orcid":true,"given":"Kathleen S Metz","family":"Reed","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}],"name":"National Cancer Institute, National Institutes of Health","place":["Bethesda, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Andrew","family":"Fritz","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0155zta11","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine","place":["Burlington, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Haley","family":"Greenyer","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0155zta11","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine","place":["Burlington, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Kerstin","family":"Heselmeyer-Haddad","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}],"name":"OMICS Technology Facility, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health","place":["Bethesda, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Seth","family":"Frietze","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0155zta11","id-type":"ROR","asserted-by":"publisher"}],"name":"College of Nursing and Health Sciences, University of Vermont Cancer Center","place":["Burlington, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"data-curation","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"}]},{"given":"Janet","family":"Stein","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0155zta11","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine","place":["Burlington, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8762-5422","authenticated-orcid":true,"given":"Gary","family":"Stein","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0155zta11","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biochemistry and University of Vermont Cancer Center, University of Vermont Larner College of Medicine","place":["Burlington, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"corresponding-author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3530-3020","authenticated-orcid":true,"given":"Tom","family":"Misteli","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}],"name":"National Cancer Institute, National Institutes of Health","place":["Bethesda, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"corresponding-author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]}],"member":"4374","published-online":{"date-parts":[[2026,6,16]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","DOI":"10.1101\/2023.02.13.528389","type":"preprint","article-title":"Pairtools: from sequencing data to chromosome contacts","volume-title":"bioRxiv","author":"Abdennur","year":"2023"},{"key":"bib2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-45839-z","type":"journal-article","article-title":"The ENCODE blacklist: identification of problematic regions of the genome","volume":"9","author":"Amemiya","year":"2019","journal-title":"Scientific Reports"},{"key":"bib3","doi-asserted-by":"publisher","DOI":"10.1016\/j.gde.2024.102307","type":"journal-article","article-title":"Rewiring cancer: 3D genome determinants of cancer hallmarks","volume":"91","author":"Amodeo","year":"2025","journal-title":"Current Opinion in Genetics & Development"},{"key":"bib4","type":"web-resource","article-title":"Trim Galorel","author":"Babraham Bioinformatics","year":"2017","unstructured":"Babraham Bioinformatics. 2017. Trim Galorel. http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/trim_galore\/ [Accessed February 15, 2017]."},{"key":"bib5","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0768-0","type":"journal-article","article-title":"Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells","volume":"16","author":"Barutcu","year":"2015","journal-title":"Genome Biology"},{"key":"bib6","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1016\/j.molcel.2019.07.038","type":"journal-article","article-title":"Decreased enhancer-promoter proximity accompanying enhancer activation","volume":"76","author":"Benabdallah","year":"2019","journal-title":"Molecular Cell"},{"key":"bib7","doi-asserted-by":"publisher","first-page":"19645","DOI":"10.18632\/oncotarget.14902","type":"journal-article","article-title":"Regulation of miRNA-29c and its downstream pathways in preneoplastic progression of triple-negative breast cancer","volume":"8","author":"Bhardwaj","year":"2017","journal-title":"Oncotarget"},{"key":"bib8","type":"web-resource","article-title":"FastQC: A quality control tool for high throughput sequence data [Internet]","author":"Bioinformatics","year":"2015","unstructured":"Bioinformatics B. 2015. FastQC: A quality control tool for high throughput sequence data [Internet]. http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/ [Accessed February 15, 2017]."},{"key":"bib9","doi-asserted-by":"publisher","first-page":"1972","DOI":"10.1158\/0008-5472.CAN-14-2761","type":"journal-article","article-title":"Paracrine WNT5A signaling inhibits expansion of tumor-initiating cells","volume":"75","author":"Borcherding","year":"2015","journal-title":"Cancer Research"},{"key":"bib10","doi-asserted-by":"publisher","DOI":"10.1016\/j.tranon.2024.101879","type":"journal-article","article-title":"Increased heterogeneity in expression of genes associated with cancer progression and drug resistance","volume":"41","author":"Bose","year":"2024","journal-title":"Translational Oncology"},{"key":"bib11","doi-asserted-by":"publisher","first-page":"941","DOI":"10.3892\/IJO.31.4.941\/HTML","type":"journal-article","article-title":"Differential expression of acidic proteins with progression in the MCF10 model of human breast disease","volume":"31","author":"Buchanan","year":"2007","journal-title":"International Journal of Oncology"},{"key":"bib12","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-20940-y","type":"journal-article","article-title":"H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions","volume":"12","author":"Cai","year":"2021","journal-title":"Nature Communications"},{"key":"bib13","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1038\/s41576-020-00300-0","type":"journal-article","article-title":"The epigenetic basis of cellular heterogeneity","volume":"22","author":"Carter","year":"2021","journal-title":"Nature Reviews. Genetics"},{"key":"bib14","doi-asserted-by":"publisher","DOI":"10.1101\/2024.08.03.606480","type":"preprint","article-title":"Structural perturbation of chromatin domains with multiple developmental regulators can severely impact gene regulation and development","volume-title":"bioRxiv","author":"Chakraborty","year":"2024"},{"key":"bib15","doi-asserted-by":"publisher","first-page":"1838","DOI":"10.1016\/j.devcel.2025.02.002","type":"journal-article","article-title":"Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development","volume":"60","author":"Chakraborty","year":"2025","journal-title":"Developmental Cell"},{"key":"bib16","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2025.115450","type":"journal-article","article-title":"Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity informing a looping-mediated therapeutic avenue","volume":"44","author":"Choppavarapu","year":"2025","journal-title":"Cell Reports"},{"key":"bib17","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1016\/j.cell.2015.09.033","type":"journal-article","article-title":"Comprehensive molecular portraits of invasive lobular breast cancer","volume":"163","author":"Ciriello","year":"2015","journal-title":"Cell"},{"key":"bib18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.gde.2016.01.002","type":"journal-article","article-title":"The three-dimensional cancer genome","volume":"36","author":"Corces","year":"2016","journal-title":"Current Opinion in Genetics & Development"},{"key":"bib19","doi-asserted-by":"publisher","first-page":"959","DOI":"10.1038\/nmeth.4396","type":"journal-article","article-title":"An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues","volume":"14","author":"Corces","year":"2017","journal-title":"Nature Methods"},{"key":"bib20","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1146\/annurev-genom-120121-101149","type":"journal-article","article-title":"Structural variation in cancer: role, prevalence, and mechanisms","volume":"23","author":"Cosenza","year":"2022","journal-title":"Annual Review of Genomics and Human Genetics"},{"key":"bib21","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-020-03652-w","type":"journal-article","article-title":"SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering","volume":"21","author":"Cresswell","year":"2020","journal-title":"BMC Bioinformatics"},{"key":"bib22","doi-asserted-by":"publisher","first-page":"21931","DOI":"10.1073\/PNAS.1016071107\/SUPPL_FILE\/ST01.XLSX","type":"journal-article","article-title":"Histone H3K27ac separates active from poised enhancers and predicts developmental state","volume":"107","author":"Creyghton","year":"2010","journal-title":"PNAS"},{"key":"bib23","doi-asserted-by":"publisher","first-page":"932","DOI":"10.1038\/s41590-018-0184-1","type":"journal-article","article-title":"Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation","volume":"19","author":"Cuartero","year":"2018","journal-title":"Nature Immunology"},{"key":"bib24","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2023.102622","type":"journal-article","article-title":"TADs: Dynamic structures to create stable regulatory functions","volume":"81","author":"da Costa-Nunes","year":"2023","journal-title":"Current Opinion in Structural Biology"},{"key":"bib25","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1038\/nrclinonc.2017.166","type":"journal-article","article-title":"Tumour heterogeneity and resistance to cancer therapies","volume":"15","author":"Dagogo-Jack","year":"2018","journal-title":"Nature Reviews. Clinical Oncology"},{"key":"bib26","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/gigascience\/giab008","type":"journal-article","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"bib27","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1038\/s41580-021-00349-7","type":"journal-article","article-title":"Genome folding through loop extrusion by SMC complexes","volume":"22","author":"Davidson","year":"2021","journal-title":"Nature Reviews. Molecular Cell Biology"},{"key":"bib28","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btae352","type":"journal-article","article-title":"Mariner: explore the Hi-Cs","volume":"40","author":"Davis","year":"2024","journal-title":"Bioinformatics"},{"key":"bib29","first-page":"313","type":"journal-article","article-title":"MCF10AT: a model for the evolution of cancer from proliferative breast disease","volume":"148","author":"Dawson","year":"1996","journal-title":"The American Journal of Pathology"},{"key":"bib30","doi-asserted-by":"publisher","first-page":"1110","DOI":"10.1016\/j.cell.2016.02.007","type":"journal-article","article-title":"The 3D genome as moderator of chromosomal communication","volume":"164","author":"Dekker","year":"2016","journal-title":"Cell"},{"key":"bib31","doi-asserted-by":"publisher","DOI":"10.3389\/FCELL.2023.1303862\/BIBTEX","type":"journal-article","article-title":"Enhancers dysfunction in the 3D genome of cancer cells","volume":"11","author":"Della Chiara","year":"2023","journal-title":"Frontiers in Cell and Developmental Biology"},{"key":"bib32","doi-asserted-by":"publisher","first-page":"1263","DOI":"10.1038\/s41588-019-0466-z","type":"journal-article","article-title":"Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture","volume":"51","author":"Despang","year":"2019","journal-title":"Nature Genetics"},{"key":"bib33","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1038\/s41576-022-00530-4","type":"journal-article","article-title":"New insights into genome folding by loop extrusion from inducible degron technologies","volume":"24","author":"de Wit","year":"2023","journal-title":"Nature Reviews. Genetics"},{"key":"bib34","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1016\/j.cels.2018.06.007","type":"journal-article","article-title":"Pre-established chromatin interactions mediate the genomic response to glucocorticoids","volume":"7","author":"D\u2019Ippolito","year":"2018","journal-title":"Cell Systems"},{"key":"bib35","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","type":"journal-article","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"bib36","doi-asserted-by":"publisher","DOI":"10.3389\/FONC.2023.1268977\/FULL","type":"journal-article","article-title":"m6A regulates breast cancer proliferation and migration through stage-dependent changes in Epithelial to Mesenchymal Transition gene expression","volume":"13","author":"Dorgham","year":"2023","journal-title":"Frontiers in Oncology"},{"key":"bib37","type":"web-resource","article-title":"Welcome to the Dovetail Linked-Read Analysis Page","author":"Dovetail","year":"2025","unstructured":"Dovetail. 2025. Welcome to the Dovetail Linked-Read Analysis Page. https:\/\/dovetail-analysis.readthedocs.io\/en\/latest\/index.html [Accessed March 27, 2025]."},{"key":"bib38","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","type":"journal-article","article-title":"Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Systems"},{"key":"bib39","doi-asserted-by":"publisher","first-page":"1728","DOI":"10.1038\/nprot.2012.101","type":"journal-article","article-title":"Identifying ChIP-seq enrichment using MACS","volume":"7","author":"Feng","year":"2012","journal-title":"Nature Protocols"},{"key":"bib40","doi-asserted-by":"publisher","DOI":"10.3390\/cells11244058","type":"journal-article","article-title":"Regulation of gene expression in cancer-an overview","volume":"11","author":"Ferlier","year":"2022","journal-title":"Cells"},{"key":"bib41","doi-asserted-by":"publisher","DOI":"10.1126\/science.aal2380","type":"journal-article","article-title":"Epigenetic plasticity and the hallmarks of cancer","volume":"357","author":"Flavahan","year":"2017","journal-title":"Science"},{"key":"bib42","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1002\/jcp.25996","type":"journal-article","article-title":"Intranuclear and higher-order chromatin organization of the major histone gene cluster in breast cancer","volume":"233","author":"Fritz","year":"2018","journal-title":"Journal of Cellular Physiology"},{"key":"bib43","doi-asserted-by":"publisher","first-page":"1664","DOI":"10.1038\/s41588-019-0538-0","type":"journal-article","article-title":"Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations","volume":"51","author":"Fulco","year":"2019","journal-title":"Nature Genetics"},{"key":"bib44","doi-asserted-by":"publisher","first-page":"598","DOI":"10.1038\/s41586-023-06130-4","type":"journal-article","article-title":"Hallmarks of transcriptional intratumour heterogeneity across a thousand tumours","volume":"618","author":"Gavish","year":"2023","journal-title":"Nature"},{"key":"bib45","doi-asserted-by":"publisher","DOI":"10.1101\/2023.10.13.562171","type":"preprint","article-title":"Active regulatory elements recruit cohesin to establish cell-specific chromatin domains","volume-title":"bioRxiv","author":"Georgiades","year":"2023"},{"key":"bib46","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2023.147441","type":"journal-article","article-title":"Spatiotemporal higher-order chromatin landscape of human histone gene clusters at histone locus bodies during the cell cycle in breast cancer progression","volume":"872","author":"Ghule","year":"2023","journal-title":"Gene"},{"key":"bib47","type":"web-resource","article-title":"ENCODE [Internet]","author":"Glossary","year":"2025","unstructured":"Glossary. 2025. ENCODE [Internet]. https:\/\/www.encodeproject.org\/glossary\/ [Accessed March 8, 2025]."},{"key":"bib48","doi-asserted-by":"publisher","first-page":"1048","DOI":"10.1038\/s41588-023-01391-1","type":"journal-article","article-title":"Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments","volume":"55","author":"Goel","year":"2023","journal-title":"Nature Genetics"},{"key":"bib49","doi-asserted-by":"publisher","first-page":"675","DOI":"10.1038\/s41587-020-0546-8","type":"journal-article","article-title":"Visualizing and interpreting cancer genomics data via the Xena platform","volume":"38","author":"Goldman","year":"2020","journal-title":"Nature Biotechnology"},{"key":"bib50","doi-asserted-by":"publisher","DOI":"10.1101\/2024.07.12.603288","type":"preprint","article-title":"Cohesin-mediated 3D contacts tune enhancer-promoter regulation","volume-title":"bioRxiv","author":"Guckelberger","year":"2024"},{"key":"bib51","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-03828-2","type":"journal-article","article-title":"Mutation hotspots at CTCF binding sites coupled to chromosomal instability in gastrointestinal cancers","volume":"9","author":"Guo","year":"2018","journal-title":"Nature Communications"},{"key":"bib52","doi-asserted-by":"publisher","DOI":"10.1186\/s40364-019-0174-y","type":"journal-article","article-title":"Epigenetic heterogeneity in cancer","volume":"7","author":"Guo","year":"2019","journal-title":"Biomarker Research"},{"key":"bib53","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1016\/J.CELL.2011.02.013\/ASSET\/2067D218-2368-451A-B4DA-CF9EF4807B23\/MAIN.ASSETS\/GR1.JPG","type":"journal-article","article-title":"Hallmarks of cancer: The next generation","volume":"144","author":"Hanahan","year":"2011","journal-title":"Cell"},{"key":"bib54","doi-asserted-by":"publisher","DOI":"10.1101\/2024.10.04.615095","type":"preprint","article-title":"Synergy between Cis -regulatory elements can render cohesin dispensable for distal enhancer function","volume-title":"bioRxiv","author":"Hansen","year":"2024"},{"key":"bib55","doi-asserted-by":"publisher","DOI":"10.1038\/srep23216","type":"journal-article","article-title":"Suppression of Spry1 inhibits triple-negative breast cancer malignancy by decreasing EGF\/EGFR mediated mesenchymal phenotype","volume":"6","author":"He","year":"2016","journal-title":"Scientific Reports"},{"key":"bib56","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1038\/ng1966","type":"journal-article","article-title":"Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome","volume":"39","author":"Heintzman","year":"2007","journal-title":"Nature Genetics"},{"key":"bib57","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","type":"journal-article","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Molecular Cell"},{"key":"bib58","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1016\/j.molcel.2020.03.002","type":"journal-article","article-title":"Resolving the 3D landscape of transcription-linked mammalian chromatin folding","volume":"78","author":"Hsieh","year":"2020","journal-title":"Molecular Cell"},{"key":"bib59","doi-asserted-by":"publisher","first-page":"1919","DOI":"10.1038\/s41588-022-01223-8","type":"journal-article","article-title":"Enhancer-promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1","volume":"54","author":"Hsieh","year":"2022","journal-title":"Nature Genetics"},{"key":"bib60","doi-asserted-by":"publisher","first-page":"85","DOI":"10.22514\/ejgo.2022.045","type":"journal-article","article-title":"COL12A1 as a prognostic biomarker in HER2-enriched breast cancer and its association with immune infiltration","volume":"43","author":"Hu","year":"2022","journal-title":"European Journal of Gynaecological Oncology"},{"key":"bib61","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1038\/s41580-021-00362-w","type":"journal-article","article-title":"Understanding 3D genome organization by multidisciplinary methods","volume":"22","author":"Jerkovic\u00b4","year":"2021","journal-title":"Nature Reviews Molecular Cell Biology"},{"key":"bib62","doi-asserted-by":"publisher","first-page":"1474","DOI":"10.1016\/j.cell.2020.07.030","type":"journal-article","article-title":"Large-scale topological changes restrain malignant progression in colorectal cancer","volume":"182","author":"Johnstone","year":"2020","journal-title":"Cell"},{"key":"bib63","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009201","type":"journal-article","article-title":"Delineating genetic alterations for tumor progression in the MCF10A series of breast cancer cell lines","volume":"5","author":"Kadota","year":"2010","journal-title":"PLOS ONE"},{"key":"bib64","doi-asserted-by":"publisher","first-page":"891","DOI":"10.1038\/s41594-022-00821-8","type":"journal-article","article-title":"Cohesin is required for long-range enhancer action at the Shh locus","volume":"29","author":"Kane","year":"2022","journal-title":"Nature Structural & Molecular Biology"},{"key":"bib65","doi-asserted-by":"publisher","first-page":"818","DOI":"10.1038\/ng.3335","type":"journal-article","article-title":"CTCF\/cohesin-binding sites are frequently mutated in cancer","volume":"47","author":"Katainen","year":"2015","journal-title":"Nature Genetics"},{"key":"bib66","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1038\/s12276-022-00768-2","type":"journal-article","article-title":"Comparative characterization of 3D chromatin organization in triple-negative breast cancers","volume":"54","author":"Kim","year":"2022","journal-title":"Experimental & Molecular Medicine"},{"key":"bib67","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1038\/nature11412","type":"journal-article","article-title":"Comprehensive molecular portraits of human breast tumours","volume":"490","author":"Koboldt","year":"2012","journal-title":"Nature"},{"key":"bib68","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.24956.2","type":"journal-article","article-title":"gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler","volume":"9","author":"Kolberg","year":"2020","journal-title":"F1000Research"},{"key":"bib69","doi-asserted-by":"publisher","first-page":"2042","DOI":"10.1093\/bioinformatics\/btac057","type":"journal-article","article-title":"Plotgardener: cultivating precise multi-panel figures in R","volume":"38","author":"Kramer","year":"2022","journal-title":"Bioinformatics"},{"key":"bib70","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02215-9","type":"journal-article","article-title":"FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data","volume":"21","author":"Kruse","year":"2020","journal-title":"Genome Biology"},{"key":"bib71","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1038\/s41594-020-00539-5","type":"journal-article","article-title":"Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation","volume":"28","author":"Kubo","year":"2021","journal-title":"Nature Structural & Molecular Biology"},{"key":"bib72","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","type":"journal-article","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nature Methods"},{"key":"bib73","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003118","type":"journal-article","article-title":"Software for computing and annotating genomic ranges","volume":"9","author":"Lawrence","year":"2013","journal-title":"PLOS Computational Biology"},{"key":"bib74","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","type":"journal-article","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"bib75","doi-asserted-by":"publisher","first-page":"1752","DOI":"10.1214\/11-AOAS466","type":"journal-article","article-title":"Measuring reproducibility of high-throughput experiments","volume":"5","author":"Li","year":"2011","journal-title":"The Annals of Applied Statistics"},{"key":"bib76","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S13148-021-01167-6\/FIGURES\/6","type":"journal-article","article-title":"Hi-C profiling of cancer spheroids identifies 3D-growth-specific chromatin interactions in breast cancer endocrine resistance","volume":"13","author":"Li","year":"2021","journal-title":"Clinical Epigenetics"},{"key":"bib77","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","type":"journal-article","article-title":"The molecular signatures database (MSigDB) hallmark gene set collection","volume":"1","author":"Liberzon","year":"2015","journal-title":"Cell Systems"},{"key":"bib78","doi-asserted-by":"publisher","DOI":"10.1177\/1534735419836494","type":"journal-article","article-title":"Analyses of BMAL1 and PER2 oscillations in a model of breast cancer progression reveal changes with malignancy","volume":"18","author":"Lin","year":"2019","journal-title":"Integrative Cancer Therapies"},{"key":"bib79","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-22666-3","type":"journal-article","article-title":"Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes","volume":"12","author":"Liu","year":"2021","journal-title":"Nature Communications"},{"key":"bib80","doi-asserted-by":"publisher","first-page":"3075","DOI":"10.1038\/s41588-025-02297-w","type":"journal-article","article-title":"Tracing the evolution of single-cell 3D genomes in Kras-driven cancers","volume":"57","author":"Liu","year":"2025","journal-title":"Nature Genetics"},{"key":"bib81","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S13059-014-0550-8\/FIGURES\/9","type":"journal-article","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biology"},{"key":"bib82","type":"software","article-title":"Nullranges: generation of null ranges via bootstrapping or covariate matching [internet]","volume-title":"Github","author":"Love M Davis","year":"2022","unstructured":"Love M Davis E, Phanstiel D, Lee S. 2022. Nullranges: generation of null ranges via bootstrapping or covariate matching [internet]. Github. ffc311b. https:\/\/github.com\/nullranges\/nullranges."},{"key":"bib83","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.8759.2","type":"journal-article","article-title":"Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments","volume":"5","author":"Lun","year":"2016","journal-title":"F1000Research"},{"key":"bib84","doi-asserted-by":"publisher","first-page":"5974","DOI":"10.1073\/pnas.0931261100","type":"journal-article","article-title":"Gene expression profiles of human breast cancer progression","volume":"100","author":"Ma","year":"2003","journal-title":"PNAS"},{"key":"bib85","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1002\/path.4778","type":"journal-article","article-title":"Three-dimensional modelling identifies novel genetic dependencies associated with breast cancer progression in the isogenic MCF10 model","volume":"240","author":"Maguire","year":"2016","journal-title":"The Journal of Pathology"},{"key":"bib86","doi-asserted-by":"publisher","DOI":"10.1016\/j.xpro.2021.100854","type":"journal-article","article-title":"An optimized ATAC-seq protocol for genome-wide mapping of active regulatory elements in primary mouse cortical neurons","volume":"2","author":"Maor-Nof","year":"2021","journal-title":"STAR Protocols"},{"key":"bib87","doi-asserted-by":"publisher","first-page":"5946","DOI":"10.1158\/0008-5472.CAN-09-0420","type":"journal-article","article-title":"Cytogenetic and cDNA microarray expression analysis of MCF10 human breast cancer progression cell lines","volume":"69","author":"Marella","year":"2009","journal-title":"Cancer Research"},{"key":"bib88","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1016\/j.cell.2020.09.014","type":"journal-article","article-title":"The self-organizing genome: principles of genome architecture and function","volume":"183","author":"Misteli","year":"2020","journal-title":"Cell"},{"key":"bib89","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1038\/nrc2091","type":"journal-article","article-title":"The impact of translocations and gene fusions on cancer causation","volume":"7","author":"Mitelman","year":"2007","journal-title":"Nature Reviews. Cancer"},{"key":"bib90","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-50387-w","type":"journal-article","article-title":"3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression","volume":"15","author":"Mortenson","year":"2024","journal-title":"Nature Communications"},{"key":"bib91","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0113354","type":"journal-article","article-title":"Estrogen induces global reorganization of chromatin structure in human breast cancer cells","volume":"9","author":"Mourad","year":"2014","journal-title":"PLOS ONE"},{"key":"bib92","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1038\/s41588-023-01649-8","type":"journal-article","article-title":"In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization","volume":"56","author":"Oberbeckmann","year":"2024","journal-title":"Nature Genetics"},{"key":"bib93","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1007\/978-1-60761-753-2_27","type":"journal-article","article-title":"Using ChIP-seq technology to identify targets of zinc finger transcription factors","volume":"649","author":"O\u2019Geen","year":"2010","journal-title":"Methods in Molecular Biology"},{"key":"bib94","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-32255-7","type":"journal-article","article-title":"Temporal profiling of the breast tumour microenvironment reveals collagen XII as a driver of metastasis","volume":"13","author":"Papanicolaou","year":"2022","journal-title":"Nature Communications"},{"key":"bib95","doi-asserted-by":"publisher","first-page":"4958","DOI":"10.1093\/nar\/gkq244","type":"journal-article","article-title":"Characterization of an antagonistic switch between histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of Polycomb group target genes","volume":"38","author":"Pasini","year":"2010","journal-title":"Nucleic Acids Research"},{"key":"bib96","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.4323183","type":"software","article-title":"Nf-core\/rnaseq: nf-core\/rnaseq v3.0 - silver shark [internet]","volume-title":"Zenodo","author":"Patel","year":"2020","unstructured":"Patel H, Ewels P, Peltzer A, Hammar\u00e9n R, Botvinnik O, Sturm G. 2020. Nf-core\/rnaseq: nf-core\/rnaseq v3.0 - silver shark [internet]. Zenodo. 3.0. https:\/\/doi.org\/10.5281\/zenodo.4323183."},{"key":"bib97","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nmeth.4197","type":"journal-article","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nature Methods"},{"key":"bib98","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2022.879465","type":"journal-article","article-title":"Regulation of 3D organization and its role in cancer biology","volume":"10","author":"Peng","year":"2022","journal-title":"Frontiers in Cell and Developmental Biology"},{"key":"bib99","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1038\/nrm3965","type":"journal-article","article-title":"Three-dimensional genome architecture: players and mechanisms","volume":"16","author":"Pombo","year":"2015","journal-title":"Nature Reviews. Molecular Cell Biology"},{"key":"bib100","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2022.102117","type":"journal-article","article-title":"Coming full circle: On the origin and evolution of the looping model for enhancer-promoter communication","volume":"298","author":"Popay","year":"2022","journal-title":"The Journal of Biological Chemistry"},{"key":"bib101","doi-asserted-by":"publisher","DOI":"10.1101\/2024.10.02.616323","type":"preprint","article-title":"Genome-wide in Vivo dynamics of cohesin-mediated loop extrusion and its role in transcription activation","volume-title":"bioRxiv","author":"Popay","year":"2024"},{"key":"bib102","doi-asserted-by":"publisher","first-page":"4183","DOI":"10.1158\/0008-5472.CAN-21-1939","type":"journal-article","article-title":"The MCF10 model of breast tumor progression","volume":"81","author":"Puleo","year":"2021","journal-title":"Cancer Research"},{"key":"bib103","doi-asserted-by":"publisher","first-page":"W160","DOI":"10.1093\/nar\/gkw257","type":"journal-article","article-title":"deepTools2: a next generation web server for deep-sequencing data analysis","volume":"44","author":"Ram\u00edrez","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"bib104","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1016\/j.cell.2017.09.026","type":"journal-article","article-title":"Cohesin loss eliminates all loop domains","volume":"171","author":"Rao","year":"2017","journal-title":"Cell"},{"key":"bib105","type":"software","article-title":"MCF10-microc","volume-title":"Software Heritage","author":"Reed","year":"2025","unstructured":"Reed KSM. 2025. MCF10-microc. Software Heritage. swh:1:rev:513532d48f436b1cbbdfda894601909166bc2cdb. https:\/\/archive.softwareheritage.org\/swh:1:dir:e662a6b50726f3f993a41cb0bbe858c937879b12;origin=https:\/\/github.com\/ksmetz\/MCF10-MicroC;visit=swh:1:snp:90dafbab49f06c1b52242cd1775c51ed94088905;anchor=swh:1:rev:513532d48f436b1cbbdfda894601909166bc2cdb."},{"key":"bib106","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2025.1597245","type":"journal-article","article-title":"Integration of chromosome conformation and gene expression networks reveals regulatory mechanisms in triple negative breast cancer","volume":"13","author":"Reyes-Gopar","year":"2025","journal-title":"Frontiers in Cell and Developmental Biology"},{"key":"bib107","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1016\/j.ygeno.2008.08.005","type":"journal-article","article-title":"Molecular signatures associated with transformation and progression to breast cancer in the isogenic MCF10 model","volume":"92","author":"Rhee","year":"2008","journal-title":"Genomics"},{"key":"bib108","doi-asserted-by":"publisher","first-page":"9083","DOI":"10.1073\/PNAS.1112570109\/-\/DCSUPPLEMENTAL","type":"journal-article","article-title":"Oncogene-mediated alterations in chromatin conformation","volume":"109","author":"Rickman","year":"2012","journal-title":"PNAS"},{"key":"bib109","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1038\/s41594-022-00787-7","type":"journal-article","article-title":"Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes","volume":"29","author":"Rinzema","year":"2022","journal-title":"Nature Structural & Molecular Biology"},{"key":"bib110","doi-asserted-by":"publisher","DOI":"10.1186\/bcr2244","type":"journal-article","article-title":"Loss of TGF-beta or Wnt5a results in an increase in Wnt\/beta-catenin activity and redirects mammary tumour phenotype","volume":"11","author":"Roarty","year":"2009","journal-title":"Breast Cancer Research"},{"key":"bib111","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","type":"journal-article","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"bib112","doi-asserted-by":"publisher","DOI":"10.1101\/2023.11.26.568711","type":"preprint","article-title":"Loss of multi-level 3D genome organization during breast cancer progression","volume-title":"bioRxiv","author":"Rossini","year":"2024"},{"key":"bib113","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1038\/s41576-018-0060-8","type":"journal-article","article-title":"Organizational principles of 3D genome architecture","volume":"19","author":"Rowley","year":"2018","journal-title":"Nature Reviews. Genetics"},{"key":"bib114","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1101\/gr.257832.119","type":"journal-article","article-title":"Analysis of Hi-C data using SIP effectively identifies loops in organisms from C. elegans to mammals","volume":"30","author":"Rowley","year":"2020","journal-title":"Genome Research"},{"key":"bib115","doi-asserted-by":"publisher","first-page":"E6456","DOI":"10.1073\/PNAS.1518552112\/SUPPL_FILE\/PNAS.1518552112.ST01.XLSX","type":"journal-article","article-title":"Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes","volume":"112","author":"Sanborn","year":"2015","journal-title":"PNAS"},{"key":"bib116","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1023\/a:1006461422273","type":"journal-article","article-title":"Malignant MCF10CA1 cell lines derived from premalignant human breast epithelial MCF10AT cells","volume":"65","author":"Santner","year":"2001","journal-title":"Breast Cancer Research and Treatment"},{"key":"bib117","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1038\/s41576-019-0128-0","type":"journal-article","article-title":"Long-range enhancer-promoter contacts in gene expression control","volume":"20","author":"Schoenfelder","year":"2019","journal-title":"Nature Reviews. Genetics"},{"key":"bib118","doi-asserted-by":"publisher","DOI":"10.1101\/2024.10.04.616668","type":"preprint","article-title":"Heterogeneity in chromatin structure drives core regulatory pathways in B-cell acute lymphoblastic leukemia","volume-title":"bioRxiv","author":"Sen","year":"2024"},{"key":"bib119","first-page":"31","type":"journal-article","article-title":"Differential expression of key signaling proteins in MCF10 cell lines, a human breast cancer progression model","volume":"4","author":"So","year":"2012","journal-title":"Molecular and Cellular Pharmacology"},{"key":"bib120","doi-asserted-by":"publisher","DOI":"10.3390\/cancers15051480","type":"journal-article","article-title":"COL12A1 acts as a novel prognosis biomarker and activates cancer-associated fibroblasts in pancreatic cancer through bioinformatics and experimental validation","volume":"15","author":"Song","year":"2023","journal-title":"Cancers"},{"key":"bib121","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1016\/j.gde.2021.10.004","type":"journal-article","article-title":"The stochastic nature of genome organization and function","volume":"72","author":"Sood","year":"2022","journal-title":"Current Opinion in Genetics & Development"},{"key":"bib122","first-page":"6075","type":"journal-article","article-title":"Isolation and characterization of a spontaneously immortalized human breast epithelial cell line, MCF-10","volume":"50","author":"Soule","year":"1990","journal-title":"Cancer Research"},{"key":"bib123","doi-asserted-by":"publisher","DOI":"10.1101\/2023.09.07.556660","type":"preprint","article-title":"Loop extrusion by cohesin plays a key role in enhancer-activated gene expression during differentiation","volume-title":"bioRxiv","author":"Stolper","year":"2023"},{"key":"bib124","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","type":"journal-article","article-title":"Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"PNAS"},{"key":"bib125","doi-asserted-by":"publisher","first-page":"719","DOI":"10.1101\/gr.201517.115","type":"journal-article","article-title":"Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations","volume":"26","author":"Taberlay","year":"2016","journal-title":"Genome Research"},{"key":"bib126","doi-asserted-by":"publisher","first-page":"W98","DOI":"10.1093\/nar\/gkx247","type":"journal-article","article-title":"GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses","volume":"45","author":"Tang","year":"2017","journal-title":"Nucleic Acids Research"},{"key":"bib127","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2020.107929","type":"journal-article","article-title":"Cohesin-Dependent and -independent mechanisms mediate chromosomal contacts between promoters and enhancers","volume":"32","author":"Thiecke","year":"2020","journal-title":"Cell Reports"},{"key":"bib128","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2025.113268","type":"journal-article","article-title":"A 3D genome compendium of breast cancer progression","volume":"28","author":"van den Brand","year":"2025","journal-title":"iScience"},{"key":"bib129","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1038\/s41592-021-01164-w","type":"journal-article","article-title":"Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes","volume":"18","author":"Wang","year":"2021","journal-title":"Nature Methods"},{"key":"bib130","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S12860-022-00433-6\/FIGURES\/1","type":"journal-article","article-title":"Chromatin structure in cancer","volume":"23","author":"Wang","year":"2022","journal-title":"BMC Mol Cell Biol"},{"key":"bib131","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.64320","type":"journal-article","article-title":"How subtle changes in 3D structure can create large changes in transcription","volume":"10","author":"Xiao","year":"2021","journal-title":"eLife"},{"key":"bib132","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbagrm.2020.194631","type":"journal-article","article-title":"The 3D genomic landscape of differential response to EGFR\/HER2 inhibition in endocrine-resistant breast cancer cells","volume":"1863","author":"Yang","year":"2020","journal-title":"Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms"},{"key":"bib133","doi-asserted-by":"publisher","DOI":"10.1016\/j.prp.2022.154175","type":"journal-article","article-title":"Aberrant inactivation of SCNN1G promotes the motility of head and neck squamous cell carcinoma","volume":"240","author":"Yang","year":"2022","journal-title":"Pathology, Research and Practice"},{"key":"bib134","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1038\/s41580-024-00710-6","type":"journal-article","article-title":"Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation","volume":"25","author":"Yang","year":"2024","journal-title":"Nature Reviews. Molecular Cell Biology"},{"key":"bib135","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1038\/s41588-025-02188-0","type":"journal-article","article-title":"Three-dimensional genome landscape of primary human cancers","volume":"57","author":"Yost","year":"2025","journal-title":"Nature Genetics"},{"key":"bib136","doi-asserted-by":"publisher","first-page":"5058","DOI":"10.12659\/msm.902022","type":"journal-article","article-title":"Multiple roles of WNT5A in breast cancer","volume":"22","author":"Zeng","year":"2016","journal-title":"Medical Science Monitor"},{"key":"bib137","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-9-r137","type":"journal-article","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biology"},{"key":"bib138","doi-asserted-by":"publisher","DOI":"10.1002\/ctd2.17","type":"journal-article","article-title":"Disorder of three\u2010dimensional chromosome structure plays a role in carcinogenesis","volume":"1","author":"Zhang","year":"2021","journal-title":"Clinical and Translational Discovery"},{"key":"bib139","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09320-9","type":"journal-article","article-title":"Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance","volume":"10","author":"Zhou","year":"2019","journal-title":"Nature Communications"},{"key":"dataset1","type":"dataset","article-title":"Genome reorganization and its functional impact during breast cancer progression","volume-title":"NCBI Gene Expression Omnibus","author":"Metz Reed","year":"2026","unstructured":"Metz Reed KS, Misteli T, Fritz A, Greenyer H, Frietze S, Stein J, Stein G. 2026. Genome reorganization and its functional impact during breast cancer progression. NCBI Gene Expression Omnibus. https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE320319. GSE320319."},{"key":"dataset2","type":"dataset","article-title":"Genome reorganization and its functional impact during breast cancer progression [Micro-C]","volume-title":"NCBI Gene Expression Omnibus","author":"Metz","year":"2025","unstructured":"Metz RKS, Misteli T, Fritz A, Greenyer H, Frietze S, Stein J, Stein G. 2025. Genome reorganization and its functional impact during breast cancer progression [Micro-C]. NCBI Gene Expression Omnibus. https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE254045. GSE254045."},{"key":"dataset3","type":"dataset","article-title":"Genome reorganization and its functional impact during breast cancer progression [ATAC-Seq]","volume-title":"NCBI Gene Expression Omnibus","author":"Reed","year":"2026","unstructured":"Reed KS, Misteli T, Fritz A, Greenyer H, Frietze S, Stein J, Stein G. 2026. Genome reorganization and its functional impact during breast cancer progression [ATAC-Seq]. NCBI Gene Expression Omnibus. https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE320215. GSE320215."},{"key":"dataset4","type":"dataset","article-title":"Genome reorganization and its functional impact during breast cancer progression [RNA-Seq]","volume-title":"NCBI Gene Expression Omnibus","author":"Reed","year":"2026","unstructured":"Reed KS, Misteli T, Fritz A, Greenyer H, Frietze S, Stein J, Stein G. 2026. Genome reorganization and its functional impact during breast cancer progression [RNA-Seq]. NCBI Gene Expression Omnibus. https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE320216. GSE320216."},{"key":"dataset5","type":"dataset","article-title":"Chromatin structure and CTCF across the MCF10 breast cancer progression series (ChIP-Seq)","volume-title":"NCBI Gene Expression Omnibus","author":"Fritz","year":"2017","unstructured":"Fritz A, Boyd J, Tye C, Lian J, Stein G. 2017. Chromatin structure and CTCF across the MCF10 breast cancer progression series (ChIP-Seq). NCBI Gene Expression Omnibus. https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE98551. GSE98551."},{"key":"dataset6","type":"dataset","article-title":"Long-range genomic contacts and spatiotemporal chromatin landscape of human histone gene clusters at Histone Locus Bodies during the cell cycle in breast cancer [ChIP-seq]","volume-title":"NCBI Gene Expression Omnibus","author":"Stein","year":"2023","unstructured":"Stein G, Boyd JR, Ghule P, Frietze S. 2023. Long-range genomic contacts and spatiotemporal chromatin landscape of human histone gene clusters at Histone Locus Bodies during the cell cycle in breast cancer [ChIP-seq]. NCBI Gene Expression Omnibus. https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE229295. GSE229295."}],"container-title":["eLife"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/cdn.elifesciences.org\/articles\/108135\/elife-108135-v1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/cdn.elifesciences.org\/articles\/108135\/elife-108135-v1.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/elifesciences.org\/articles\/108135","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T08:56:52Z","timestamp":1787561812000},"score":1,"resource":{"primary":{"URL":"https:\/\/elifesciences.org\/articles\/108135"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,16]]},"references-count":145,"alternative-id":["10.7554\/eLife.108135"],"URL":"https:\/\/doi.org\/10.7554\/elife.108135","archive":["CLOCKSS"],"relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.05.14.654144","asserted-by":"subject"}],"references":[{"id-type":"accession","id":"GSE98551","asserted-by":"subject"},{"id-type":"accession","id":"GSE229295","asserted-by":"subject"}],"is-same-as":[{"id-type":"doi","id":"10.7554\/eLife.108135.3","asserted-by":"subject"}],"is-version-of":[{"id-type":"doi","id":"10.7554\/eLife.108135.1","asserted-by":"subject"},{"id-type":"doi","id":"10.7554\/eLife.108135.2","asserted-by":"subject"}],"is-supplemented-by":[{"id-type":"accession","id":"GSE320319","asserted-by":"subject"},{"id-type":"accession","id":"GSE254045","asserted-by":"subject"},{"id-type":"accession","id":"GSE320215","asserted-by":"subject"},{"id-type":"accession","id":"GSE320216","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/archive.softwareheritage.org\/swh:1:dir:e662a6b50726f3f993a41cb0bbe858c937879b12;origin=https:\/\/github.com\/ksmetz\/MCF10-MicroC;visit=swh:1:snp:90dafbab49f06c1b52242cd1775c51ed94088905;anchor=swh:1:rev:513532d48f436b1cbbdfda894601909166bc2cdb","asserted-by":"subject"}]},"ISSN":["2050-084X"],"issn-type":[{"value":"2050-084X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,16]]},"assertion":[{"value":"single anonymised","name":"peer_review_transparency","label":"Peer review transparency","group":{"name":"peer_review_taxonomy"}},{"value":"other reviewer(s), editor","name":"peer_review_interaction","label":"Peer review interaction","group":{"name":"peer_review_taxonomy"}},{"value":"review summaries, review reports, author\/editor communication, reviewer identities reviewer opt in, editor identities","name":"peer_review_published","label":"Peer review published","group":{"name":"peer_review_taxonomy"}},{"value":"open (sign in with ORCID iD required)","name":"post_publication_commenting","label":"Post publication commenting","group":{"name":"post_publication_commenting"}}],"article-number":"RP108135"}}