{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T04:44:59Z","timestamp":1781239499908,"version":"3.54.1"},"reference-count":66,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2025,8,22]],"date-time":"2025-08-22T00:00:00Z","timestamp":1755820800000},"content-version":"vor","delay-in-days":11,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","award":["CEX2020-001049-S"],"award-info":[{"award-number":["CEX2020-001049-S"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","award":["MCIN\/AEI \/10.13039\/501100011033"],"award-info":[{"award-number":["MCIN\/AEI \/10.13039\/501100011033"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002809","name":"Generalitat de Catalunya","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union's Horizon Europe Programme","award":["101039265"],"award-info":[{"award-number":["101039265"]}]},{"name":"European Union's Horizon Europe Programme","award":["101088408"],"award-info":[{"award-number":["101088408"]}]},{"name":"Swedish Cancer Research Foundation","award":["22 2240 Pj 01 H"],"award-info":[{"award-number":["22 2240 Pj 01 H"]}]},{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["2020-02657_3"],"award-info":[{"award-number":["2020-02657_3"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004410","name":"EMBO","doi-asserted-by":"publisher","award":["10156"],"award-info":[{"award-number":["10156"]}],"id":[{"id":"10.13039\/100004410","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","award":["PRE2019-087574"],"award-info":[{"award-number":["PRE2019-087574"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"name":"EMERALD International PhD Programme","award":["101034290"],"award-info":[{"award-number":["101034290"]}]},{"DOI":"10.13039\/100005910","name":"AEI","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005910","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","award":["JDC2022-049014-I"],"award-info":[{"award-number":["JDC2022-049014-I"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"ERC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,8,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Chromosomal translocations have largely been implicated in tumor development. However, beyond the consequences of aberrant gene expression near the breakpoint, their effects remain underexplored. In this work, we characterize the interplay between translocations, chromatin organization and gene expression using mantle cell lymphoma (MCL) as a model. We show by in vitro genomic engineering and in MCL patient samples that translocations can drive transcriptional changes at entire chromosome arms affecting multiple genes in a regulon-like fashion. Moreover, we demonstrate a clear link between the translocation-induced transcriptional alterations and genome organization, with genes most susceptible to change expression forming pre-existing ultra-long-range interactions spanning 50 megabases. The translocation involves the strong immunoglobulin enhancer into this 3D interaction, allowing the spread of its regulatory potential over the entire affected chromosome arm. Finally, we show that translocation-induced effects mainly represent expression enhancement of genes already active prior to translocation formation, highlighting the importance of the epigenetic state of the cell in which this initial hit occurs. In summary, by studying genome organization principles in the context of translocations, we describe a new principle of gene regulation, showing that strong enhancers can induce substantial gene expression enhancement through ultra-long-range interactions affecting entire chromosome arms, representing an important new mechanism in health and disease.<\/jats:p>","DOI":"10.1093\/nar\/gkaf677","type":"journal-article","created":{"date-parts":[[2025,8,22]],"date-time":"2025-08-22T00:02:32Z","timestamp":1755820952000},"source":"Crossref","is-referenced-by-count":2,"title":["Translocations can drive expression changes of multiple genes in regulons covering entire chromosome arms"],"prefix":"10.1093","volume":"53","author":[{"given":"Anna","family":"Oncins","sequence":"first","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , C. Dr. Aiguader 88, Barcelona 08003,","place":["Spain"]},{"name":"Universitat Pompeu Fabra (UPF) Department of Medicine and Life Sciences, , Barcelona 08003,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roser","family":"Zaurin","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , C. Dr. Aiguader 88, Barcelona 08003,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Houyem","family":"Toukabri","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , C. Dr. Aiguader 88, Barcelona 08003,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kimberly","family":"Quililan","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , C. Dr. Aiguader 88, Barcelona 08003,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9\u00a0R","family":"Hern\u00e1ndez\u00a0Mora","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , C. Dr. Aiguader 88, Barcelona 08003,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Magdalena\u00a0A","family":"Karpinska","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Multidisciplinary Sciences Department of\u00a0Genome Organization and Regulation, , G\u00f6ttingen 37077,","place":["Germany"]},{"name":"aculty of Biology and Psychology, Georg August University of G\u00f6ttingen F , G\u00f6ttingen 37073,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erik","family":"Wernersson","sequence":"additional","affiliation":[{"name":"Tumor and Cell Biology, Karolinska Institutet Department of Microbiology, , Stockholm 17165 ,","place":["Sweden"]},{"name":"Science for Life Laboratory Department of Cell and Molecular Biology, , Solna 17165,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alastair","family":"Smith","sequence":"additional","affiliation":[{"name":"MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford , Oxford\u00a0OX3 9DS ,","place":["UK"]},{"name":"MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford , Oxford\u00a0OX3 9DS ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agostina","family":"Bianchi","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , C. Dr. Aiguader 88, Barcelona 08003,","place":["Spain"]},{"name":"Universitat Pompeu Fabra (UPF) Department of Medicine and Life Sciences, , Barcelona 08003,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leone","family":"Albinati","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , C. Dr. Aiguader 88, Barcelona 08003,","place":["Spain"]},{"name":"Universitat Pompeu Fabra (UPF) Department of Medicine and Life Sciences, , Barcelona 08003,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luca","family":"Cozzuto","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , C. Dr. Aiguader 88, Barcelona 08003,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Rivero","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , C. Dr. Aiguader 88, Barcelona 08003,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chloe","family":"Gulliver","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , C. Dr. Aiguader 88, Barcelona 08003,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"Velten","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , C. Dr. Aiguader 88, Barcelona 08003,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johanna","family":"Denkena","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , C. Dr. Aiguader 88, Barcelona 08003,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fran\u00e7ois","family":"Serra","sequence":"additional","affiliation":[{"name":"Barcelona Supercomputing Center Life Sciences Department, , Barcelona\u00a008034 ,","place":["Spain"]},{"name":"Carlos Simon Foundation Present: , 46980 Paterna, Valencia,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ra\u00fal","family":"G\u00f3mez","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , C. Dr. Aiguader 88, Barcelona 08003,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristina","family":"L\u00f3pez","sequence":"additional","affiliation":[{"name":"Lymphoid Neoplasms Program, Institut d\u2019Investigacions Biom\u00e8diques August Pi i Sunyer (IDIBAPS) , Barcelona 08036,","place":["Spain"]},{"name":"Departamento de Tumores Hematol\u00f3gicos, Centro de Investigaci\u00f3n Biom\u00e9dica en Red de C\u00e1ncer (CIBERONC) , Madrid 28029,","place":["Spain"]},{"name":"Departament de Fonaments Cl\u00ednics,\u00a0University of Barcelona , Barcelona\u00a008036 ,","place":["Spain"]},{"name":"Hospital Cl\u00ednic Barcelona Hematopathology Section, Pathology Department, , Barcelona \u00a008036,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S\u00edlvia","family":"Be\u00e0","sequence":"additional","affiliation":[{"name":"Lymphoid Neoplasms Program, Institut d\u2019Investigacions Biom\u00e8diques August Pi i Sunyer (IDIBAPS) , Barcelona 08036,","place":["Spain"]},{"name":"Departamento de Tumores Hematol\u00f3gicos, Centro de Investigaci\u00f3n Biom\u00e9dica en Red de C\u00e1ncer (CIBERONC) , Madrid 28029,","place":["Spain"]},{"name":"Departament de Fonaments Cl\u00ednics,\u00a0University of Barcelona , Barcelona\u00a008036 ,","place":["Spain"]},{"name":"Hospital Cl\u00ednic Barcelona Hematopathology Section, Pathology Department, , Barcelona \u00a008036,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7918-5495","authenticated-orcid":false,"given":"Jonas","family":"Paulsen","sequence":"additional","affiliation":[{"name":"Faculty of Mathematics and Natural Sciences, University of Oslo Department of Biosciences, , 0316 Oslo ,","place":["Norway"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadia","family":"Halidi","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , C. Dr. Aiguader 88, Barcelona 08003,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[{"name":"Barcelona Supercomputing Center Life Sciences Department, , Barcelona\u00a008034 ,","place":["Spain"]},{"name":"Instituci\u00f3 Catalana de Recerca Avan\u00e7ada (ICREA) Department of Life & Medical Sciences, , Barcelona 08010,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Magda","family":"Bienko","sequence":"additional","affiliation":[{"name":"Tumor and Cell Biology, Karolinska Institutet Department of Microbiology, , Stockholm 17165 ,","place":["Sweden"]},{"name":"Science for Life Laboratory Department of Cell and Molecular Biology, , Solna 17165,","place":["Sweden"]},{"name":"Human Technopole , Viale Rita Levi-Montalcini 1, 20157 Milan ,","place":["Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A\u00a0Marieke","family":"Oudelaar","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Multidisciplinary Sciences Department of\u00a0Genome Organization and Regulation, , G\u00f6ttingen 37077,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7081-7874","authenticated-orcid":false,"given":"Ren\u00e9e","family":"Beekman","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , C. Dr. Aiguader 88, Barcelona 08003,","place":["Spain"]},{"name":"Universitat Pompeu Fabra (UPF) Department of Medicine and Life Sciences, , Barcelona 08003,","place":["Spain"]},{"name":"Lymphoid Neoplasms Program, Institut d\u2019Investigacions Biom\u00e8diques August Pi i Sunyer (IDIBAPS) , Barcelona 08036,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,8,22]]},"reference":[{"key":"2025082120022716300_B1","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1038\/35066075","article-title":"Chromosome territories, nuclear architecture and gene regulation in mammalian cells","volume":"2","author":"Cremer","year":"2001","journal-title":"Nat Rev Genet"},{"key":"2025082120022716300_B2","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1093\/hmg\/10.3.211","article-title":"The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells","volume":"10","author":"Boyle","year":"2001","journal-title":"Hum Mol Genet"},{"key":"2025082120022716300_B3","doi-asserted-by":"crossref","first-page":"2038","DOI":"10.1016\/j.celrep.2016.04.085","article-title":"Formation of chromosomal domains by loop extrusion","volume":"15","author":"Fudenberg","year":"2016","journal-title":"Cell Rep"},{"key":"2025082120022716300_B4","doi-asserted-by":"publisher","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","article-title":"A three-dimensional map of the human genome at kilobase resolution reveals principles of chromatin looping","volume":"159","author":"Rao","year":"2014","journal-title":"Cell"},{"key":"2025082120022716300_B5","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1038\/nature11082","article-title":"Topological domains in mammalian genomes identified by analysis of chromatin interactions","volume":"485","author":"Dixon","year":"2012","journal-title":"Nature"},{"key":"2025082120022716300_B6","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1126\/science.1181369","article-title":"Comprehensive mapping of long range interactions reveals folding principles of the human genome","volume":"326","author":"Aiden","year":"2009","journal-title":"Science"},{"key":"2025082120022716300_B7","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1038\/s41594-020-0506-5","article-title":"Multi-contact 3C reveals that the human genome during interphase is largely not entangled","volume":"27","author":"Tavares-Cadete","year":"2020","journal-title":"Nat Struct Mol Biol"},{"key":"2025082120022716300_B8","doi-asserted-by":"publisher","first-page":"1184","DOI":"10.1038\/s41587-020-0519-y","article-title":"GPSeq reveals the radial organization of chromatin in the cell nucleus","volume":"38","author":"Girelli","year":"2020","journal-title":"Nat Biotechnol"},{"key":"2025082120022716300_B9","doi-asserted-by":"publisher","first-page":"948","DOI":"10.1038\/nature06947","article-title":"Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions","volume":"453","author":"Guelen","year":"2008","journal-title":"Nature"},{"key":"2025082120022716300_B10","first-page":"85","article-title":"Chromosome studies in normal and leukemic Human leukocytes","volume":"25","author":"Nowell","year":"1960","journal-title":"J Natl Cancer Inst"},{"key":"2025082120022716300_B11","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/0092-8674(84)90077-1","article-title":"Philadelphia chromosomal breakpoints are clustered within a limited region, bcr, on chromosome 22","volume":"36","author":"Groffen","year":"1984","journal-title":"Cell"},{"key":"2025082120022716300_B12","doi-asserted-by":"publisher","first-page":"675","DOI":"10.1016\/0092-8674(91)90113-D","article-title":"The PML-RAR\u03b1 fusion mRNA generated by the t(15;17) translocation in acute promyelocytic leukemia encodes a functionally altered RAR","volume":"66","author":"de\u00a0Th\u00e9","year":"1991","journal-title":"Cell"},{"key":"2025082120022716300_B13","first-page":"607","article-title":"The chronic myelocytic cell line K562 contains a breakpoint in bcr and produces a chimeric bcr \/c - abl transcript","volume":"6","author":"Grosveld","year":"1986","journal-title":"Mol Cell Biol"},{"key":"2025082120022716300_B14","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1016\/j.cell.2014.02.019","article-title":"A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in Leukemia","volume":"157","author":"Gr\u00f6schel","year":"2014","journal-title":"Cell"},{"key":"2025082120022716300_B15","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1016\/j.jsb.2006.05.005","article-title":"Localization of genetic elements of intact and derivative chromosome 11 and 22 territories in nuclei of Ewing sarcoma cells","volume":"155","author":"Taslerov\u00e1","year":"2006","journal-title":"J Struct Biol"},{"key":"2025082120022716300_B16","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1007\/s00439-002-0847-7","article-title":"Arrangement of chromosome 11 and 22 territories, EWSR1 and FLI1 genes, and other genetic elements of these chromosomes in human lymphocytes and Ewing sarcoma cells","volume":"112","author":"Taslerov\u00e1","year":"2003","journal-title":"Hum Genet"},{"key":"2025082120022716300_B17","doi-asserted-by":"publisher","first-page":"16044","DOI":"10.3390\/ijms242216044","article-title":"Trisomies reorganize Human 3D genome","volume":"24","author":"Zhegalova","year":"2023","journal-title":"Int J Mol Sci"},{"key":"2025082120022716300_B18","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1038\/nrc1589","article-title":"Mechanisms of B-cell lymphoma pathogenesis","volume":"5","author":"K\u00fcppers","year":"2005","journal-title":"Nat Rev Cancer"},{"key":"2025082120022716300_B19","doi-asserted-by":"publisher","first-page":"750","DOI":"10.1038\/nrc2230","article-title":"Genetic and molecular pathogenesis of mantle cell lymphoma: perspectives for new targeted therapeutics","volume":"7","author":"Jares","year":"2007","journal-title":"Nat Rev Cancer"},{"key":"2025082120022716300_B20","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1002\/hon.3149","article-title":"Mantle cell lymphoma\u2014Update on molecular biology, prognostication and treatment approaches","volume":"41","author":"Silkenstedt","year":"2023","journal-title":"Hematol Oncol"},{"key":"2025082120022716300_B21","doi-asserted-by":"publisher","first-page":"795","DOI":"10.1016\/j.hoc.2020.05.002","article-title":"Molecular pathogenesis of mantle cell lymphoma","volume":"34","author":"Navarro","year":"2020","journal-title":"Hematol Oncol Clin North Am"},{"key":"2025082120022716300_B22","doi-asserted-by":"publisher","first-page":"2124","DOI":"10.1002\/j.1460-2075.1994.tb06488.x","article-title":"Cyclin D1 transgene impedes lymphocyte maturation and collaborates in lymphomagenesis with the myc gene","volume":"13","author":"Bodrug","year":"1994","journal-title":"EMBO J"},{"key":"2025082120022716300_B23","doi-asserted-by":"publisher","first-page":"3487","DOI":"10.1002\/j.1460-2075.1994.tb06655.x","article-title":"Cyclin D1\/bcl-1 cooperates with myc genes in the generation of B-cell lymphoma in transgenic mice","volume":"13","author":"Lovec","year":"1994","journal-title":"EMBO J"},{"key":"2025082120022716300_B24","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-020-20849-y","article-title":"Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation","volume":"12","author":"Vilarrasa-Blasi","year":"2021","journal-title":"Nat Commun"},{"key":"2025082120022716300_B25","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1038\/s41467-018-07885-5","article-title":"Selective single molecule sequencing and assembly of a human Y chromosome of African origin","volume":"10","author":"Kuderna","year":"2019","journal-title":"Nat Commun"},{"key":"2025082120022716300_B26","doi-asserted-by":"publisher","first-page":"e63","DOI":"10.1002\/cphg.63","article-title":"Capture hi-C library generation and analysis to detect chromatin interactions","volume":"98","author":"Orlando","year":"2018","journal-title":"CP Human Genetics"},{"key":"2025082120022716300_B27","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pcbi.1005665","article-title":"Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors","volume":"13","author":"Serra","year":"2017","journal-title":"PLoS Comput Biol"},{"key":"2025082120022716300_B28","doi-asserted-by":"publisher","first-page":"18250","DOI":"10.1073\/pnas.1314608110","article-title":"Landscape of somatic mutations and clonal evolution in mantle cell lymphoma","volume":"110","author":"Be\u00e0","year":"2013","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025082120022716300_B29","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1016\/j.ymeth.2012.04.009","article-title":"Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation","volume":"58","author":"Splinter","year":"2012","journal-title":"Methods"},{"key":"2025082120022716300_B30","doi-asserted-by":"crossref","unstructured":"Danecek P, Bonfield JK, Liddle J \u00a0et al. \u00a0Twelve years of SAMtools and BCFtools. Gigascience. 2021; 10:giab00810.1093\/gigascience\/giab008.","DOI":"10.1093\/gigascience\/giab008"},{"key":"2025082120022716300_B31","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2025082120022716300_B32","doi-asserted-by":"publisher","first-page":"868","DOI":"10.1038\/s41591-018-0028-4","article-title":"The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia","volume":"24","author":"Beekman","year":"2018","journal-title":"Nat Med"},{"key":"2025082120022716300_B33","doi-asserted-by":"publisher","first-page":"2722","DOI":"10.1038\/s41467-020-16598-7","article-title":"Dynamics of the 4D genome during in vivo lineage specification and differentiation","volume":"11","author":"Oudelaar","year":"2020","journal-title":"Nat Commun"},{"key":"2025082120022716300_B34","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1038\/s41596-021-00651-w","article-title":"Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture","volume":"17","author":"Downes","year":"2022","journal-title":"Nat Protoc"},{"key":"2025082120022716300_B35","first-page":"999","article-title":"Iterative correction of hi-C data reveals hallmarks of","volume":"9","author":"Imakaev","year":"2012","journal-title":"Nature"},{"key":"2025082120022716300_B36","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1046\/j.1365-2818.2000.00754.x","article-title":"An efficient algorithm for measurement and correction of chromatic aberrations in fluorescence microscopy","volume":"200","author":"Kozubek","year":"2000","journal-title":"J Microsc"},{"key":"2025082120022716300_B37","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1111\/j.2517-6161.1986.tb01412.x","article-title":"On the statistical analysis of dirty pictures","volume":"48","author":"Besag","year":"1986","journal-title":"J R Stat Soc Ser B Stat Methodol"},{"key":"2025082120022716300_B38","doi-asserted-by":"publisher","first-page":"1362","DOI":"10.1109\/TPAMI.2008.173","article-title":"Watershed cuts: minimum spanning forests and the drop of water principle","volume":"31","author":"Cousty","year":"2009","journal-title":"IEEE Trans Pattern Anal Mach Intell"},{"key":"2025082120022716300_B39","first-page":"331","article-title":"A general algorithm for computing distance transforms in linear time","volume-title":"Math Morphol Its Appl to Image Signal Procesing","author":"Meijster","year":"2000"},{"key":"2025082120022716300_B40","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1186\/s13059-016-1146-2","article-title":"Chrom3D: three-dimensional genome modeling from hi-C and nuclear lamin-genome contacts","volume":"18","author":"Paulsen","year":"2017","journal-title":"Genome Biol"},{"key":"2025082120022716300_B41","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1186\/s13059-017-1156-8","article-title":"Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types","volume":"18","author":"Ecker","year":"2017","journal-title":"Genome Biol"},{"key":"2025082120022716300_B42","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2025082120022716300_B43","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"ClusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS"},{"key":"2025082120022716300_B44","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1186\/1471-2105-14-128","article-title":"Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool","volume":"14","author":"Chen","year":"2013","journal-title":"BMC Bioinf"},{"key":"2025082120022716300_B45","doi-asserted-by":"publisher","first-page":"W90","DOI":"10.1093\/nar\/gkw377","article-title":"Enrichr: a comprehensive gene set enrichment analysis web server 2016 update","volume":"44","author":"Kuleshov","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2025082120022716300_B46","doi-asserted-by":"publisher","first-page":"1096","DOI":"10.1038\/nmeth.2639","article-title":"Smart-seq2 for sensitive full-length transcriptome profiling in single cells","volume":"10","author":"Picelli","year":"2013","journal-title":"Nat Methods"},{"key":"2025082120022716300_B47","doi-asserted-by":"publisher","first-page":"e109457","DOI":"10.15252\/embj.2021109457","article-title":"Controlled X-chromosome dynamics defines meiotic potential of female mouse in vitro germ cells","volume":"41","author":"Severino","year":"2022","journal-title":"EMBO J"},{"key":"2025082120022716300_B48","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1038\/msb.2011.54","article-title":"AlleleSeq: analysis of allele-specific expression and binding in a network framework","volume":"7","author":"Rozowsky","year":"2011","journal-title":"Mol Syst Biol"},{"key":"2025082120022716300_B49","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2025082120022716300_B50","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1038\/nmeth.3582","article-title":"WASP: allele-specific software for robust molecular quantitative trait locus discovery","volume":"12","author":"van de Geijn","year":"2015","journal-title":"Nat Methods"},{"key":"2025082120022716300_B51","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1016\/S0027-5107(02)00077-5","article-title":"Non-random radial arrangements of interphase chromosome territories: evolutionary considerations and functional implications","volume":"504","author":"Tanabe","year":"2002","journal-title":"Mutat Res"},{"key":"2025082120022716300_B52","doi-asserted-by":"publisher","first-page":"0826","DOI":"10.1371\/journal.pbio.0030157","article-title":"Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes","volume":"3","author":"Bolzer","year":"2005","journal-title":"PLoS Biol"},{"key":"2025082120022716300_B53","doi-asserted-by":"publisher","first-page":"4424","DOI":"10.1073\/pnas.072618599","article-title":"Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates","volume":"99","author":"Tanabe","year":"2002","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025082120022716300_B54","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1016\/S0145-2126(97)00191-4","article-title":"Z-138: a new mature B-cell acute lymphoblastic leukemia cell line from a patient with transformed chronic lymphocytic leukemia","volume":"22","author":"Estrov","year":"1998","journal-title":"Leuk Res"},{"key":"2025082120022716300_B55","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/j.bbcan.2008.07.005","article-title":"Chromosomal translocations in cancer","volume":"1786","author":"Nambiar","year":"2008","journal-title":"Biochim Biophys Acta (BBA)"},{"key":"2025082120022716300_B56","doi-asserted-by":"publisher","first-page":"a006157","DOI":"10.1101\/mcs.a006157","article-title":"Hi-C detects genomic structural variants in peripheral blood of pediatric leukemia patients","volume":"8","author":"Mallard","year":"2022","journal-title":"Cold Spring Harb Mol Case Stud"},{"key":"2025082120022716300_B57","doi-asserted-by":"publisher","first-page":"2313","DOI":"10.1038\/sj.leu.2403954","article-title":"Translocation t(14;18) and gain of chromosome 18\/BCL2: effects on BCL2 expression and apoptosis in B-cell non-hodgkin's lymphomas","volume":"19","author":"Galteland","year":"2005","journal-title":"Leukemia"},{"key":"2025082120022716300_B58","doi-asserted-by":"publisher","first-page":"6209","DOI":"10.1002\/j.1460-2075.1995.tb00311.x","article-title":"Chromosomal translocations cause deregulated BCL6 expression by promoter substitution in B cell lymphoma","volume":"14","author":"Ye","year":"1995","journal-title":"EMBO J"},{"key":"2025082120022716300_B59","first-page":"575","article-title":"Understanding MYC-driven aggressive B-cell lymphomas: pathogenesis and classification","author":"Ott","year":"2013"},{"key":"2025082120022716300_B60","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1023\/A:1012495201697","article-title":"Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells","volume":"9","author":"Cremer","year":"2001","journal-title":"Chromosom Res"},{"key":"2025082120022716300_B61","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1083\/jcb.145.6.1119","article-title":"Differences in the localization and morphology of chromosomes in the human nucleus","volume":"145","author":"Croft","year":"1999","journal-title":"J Cell Biol"},{"key":"2025082120022716300_B62","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1016\/S0006-3495(00)76282-5","article-title":"Size-dependent positioning of human chromosomes in interphase nuclei","volume":"79","author":"Sun","year":"2000","journal-title":"Biophys J"},{"key":"2025082120022716300_B63","doi-asserted-by":"publisher","first-page":"8303571","DOI":"10.1155\/2018\/8303571","article-title":"Blastoid variant mantle cell lymphoma expressing aberrant CD3 and CD10 with concurrent small lymphocytic lymphoma: establishment of a clonal relationship by B- and T-cell receptor gene rearrangements","volume":"2018","author":"Felten","year":"2018","journal-title":"Case Rep Hematol"},{"key":"2025082120022716300_B64","doi-asserted-by":"publisher","first-page":"1388","DOI":"10.1182\/blood-2017-05-783274","article-title":"Cyclin D1\u2212negative mantle cell lymphoma with aberrant CD3 expression","volume":"130","author":"Malek","year":"2017","journal-title":"Blood"},{"key":"2025082120022716300_B65","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1038\/s42003-023-05719-9","article-title":"A biphenotypic lymphocyte subset displays both T- and B-cell functionalities","volume":"7","author":"zhang","year":"2024","journal-title":"Commun Biol"},{"key":"2025082120022716300_B66","doi-asserted-by":"publisher","first-page":"9289417","DOI":"10.1155\/2018\/9289417","article-title":"CD3+ B-1a cells as a mediator of disease progression in autoimmune-prone mice","volume":"2018","author":"Yamamoto","year":"2018","journal-title":"Mediat Inflamm"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/53\/15\/gkaf677\/64039540\/gkaf677.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/53\/15\/gkaf677\/64039540\/gkaf677.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,22]],"date-time":"2025-08-22T00:02:36Z","timestamp":1755820956000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/doi\/10.1093\/nar\/gkaf677\/8234008"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,11]]},"references-count":66,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2025,8,11]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaf677","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,8,28]]},"published":{"date-parts":[[2025,8,11]]},"article-number":"gkaf677"}}