{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T03:12:34Z","timestamp":1792725154914,"version":"4.5.0"},"reference-count":79,"publisher":"Springer Science and Business Media LLC","issue":"7","license":[{"start":{"date-parts":[[2025,5,16]],"date-time":"2025-05-16T00:00:00Z","timestamp":1747353600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,5,16]],"date-time":"2025-05-16T00:00:00Z","timestamp":1747353600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Struct Mol Biol"],"published-print":{"date-parts":[[2025,7]]},"DOI":"10.1038\/s41594-025-01559-9","type":"journal-article","created":{"date-parts":[[2025,5,16]],"date-time":"2025-05-16T05:02:28Z","timestamp":1747371748000},"page":"1193-1204","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["DEK\u2013nucleosome structure shows DEK modulates H3K27me3 and stem cell fate"],"prefix":"10.1038","volume":"32","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-8515-3104","authenticated-orcid":false,"given":"Yunfan","family":"Shen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanhong","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maochao","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Song","family":"Mao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3821-0436","authenticated-orcid":false,"given":"Rui","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengran","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhengbo","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wan","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fang","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2502-9785","authenticated-orcid":false,"given":"Baixing","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7477-5376","authenticated-orcid":false,"given":"Chongyuan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3263-1627","authenticated-orcid":false,"given":"Wei","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6190-6135","authenticated-orcid":false,"given":"Huanhuan","family":"Cui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7002-5703","authenticated-orcid":false,"given":"Kai","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6741-7677","authenticated-orcid":false,"given":"Hongda","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,5,16]]},"reference":[{"key":"1559_CR1","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1016\/j.exphem.2023.05.002","volume":"123","author":"KE Wilcher","year":"2023","unstructured":"Wilcher, K. E., Page, E. R. H. & Privette Vinnedge, L. M. The impact of the chromatin binding DEK protein in hematopoiesis and acute myeloid leukemia. Exp. Hematol. 123, 18\u201327 (2023).","journal-title":"Exp. Hematol."},{"key":"1559_CR2","doi-asserted-by":"publisher","first-page":"106517","DOI":"10.1155\/2015\/106517","volume":"2015","author":"NA Pease","year":"2015","unstructured":"Pease, N. A., Wise-Draper, T. & Privette Vinnedge, L. Dissecting the potential interplay of DEK functions in inflammation and cancer. J. Oncol. 2015, 106517 (2015).","journal-title":"J. Oncol."},{"key":"1559_CR3","first-page":"1687","volume":"12","author":"M von Lindern","year":"1992","unstructured":"von Lindern, M. et al. The translocation (6;9), associated with a specific subtype of acute myeloid leukemia, results in the fusion of two genes, dek and can, and the expression of a chimeric, leukemia-specific dek\u2013can mRNA. Mol. Cell. Biol. 12, 1687\u20131697 (1992).","journal-title":"Mol. Cell. Biol."},{"key":"1559_CR4","doi-asserted-by":"publisher","first-page":"1910","DOI":"10.1038\/leu.2010.180","volume":"24","author":"C Oancea","year":"2010","unstructured":"Oancea, C., R\u00fcster, B., Henschler, R., Puccetti, E. & Ruthardt, M. The t(6;9) associated DEK\/CAN fusion protein targets a population of long-term repopulating hematopoietic stem cells for leukemogenic transformation. Leukemia 24, 1910\u20131919 (2010).","journal-title":"Leukemia"},{"key":"1559_CR5","doi-asserted-by":"publisher","first-page":"767","DOI":"10.1038\/s41591-019-0434-2","volume":"25","author":"W Yang","year":"2019","unstructured":"Yang, W. et al. Immunogenic neoantigens derived from gene fusions stimulate T cell responses. Nat. Med. 25, 767\u2013775 (2019).","journal-title":"Nat. Med."},{"key":"1559_CR6","doi-asserted-by":"publisher","first-page":"1632","DOI":"10.1038\/leu.2015.72","volume":"29","author":"C Sanden","year":"2015","unstructured":"Sanden, C. & Gullberg, U. The DEK oncoprotein and its emerging roles in gene regulation. Leukemia 29, 1632\u20131636 (2015).","journal-title":"Leukemia"},{"key":"1559_CR7","doi-asserted-by":"publisher","first-page":"1308","DOI":"10.1101\/gad.14.11.1308","volume":"14","author":"V Alexiadis","year":"2000","unstructured":"Alexiadis, V. et al. The protein encoded by the proto-oncogene DEK changes the topology of chromatin and reduces the efficiency of DNA replication in a chromatin-specific manner. Genes Dev. 14, 1308\u20131312 (2000).","journal-title":"Genes Dev."},{"key":"1559_CR8","doi-asserted-by":"publisher","first-page":"26317","DOI":"10.1074\/jbc.M100162200","volume":"276","author":"F Kappes","year":"2001","unstructured":"Kappes, F., Burger, K., Baack, M., Fackelmayer, F. O. & Gruss, C. Subcellular localization of the human proto-oncogene protein DEK. J. Biol. Chem. 276, 26317\u201326323 (2001).","journal-title":"J. Biol. Chem."},{"key":"1559_CR9","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1101\/gad.2036411","volume":"25","author":"F Kappes","year":"2011","unstructured":"Kappes, F. et al. The DEK oncoprotein is a Su(var) that is essential to heterochromatin integrity. Genes Dev. 25, 673\u2013678 (2011).","journal-title":"Genes Dev."},{"key":"1559_CR10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.gene.2004.08.029","volume":"343","author":"T Waldmann","year":"2004","unstructured":"Waldmann, T., Scholten, I., Kappes, F., Hu, H. G. & Knippers, R. The DEK protein\u2014an abundant and ubiquitous constituent of mammalian chromatin. Gene 343, 1\u20139 (2004).","journal-title":"Gene"},{"key":"1559_CR11","doi-asserted-by":"publisher","first-page":"1584","DOI":"10.1101\/gr.173831.114","volume":"24","author":"K Ivanauskiene","year":"2014","unstructured":"Ivanauskiene, K. et al. The PML-associated protein DEK regulates the balance of H3.3 loading on chromatin and is important for telomere integrity. Genome Res. 24, 1584\u20131594 (2014).","journal-title":"Genome Res."},{"key":"1559_CR12","doi-asserted-by":"publisher","first-page":"548","DOI":"10.1038\/nsmb1248","volume":"14","author":"MJ Gamble","year":"2007","unstructured":"Gamble, M. J. & Fisher, R. P. SET and PARP1 remove DEK from chromatin to permit access by the transcription machinery. Nat. Struct. Mol. Biol. 14, 548\u2013555 (2007).","journal-title":"Nat. Struct. Mol. Biol."},{"key":"1559_CR13","doi-asserted-by":"publisher","first-page":"556","DOI":"10.1002\/art.30138","volume":"63","author":"N Mor\u2010Vaknin","year":"2011","unstructured":"Mor\u2010Vaknin, N. et al. DEK in the synovium of patients with juvenile idiopathic arthritis: characterization of DEK antibodies and posttranslational modification of the DEK autoantigen. Arthritis Rheum. 63, 556\u2013567 (2011).","journal-title":"Arthritis Rheum."},{"key":"1559_CR14","doi-asserted-by":"publisher","first-page":"6011","DOI":"10.1128\/MCB.24.13.6011-6020.2004","volume":"24","author":"F Kappes","year":"2004","unstructured":"Kappes, F. et al. Phosphorylation by protein kinase CK2 changes the DNA binding properties of the human chromatin protein DEK. Mol. Cell. Biol. 24, 6011\u20136020 (2004).","journal-title":"Mol. Cell. Biol."},{"key":"1559_CR15","doi-asserted-by":"publisher","first-page":"31760","DOI":"10.1074\/jbc.M500884200","volume":"280","author":"J Cleary","year":"2005","unstructured":"Cleary, J. et al. p300\/CBP-associated factor drives DEK into interchromatin granule clusters. J. Biol. Chem. 280, 31760\u201331767 (2005).","journal-title":"J. Biol. Chem."},{"key":"1559_CR16","doi-asserted-by":"publisher","first-page":"3245","DOI":"10.1128\/MCB.01921-07","volume":"28","author":"F Kappes","year":"2008","unstructured":"Kappes, F. et al. DEK is a poly(ADP-ribose) acceptor in apoptosis and mediates resistance to genotoxic stress. Mol. Cell. Biol. 28, 3245\u20133257 (2008).","journal-title":"Mol. Cell. Biol."},{"key":"1559_CR17","doi-asserted-by":"publisher","first-page":"jcs261329","DOI":"10.1242\/jcs.261329","volume":"136","author":"A Pierzynska-Mach","year":"2023","unstructured":"Pierzynska-Mach, A. et al. DEK oncoprotein participates in heterochromatin replication via SUMO-dependent nuclear bodies. J. Cell Sci. 136, jcs261329 (2023).","journal-title":"J. Cell Sci."},{"key":"1559_CR18","doi-asserted-by":"publisher","first-page":"1447","DOI":"10.1002\/stem.1443","volume":"31","author":"HE Broxmeyer","year":"2013","unstructured":"Broxmeyer, H. E. et al. Concise review: role of DEK in stem\/progenitor cell biology. Stem Cells 31, 1447\u20131453 (2013).","journal-title":"Stem Cells"},{"key":"1559_CR19","doi-asserted-by":"publisher","first-page":"51","DOI":"10.4161\/cc.23121","volume":"12","author":"LM Privette Vinnedge","year":"2013","unstructured":"Privette Vinnedge, L. M., Kappes, F., Nassar, N. & Wells, S. I. Stacking the DEK: from chromatin topology to cancer stem cells. Cell Cycle 12, 51\u201366 (2013).","journal-title":"Cell Cycle"},{"key":"1559_CR20","doi-asserted-by":"publisher","first-page":"e20201974","DOI":"10.1084\/jem.20201974","volume":"218","author":"Z Chen","year":"2021","unstructured":"Chen, Z. et al. Nuclear DEK preserves hematopoietic stem cells potential via NCoR1\/HDAC3\u2013Akt1\/2\u2013mTOR axis. J. Exp. Med. 218, e20201974 (2021).","journal-title":"J. Exp. Med."},{"key":"1559_CR21","doi-asserted-by":"publisher","first-page":"2624","DOI":"10.1038\/s41388-022-02278-x","volume":"41","author":"YS Yang","year":"2022","unstructured":"Yang, Y. S. et al. Exosomal DEK removes chemoradiotherapy resistance by triggering quiescence exit of breast cancer stem cells. Oncogene 41, 2624\u20132637 (2022).","journal-title":"Oncogene"},{"key":"1559_CR22","doi-asserted-by":"publisher","first-page":"2252","DOI":"10.1110\/ps.04797104","volume":"13","author":"M Devany","year":"2004","unstructured":"Devany, M., Kotharu, N. P. & Matsuo, H. Solution NMR structure of the C-terminal domain of the human protein DEK. Protein Sci. 13, 2252\u20132259 (2004).","journal-title":"Protein Sci."},{"key":"1559_CR23","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1110\/ps.073244108","volume":"17","author":"M Devany","year":"2008","unstructured":"Devany, M., Kappes, F., Chen, K. M., Markovitz, D. M. & Matsuo, H. Solution NMR structure of the N-terminal domain of the human DEK protein. Protein Sci. 17, 205\u2013215 (2008).","journal-title":"Protein Sci."},{"key":"1559_CR24","doi-asserted-by":"publisher","first-page":"1438","DOI":"10.1002\/1873-3468.14070","volume":"595","author":"H Guo","year":"2021","unstructured":"Guo, H. et al. Bacterial growth inhibition screen (BGIS) identifies a loss-of-function mutant of the DEK oncogene, indicating DNA modulating activities of DEK in chromatin. FEBS Lett. 595, 1438\u20131453 (2021).","journal-title":"FEBS Lett."},{"key":"1559_CR25","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1101\/gad.1857410","volume":"24","author":"S Sawatsubashi","year":"2010","unstructured":"Sawatsubashi, S. et al. A histone chaperone, DEK, transcriptionally coactivates a nuclear receptor. Genes Dev. 24, 159\u2013170 (2010).","journal-title":"Genes Dev."},{"key":"1559_CR26","doi-asserted-by":"publisher","DOI":"10.1186\/1476-4598-13-215","volume":"13","author":"C Sand\u00e9n","year":"2014","unstructured":"Sand\u00e9n, C. et al. The DEK oncoprotein binds to highly and ubiquitously expressed genes with a dual role in their transcriptional regulation. Mol. Cancer 13, 215 (2014).","journal-title":"Mol. Cancer"},{"key":"1559_CR27","doi-asserted-by":"publisher","first-page":"2843","DOI":"10.1016\/j.cell.2021.04.020","volume":"184","author":"H Shen","year":"2021","unstructured":"Shen, H. et al. Mouse totipotent stem cells captured and maintained through spliceosomal repression. Cell 184, 2843\u20132859 (2021).","journal-title":"Cell"},{"key":"1559_CR28","doi-asserted-by":"crossref","unstructured":"The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57 (2012).","DOI":"10.1038\/nature11247"},{"key":"1559_CR29","doi-asserted-by":"publisher","first-page":"807","DOI":"10.1038\/s41592-020-0907-8","volume":"17","author":"A Sethi","year":"2020","unstructured":"Sethi, A. et al. Supervised enhancer prediction with epigenetic pattern recognition and targeted validation. Nat. Methods 17, 807\u2013814 (2020).","journal-title":"Nat. Methods"},{"key":"1559_CR30","doi-asserted-by":"publisher","first-page":"12019","DOI":"10.1093\/nar\/gkac230","volume":"50","author":"X Dong","year":"2022","unstructured":"Dong, X. et al. YY1 safeguard multidimensional epigenetic landscape associated with extended pluripotency. Nucleic Acids Res. 50, 12019\u201312038 (2022).","journal-title":"Nucleic Acids Res."},{"key":"1559_CR31","doi-asserted-by":"publisher","first-page":"2384","DOI":"10.1093\/brain\/awae051","volume":"147","author":"P Rodriguez-Rodriguez","year":"2024","unstructured":"Rodriguez-Rodriguez, P. et al. A cell autonomous regulator of neuronal excitability modulates tau in Alzheimer\u2019s disease vulnerable neurons. Brain 147, 2384\u20132399 (2024).","journal-title":"Brain"},{"key":"1559_CR32","doi-asserted-by":"publisher","first-page":"4328","DOI":"10.1105\/tpc.114.129254","volume":"26","author":"S Waidmann","year":"2014","unstructured":"Waidmann, S., Kusenda, B., Mayerhofer, J., Mechtler, K. & Jonak, C. A DEK domain-containing protein modulates chromatin structure and function in Arabidopsis. Plant Cell 26, 4328\u20134344 (2014).","journal-title":"Plant Cell"},{"key":"1559_CR33","doi-asserted-by":"publisher","unstructured":"Brestovitsky, A. et al. DEK influences the trade-off between growth and arrest via H2A.Z-nucleosomes in Arabidopsis. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/829226 (2019).","DOI":"10.1101\/829226"},{"key":"1559_CR34","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1111\/nph.17366","volume":"231","author":"W Zong","year":"2021","unstructured":"Zong, W. et al. DEK domain-containing proteins control flowering time in Arabidopsis. New Phytol. 231, 182\u2013192 (2021).","journal-title":"New Phytol."},{"key":"1559_CR35","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1126\/science.aay3325","volume":"375","author":"Y Ohinata","year":"2022","unstructured":"Ohinata, Y. et al. Establishment of mouse stem cells that can recapitulate the developmental potential of primitive endoderm. Science 375, 574\u2013578 (2022).","journal-title":"Science"},{"key":"1559_CR36","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1016\/j.devcel.2019.01.003","volume":"48","author":"S Schlesinger","year":"2019","unstructured":"Schlesinger, S. & Meshorer, E. Open chromatin, epigenetic plasticity, and nuclear organization in pluripotency. Dev. Cell 48, 135\u2013150 (2019).","journal-title":"Dev. Cell"},{"key":"1559_CR37","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1038\/s41586-019-1127-1","volume":"569","author":"S Nowotschin","year":"2019","unstructured":"Nowotschin, S. et al. The emergent landscape of the mouse gut endoderm at single-cell resolution. Nature 569, 361\u2013367 (2019).","journal-title":"Nature"},{"key":"1559_CR38","doi-asserted-by":"publisher","first-page":"1215","DOI":"10.1016\/j.celrep.2017.07.009","volume":"20","author":"H Mohammed","year":"2017","unstructured":"Mohammed, H. et al. Single-cell landscape of transcriptional heterogeneity and cell fate decisions during mouse early gastrulation. Cell Rep. 20, 1215\u20131228 (2017).","journal-title":"Cell Rep."},{"key":"1559_CR39","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-31938-5","volume":"13","author":"JJ Thompson","year":"2022","unstructured":"Thompson, J. J. et al. Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages. Nat. Commun. 13, 4257 (2022).","journal-title":"Nat. Commun."},{"key":"1559_CR40","doi-asserted-by":"publisher","first-page":"1238","DOI":"10.1038\/s41588-022-01132-w","volume":"54","author":"V Asimi","year":"2022","unstructured":"Asimi, V. et al. Hijacking of transcriptional condensates by endogenous retroviruses. Nat. Genet. 54, 1238\u20131247 (2022).","journal-title":"Nat. Genet."},{"key":"1559_CR41","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1038\/86912","volume":"27","author":"S Kalantry","year":"2001","unstructured":"Kalantry, S. et al. The amnionless gene, essential for mouse gastrulation, encodes a visceral-endoderm-specific protein with an extracellular cysteine-rich domain. Nat. Genet. 27, 412\u2013416 (2001).","journal-title":"Nat. Genet."},{"key":"1559_CR42","doi-asserted-by":"publisher","first-page":"6847","DOI":"10.1073\/pnas.1220751110","volume":"110","author":"AK Saha","year":"2013","unstructured":"Saha, A. K. et al. Intercellular trafficking of the nuclear oncoprotein DEK. Proc. Natl Acad. Sci. USA 110, 6847\u20136852 (2013).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"1559_CR43","doi-asserted-by":"publisher","first-page":"9415","DOI":"10.1093\/nar\/gkaa544","volume":"48","author":"A Skrajna","year":"2020","unstructured":"Skrajna, A. et al. Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding. Nucleic Acids Res. 48, 9415\u20139432 (2020).","journal-title":"Nucleic Acids Res."},{"key":"1559_CR44","doi-asserted-by":"publisher","first-page":"856","DOI":"10.1126\/science.1120541","volume":"311","author":"AJ Barbera","year":"2006","unstructured":"Barbera, A. J. et al. The nucleosomal surface as a docking station for Kaposi\u2019s sarcoma herpesvirus LANA. Science 311, 856\u2013861 (2006).","journal-title":"Science"},{"key":"1559_CR45","doi-asserted-by":"publisher","first-page":"562","DOI":"10.1038\/nature09321","volume":"467","author":"RD Makde","year":"2010","unstructured":"Makde, R. D., England, J. R., Yennawar, H. P. & Tan, S. Structure of RCC1 chromatin factor bound to the nucleosome core particle. Nature 467, 562\u2013566 (2010).","journal-title":"Nature"},{"key":"1559_CR46","doi-asserted-by":"publisher","unstructured":"Johnstone, M. et al. The chromatin remodeler DEK promotes proliferation of mammary epithelium and is associated with H3K27me3 epigenetic modifications. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2024.09.09.612116 (2024).","DOI":"10.1101\/2024.09.09.612116"},{"key":"1559_CR47","doi-asserted-by":"publisher","first-page":"e0275476","DOI":"10.1371\/journal.pone.0275476","volume":"17","author":"E \u00d6z\u00e7elik","year":"2022","unstructured":"\u00d6z\u00e7elik, E. et al. Doxorubicin induces prolonged DNA damage signal in cells overexpressing DEK isoform-2. PLoS ONE 17, e0275476 (2022).","journal-title":"PLoS ONE"},{"key":"1559_CR48","doi-asserted-by":"publisher","first-page":"1753","DOI":"10.1042\/BCJ20190169","volume":"476","author":"WH Jia","year":"2019","unstructured":"Jia, W. H. et al. DEK terminates diapause by activation of quiescent cells in the crustacean Artemia. Biochem. J. 476, 1753\u20131769 (2019).","journal-title":"Biochem. J."},{"key":"1559_CR49","doi-asserted-by":"publisher","first-page":"7003","DOI":"10.1093\/nar\/gkg864","volume":"31","author":"T Waldmann","year":"2003","unstructured":"Waldmann, T., Baack, M., Richter, N. & Gruss, C. Structure-specific binding of the proto-oncogene protein DEK to DNA. Nucleic Acids Res. 31, 7003\u20137010 (2003).","journal-title":"Nucleic Acids Res."},{"key":"1559_CR50","doi-asserted-by":"publisher","first-page":"1101","DOI":"10.1093\/nar\/gki258","volume":"33","author":"F Bohm","year":"2005","unstructured":"Bohm, F. et al. The SAF-box domain of chromatin protein DEK. Nucleic Acids Res. 33, 1101\u20131110 (2005).","journal-title":"Nucleic Acids Res."},{"key":"1559_CR51","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1016\/j.molcel.2020.10.038","volume":"81","author":"BR Zhou","year":"2021","unstructured":"Zhou, B. R. et al. Distinct structures and dynamics of chromatosomes with different human linker histone isoforms. Mol. Cell 81, 166\u2013182 (2021).","journal-title":"Mol. Cell"},{"key":"1559_CR52","doi-asserted-by":"publisher","first-page":"628","DOI":"10.1016\/j.molcel.2015.06.025","volume":"59","author":"BR Zhou","year":"2015","unstructured":"Zhou, B. R. et al. Structural mechanisms of nucleosome recognition by linker histones. Mol. Cell 59, 628\u2013638 (2015).","journal-title":"Mol. Cell"},{"key":"1559_CR53","doi-asserted-by":"publisher","first-page":"384","DOI":"10.1016\/j.molcel.2017.04.012","volume":"66","author":"J Bednar","year":"2017","unstructured":"Bednar, J. et al. Structure and dynamics of a 197\u2009bp nucleosome in complex with linker histone H1. Mol. Cell 66, 384\u2013397 (2017).","journal-title":"Mol. Cell"},{"key":"1559_CR54","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41594-022-00768-w","volume":"29","author":"M Dombrowski","year":"2022","unstructured":"Dombrowski, M., Engeholm, M., Dienemann, C., Dodonova, S. & Cramer, P. Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory. Nat. Struct. Mol. Biol. 29, 493\u2013501 (2022).","journal-title":"Nat. Struct. Mol. Biol."},{"key":"1559_CR55","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-48305-1","volume":"15","author":"M Zhang","year":"2024","unstructured":"Zhang, M. et al. Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography. Nat. Commun. 15, 4395 (2024).","journal-title":"Nat. Commun."},{"key":"1559_CR56","doi-asserted-by":"publisher","first-page":"7119","DOI":"10.1021\/bi1004365","volume":"49","author":"JR Fahrer","year":"2010","unstructured":"Fahrer, J. R. et al. High-affinity interaction of poly(ADP-ribose) and the human DEK oncoprotein depends upon chain length. Biochemistry 49, 7119\u20137130 (2010).","journal-title":"Biochemistry"},{"key":"1559_CR57","doi-asserted-by":"publisher","first-page":"e1010463","DOI":"10.1371\/journal.pgen.1010463","volume":"18","author":"C Chiriches","year":"2022","unstructured":"Chiriches, C. et al. Understanding a high-risk acute myeloid leukemia by analyzing the interactome of its major driver mutation. PLoS Genet. 18, e1010463 (2022).","journal-title":"PLoS Genet."},{"key":"1559_CR58","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1038\/s41586-021-03662-5","volume":"595","author":"JH Ahn","year":"2021","unstructured":"Ahn, J. H. et al. Phase separation drives aberrant chromatin looping and cancer development. Nature 595, 591\u2013595 (2021).","journal-title":"Nature"},{"key":"1559_CR59","doi-asserted-by":"publisher","first-page":"112884","DOI":"10.1016\/j.celrep.2023.112884","volume":"42","author":"M Oka","year":"2023","unstructured":"Oka, M. et al. Phase-separated nuclear bodies of nucleoporin fusions promote condensation of MLL1\/CRM1 and rearrangement of 3D genome structure. Cell Rep. 42, 112884 (2023).","journal-title":"Cell Rep."},{"key":"1559_CR60","doi-asserted-by":"publisher","first-page":"23068","DOI":"10.1074\/jbc.M116.735340","volume":"291","author":"SA Port","year":"2016","unstructured":"Port, S. A. et al. The oncogenic fusion proteins SET\u2013Nup214 and sequestosome-1 (SQSTM1)\u2013Nup214 form dynamic nuclear bodies and differentially affect nuclear protein and poly(A)+ RNA export. J. Biol. Chem. 291, 23068\u201323083 (2016).","journal-title":"J. Biol. Chem."},{"key":"1559_CR61","first-page":"1206","volume":"53","author":"MS Meyn","year":"1993","unstructured":"Meyn, M. S., Lu-Kuo, J. & Herzing, L. Expression cloning of multiple human cDNAs that complement the phenotypic defects of ataxia-telangiectasia group D fibroblasts. Am. J. Hum. Genet 53, 1206 (1993).","journal-title":"Am. J. Hum. Genet"},{"key":"1559_CR62","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1016\/j.biochi.2024.07.018","volume":"227","author":"R Sundaram","year":"2024","unstructured":"Sundaram, R., Gandhi, S., Jonak, C. & Vasudevan, D. Characterization of the Arabidopsis thaliana chromatin remodeler DEK3 for its interaction with histones and DNA. Biochimie 227, 248\u2013261 (2024).","journal-title":"Biochimie"},{"key":"1559_CR63","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/S0076-6879(99)04003-3","volume":"304","author":"K Luger","year":"1999","unstructured":"Luger, K., Rechsteiner, T. J. & Richmond, T. J.Preparation of nucleosome core particle from recombinant histones. Methods Enzymol. 304, 3\u201319 (1999).","journal-title":"Methods Enzymol."},{"key":"1559_CR64","doi-asserted-by":"publisher","first-page":"5349","DOI":"10.1093\/nar\/gkac303","volume":"50","author":"H Bao","year":"2022","unstructured":"Bao, H. et al. NASP maintains histone H3\u2013H4 homeostasis through two distinct H3 binding modes. Nucleic Acids Res. 50, 5349\u20135368 (2022).","journal-title":"Nucleic Acids Res."},{"key":"1559_CR65","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1006\/jmbi.1997.1494","volume":"276","author":"PT Lowary","year":"1998","unstructured":"Lowary, P. T. & Widom, J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276, 19\u201342 (1998).","journal-title":"J. Mol. Biol."},{"key":"1559_CR66","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nmeth.4169","volume":"14","author":"A Punjani","year":"2017","unstructured":"Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290\u2013296 (2017).","journal-title":"Nat. Methods"},{"key":"1559_CR67","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1038\/s41592-020-0914-9","volume":"17","author":"TC Terwilliger","year":"2020","unstructured":"Terwilliger, T. C., Ludtke, S. J., Read, R. J., Adams, P. D. & Afonine, P. V. Improvement of cryo-EM maps by density modification. Nat. Methods 17, 923\u2013927 (2020).","journal-title":"Nat. Methods"},{"key":"1559_CR68","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1107\/S0907444910007493","volume":"66","author":"P Emsley","year":"2010","unstructured":"Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486\u2013501 (2010).","journal-title":"Acta Crystallogr. D"},{"key":"1559_CR69","doi-asserted-by":"publisher","first-page":"861","DOI":"10.1107\/S2059798319011471","volume":"75","author":"D Liebschner","year":"2019","unstructured":"Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in PHENIX. Acta Crystallogr. D 75, 861\u2013877 (2019).","journal-title":"Acta Crystallogr. D"},{"key":"1559_CR70","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1002\/pro.3943","volume":"30","author":"EF Pettersen","year":"2021","unstructured":"Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70\u201382 (2021).","journal-title":"Protein Sci."},{"key":"1559_CR71","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen, E. F. et al. UCSF Chimera\u2014a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605\u20131612 (2004).","journal-title":"J. Comput. Chem."},{"key":"1559_CR72","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","volume":"17","author":"M Martin","year":"2011","unstructured":"Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10\u201312 (2011).","journal-title":"EMBnet J."},{"key":"1559_CR73","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013).","journal-title":"Bioinformatics"},{"key":"1559_CR74","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","volume":"30","author":"Y Liao","year":"2014","unstructured":"Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923\u2013930 (2014).","journal-title":"Bioinformatics"},{"key":"1559_CR75","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).","journal-title":"Genome Biol."},{"key":"1559_CR76","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-9-r137","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).","journal-title":"Genome Biol."},{"key":"1559_CR77","doi-asserted-by":"publisher","first-page":"e585","DOI":"10.1002\/cpz1.585","volume":"2","author":"Q Wang","year":"2022","unstructured":"Wang, Q. et al. Exploring epigenomic datasets by ChIPseeker. Curr. Protoc. 2, e585 (2022).","journal-title":"Curr. Protoc."},{"key":"1559_CR78","doi-asserted-by":"crossref","unstructured":"Wu, T. et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation 2, 100141 (2021).","DOI":"10.1016\/j.xinn.2021.100141"},{"key":"1559_CR79","doi-asserted-by":"publisher","first-page":"W320","DOI":"10.1093\/nar\/gku316","volume":"42","author":"X Robert","year":"2014","unstructured":"Robert, X. & Gouet, P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res. 42, W320\u2013W324 (2014).","journal-title":"Nucleic Acids Res."}],"container-title":["Nature Structural & Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41594-025-01559-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41594-025-01559-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41594-025-01559-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,6]],"date-time":"2025-09-06T16:55:57Z","timestamp":1757177757000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41594-025-01559-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,16]]},"references-count":79,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2025,7]]}},"alternative-id":["1559"],"URL":"https:\/\/doi.org\/10.1038\/s41594-025-01559-9","relation":{},"ISSN":["1545-9993","1545-9985"],"issn-type":[{"value":"1545-9993","type":"print"},{"value":"1545-9985","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,16]]},"assertion":[{"value":"28 January 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 April 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 May 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}