{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T12:53:54Z","timestamp":1793969634290,"version":"4.8.0"},"reference-count":61,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T00:00:00Z","timestamp":1761868800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T00:00:00Z","timestamp":1761868800000},"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":[[2026,1]]},"DOI":"10.1038\/s41594-025-01704-4","type":"journal-article","created":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T10:04:15Z","timestamp":1761905055000},"page":"171-183","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Mechanisms of DNMT3A\u20133L-mediated de novo DNA methylation on chromatin"],"prefix":"10.1038","volume":"33","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6656-7737","authenticated-orcid":false,"given":"Yan","family":"Yan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"X. Edward","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3631-7184","authenticated-orcid":false,"given":"Stacey L.","family":"Thomas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7405-8972","authenticated-orcid":false,"given":"Minmin","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gan-Qiang","family":"Lai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0644-166X","authenticated-orcid":false,"given":"Evan J.","family":"Worden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8309-4767","authenticated-orcid":false,"given":"Peter A.","family":"Jones","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2239-1420","authenticated-orcid":false,"given":"Ting-Hai","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,10,31]]},"reference":[{"key":"1704_CR1","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1016\/S0092-8674(00)81656-6","volume":"99","author":"M Okano","year":"1999","unstructured":"Okano, M., Bell, D. W., Haber, D. A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247\u2013257 (1999).","journal-title":"Cell"},{"key":"1704_CR2","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1038\/s41580-019-0159-6","volume":"20","author":"MVC Greenberg","year":"2019","unstructured":"Greenberg, M. V. C. & Bourc\u2019his, D. The diverse roles of DNA methylation in mammalian development and disease. Nat. Rev. Mol. Cell Biol. 20, 590\u2013607 (2019).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"1704_CR3","doi-asserted-by":"publisher","first-page":"1983","DOI":"10.1242\/dev.129.8.1983","volume":"129","author":"K Hata","year":"2002","unstructured":"Hata, K., Okano, M., Lei, H. & Li, E. Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice. Development 129, 1983\u20131993 (2002).","journal-title":"Development"},{"key":"1704_CR4","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms11453","volume":"7","author":"CE Duymich","year":"2016","unstructured":"Duymich, C. E., Charlet, J., Yang, X., Jones, P. A. & Liang, G. DNMT3B isoforms without catalytic activity stimulate gene body methylation as accessory proteins in somatic cells. Nat. Commun. 7, 11453 (2016).","journal-title":"Nat. Commun."},{"key":"1704_CR5","doi-asserted-by":"publisher","first-page":"1546","DOI":"10.1101\/gad.341925.120","volume":"34","author":"Y Zeng","year":"2020","unstructured":"Zeng, Y. et al. The inactive Dnmt3b3 isoform preferentially enhances Dnmt3b-mediated DNA methylation. Genes Dev. 34, 1546\u20131558 (2020).","journal-title":"Genes Dev."},{"key":"1704_CR6","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1038\/nature25477","volume":"554","author":"ZM Zhang","year":"2018","unstructured":"Zhang, Z. M. et al. Structural basis for DNMT3A-mediated de novo DNA methylation. Nature 554, 387\u2013391 (2018).","journal-title":"Nature"},{"key":"1704_CR7","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1016\/0092-8674(94)90342-5","volume":"76","author":"S Klimasauskas","year":"1994","unstructured":"Klimasauskas, S., Kumar, S., Roberts, R. J. & Cheng, X. HhaI methyltransferase flips its target base out of the DNA helix. Cell 76, 357\u2013369 (1994).","journal-title":"Cell"},{"key":"1704_CR8","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1038\/nature06146","volume":"449","author":"D Jia","year":"2007","unstructured":"Jia, D., Jurkowska, R. Z., Zhang, X., Jeltsch, A. & Cheng, X. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449, 248\u2013251 (2007).","journal-title":"Nature"},{"key":"1704_CR9","doi-asserted-by":"publisher","first-page":"714","DOI":"10.1038\/nature05987","volume":"448","author":"SK Ooi","year":"2007","unstructured":"Ooi, S. K. et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714\u2013717 (2007).","journal-title":"Nature"},{"key":"1704_CR10","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1038\/s41586-020-2747-1","volume":"586","author":"TH Xu","year":"2020","unstructured":"Xu, T. H. et al. Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B. Nature 586, 151\u2013155 (2020).","journal-title":"Nature"},{"key":"1704_CR11","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1093\/nar\/gky947","volume":"47","author":"N Veland","year":"2019","unstructured":"Veland, N. et al. DNMT3L facilitates DNA methylation partly by maintaining DNMT3A stability in mouse embryonic stem cells. Nucleic Acids Res. 47, 152\u2013167 (2019).","journal-title":"Nucleic Acids Res."},{"key":"1704_CR12","doi-asserted-by":"publisher","first-page":"119","DOI":"10.4161\/epi.25799","volume":"9","author":"BF Chen","year":"2014","unstructured":"Chen, B. F., Gu, S., Suen, Y. K., Li, L. & Chan, W. Y. microRNA-199a-3p, DNMT3A, and aberrant DNA methylation in testicular cancer. Epigenetics 9, 119\u2013128 (2014).","journal-title":"Epigenetics"},{"key":"1704_CR13","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-12746-w","volume":"10","author":"HR Davies","year":"2019","unstructured":"Davies, H. R. et al. Epigenetic modifiers DNMT3A and BCOR are recurrently mutated in CYLD cutaneous syndrome. Nat. Commun. 10, 4717 (2019).","journal-title":"Nat. Commun."},{"key":"1704_CR14","doi-asserted-by":"publisher","first-page":"9048","DOI":"10.1128\/MCB.24.20.9048-9058.2004","volume":"24","author":"T Chen","year":"2004","unstructured":"Chen, T., Tsujimoto, N. & Li, E. The PWWP domain of Dnmt3a and Dnmt3b is required for directing DNA methylation to the major satellite repeats at pericentric heterochromatin. Mol. Cell Biol. 24, 9048\u20139058 (2004).","journal-title":"Mol. Cell Biol."},{"key":"1704_CR15","doi-asserted-by":"publisher","first-page":"26114","DOI":"10.1074\/jbc.M109.089433","volume":"285","author":"A Dhayalan","year":"2010","unstructured":"Dhayalan, A. et al. The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation. J. Biol. Chem. 285, 26114\u201326120 (2010).","journal-title":"J. Biol. Chem."},{"key":"1704_CR16","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1038\/s41586-019-1534-3","volume":"573","author":"DN Weinberg","year":"2019","unstructured":"Weinberg, D. N. et al. The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape. Nature 573, 281\u2013286 (2019).","journal-title":"Nature"},{"key":"1704_CR17","doi-asserted-by":"publisher","first-page":"5063","DOI":"10.1016\/j.jmb.2019.09.006","volume":"431","author":"M Dukatz","year":"2019","unstructured":"Dukatz, M. et al. H3K36me2\/3 binding and DNA binding of the DNA methyltransferase DNMT3A PWWP domain both contribute to its chromatin interaction. J. Mol. Biol. 431, 5063\u20135074 (2019).","journal-title":"J. Mol. Biol."},{"key":"1704_CR18","first-page":"217","volume":"9","author":"C Qiu","year":"2002","unstructured":"Qiu, C., Sawada, K., Zhang, X. & Cheng, X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nat. Struct. Biol. 9, 217\u2013224 (2002).","journal-title":"Nat. Struct. Biol."},{"key":"1704_CR19","doi-asserted-by":"publisher","first-page":"1235","DOI":"10.1038\/embor.2009.218","volume":"10","author":"J Otani","year":"2009","unstructured":"Otani, J. et al. Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX\u2013DNMT3\u2013DNMT3L domain. EMBO Rep. 10, 1235\u20131241 (2009).","journal-title":"EMBO Rep."},{"key":"1704_CR20","doi-asserted-by":"publisher","first-page":"4246","DOI":"10.1093\/nar\/gkq147","volume":"38","author":"Y Zhang","year":"2010","unstructured":"Zhang, Y. et al. Chromatin methylation activity of Dnmt3a and Dnmt3a\/3L is guided by interaction of the ADD domain with the histone H3 tail. Nucleic Acids Res. 38, 4246\u20134253 (2010).","journal-title":"Nucleic Acids Res."},{"key":"1704_CR21","first-page":"203","volume":"301","author":"A Jeltsch","year":"2006","unstructured":"Jeltsch, A. Molecular enzymology of mammalian DNA methyltransferases. Curr. Top. Microbiol. Immunol. 301, 203\u2013225 (2006).","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"1704_CR22","doi-asserted-by":"publisher","first-page":"27816","DOI":"10.1074\/jbc.M400181200","volume":"279","author":"I Suetake","year":"2004","unstructured":"Suetake, I., Shinozaki, F., Miyagawa, J., Takeshima, H. & Tajima, S. DNMT3L stimulates the DNA methylation activity of Dnmt3a and Dnmt3b through a direct interaction. J. Biol. Chem. 279, 27816\u201327823 (2004).","journal-title":"J. Biol. Chem."},{"key":"1704_CR23","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":"1704_CR24","doi-asserted-by":"publisher","first-page":"16916","DOI":"10.1073\/pnas.262443999","volume":"99","author":"F Chedin","year":"2002","unstructured":"Chedin, F., Lieber, M. R. & Hsieh, C. L. The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a. Proc. Natl Acad. Sci. USA 99, 16916\u201316921 (2002).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"1704_CR25","doi-asserted-by":"publisher","first-page":"13341","DOI":"10.1074\/jbc.M413412200","volume":"280","author":"H Gowher","year":"2005","unstructured":"Gowher, H., Liebert, K., Hermann, A., Xu, G. & Jeltsch, A. Mechanism of stimulation of catalytic activity of Dnmt3A and Dnmt3B DNA-(cytosine-C5)-methyltransferases by Dnmt3L. J. Biol. Chem. 280, 13341\u201313348 (2005).","journal-title":"J. Biol. Chem."},{"key":"1704_CR26","doi-asserted-by":"publisher","first-page":"41479","DOI":"10.1074\/jbc.M111.284687","volume":"286","author":"C Holz-Schietinger","year":"2011","unstructured":"Holz-Schietinger, C., Matje, D. M., Harrison, M. F. & Reich, N. O. Oligomerization of DNMT3A controls the mechanism of de novo DNA methylation. J. Biol. Chem. 286, 41479\u201341488 (2011).","journal-title":"J. Biol. Chem."},{"key":"1704_CR27","doi-asserted-by":"publisher","first-page":"640","DOI":"10.1038\/nature13899","volume":"517","author":"X Guo","year":"2015","unstructured":"Guo, X. et al. Structural insight into autoinhibition and histone H3-induced activation of DNMT3A. Nature 517, 640\u2013644 (2015).","journal-title":"Nature"},{"key":"1704_CR28","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-47398-y","volume":"15","author":"J Lu","year":"2024","unstructured":"Lu, J. et al. Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations. Nat. Commun. 15, 3111 (2024).","journal-title":"Nat. Commun."},{"key":"1704_CR29","doi-asserted-by":"publisher","first-page":"24200","DOI":"10.1074\/jbc.M111.254987","volume":"286","author":"RZ Jurkowska","year":"2011","unstructured":"Jurkowska, R. Z. et al. Oligomerization and binding of the Dnmt3a DNA methyltransferase to parallel DNA molecules: heterochromatic localization and role of Dnmt3L. J. Biol. Chem. 286, 24200\u201324207 (2011).","journal-title":"J. Biol. Chem."},{"key":"1704_CR30","doi-asserted-by":"publisher","first-page":"12476","DOI":"10.1093\/nar\/gkad972","volume":"51","author":"J Lu","year":"2023","unstructured":"Lu, J. et al. Structural basis for the allosteric regulation and dynamic assembly of DNMT3B. Nucleic Acids Res. 51, 12476\u201312491 (2023).","journal-title":"Nucleic Acids Res."},{"key":"1704_CR31","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-22665-4","volume":"12","author":"W Ren","year":"2021","unstructured":"Ren, W. et al. DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation. Nat. Commun. 12, 2490 (2021).","journal-title":"Nat. Commun."},{"key":"1704_CR32","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adp0975","volume":"10","author":"KH Gretarsson","year":"2024","unstructured":"Gretarsson, K. H. et al. Cancer-associated DNA hypermethylation of Polycomb targets requires DNMT3A dual recognition of histone H2AK119 ubiquitination and the nucleosome acidic patch. Sci. Adv. 10, eadp0975 (2024).","journal-title":"Sci. Adv."},{"key":"1704_CR33","doi-asserted-by":"publisher","first-page":"5743","DOI":"10.1038\/s44319-024-00306-3","volume":"25","author":"H Wapenaar","year":"2024","unstructured":"Wapenaar, H. et al. The N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment. EMBO Rep. 25, 5743\u20135779 (2024).","journal-title":"EMBO Rep."},{"key":"1704_CR34","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-50526-3","volume":"15","author":"X Chen","year":"2024","unstructured":"Chen, X. et al. Structural basis for the H2AK119ub1-specific DNMT3A\u2013nucleosome interaction. Nat. Commun. 15, 6217 (2024).","journal-title":"Nat. Commun."},{"key":"1704_CR35","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1016\/j.tcb.2024.06.001","volume":"35","author":"H Wang","year":"2025","unstructured":"Wang, H. & Helin, K. Roles of H3K4 methylation in biology and disease. Trends Cell Biol. 35, 115\u2013128 (2025).","journal-title":"Trends Cell Biol."},{"key":"1704_CR36","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1038\/nature14176","volume":"520","author":"T Baubec","year":"2015","unstructured":"Baubec, T. et al. Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation. Nature 520, 243\u2013247 (2015).","journal-title":"Nature"},{"key":"1704_CR37","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1038\/nature21373","volume":"543","author":"F Neri","year":"2017","unstructured":"Neri, F. et al. Intragenic DNA methylation prevents spurious transcription initiation. Nature 543, 72\u201377 (2017).","journal-title":"Nature"},{"key":"1704_CR38","doi-asserted-by":"publisher","first-page":"1172","DOI":"10.1038\/cr.2011.92","volume":"21","author":"BZ Li","year":"2011","unstructured":"Li, B. Z. et al. Histone tails regulate DNA methylation by allosterically activating de novo methyltransferase. Cell Res. 21, 1172\u20131181 (2011).","journal-title":"Cell Res."},{"key":"1704_CR39","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1038\/s41586-025-08782-w","volume":"641","author":"W Choi","year":"2025","unstructured":"Choi, W., Li, C., Chen, Y., Wang, Y. & Cheng, Y. Structural dynamics of human fatty acid synthase in the condensing cycle. Nature 641, 529\u2013536 (2025).","journal-title":"Nature"},{"key":"1704_CR40","doi-asserted-by":"publisher","first-page":"8556","DOI":"10.1093\/nar\/gkw723","volume":"44","author":"A Jeltsch","year":"2016","unstructured":"Jeltsch, A. & Jurkowska, R. Z. Allosteric control of mammalian DNA methyltransferases\u2014a new regulatory paradigm. Nucleic Acids Res. 44, 8556\u20138575 (2016).","journal-title":"Nucleic Acids Res."},{"key":"1704_CR41","doi-asserted-by":"publisher","first-page":"5123","DOI":"10.1093\/nar\/gkw124","volume":"44","author":"C Lovkvist","year":"2016","unstructured":"Lovkvist, C., Dodd, I. B., Sneppen, K. & Haerter, J. O. DNA methylation in human epigenomes depends on local topology of CpG sites. Nucleic Acids Res. 44, 5123\u20135132 (2016).","journal-title":"Nucleic Acids Res."},{"key":"1704_CR42","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1016\/B978-0-12-386931-9.00016-7","volume":"117","author":"A Jeltsch","year":"2013","unstructured":"Jeltsch, A. & Jurkowska, R. Z. Multimerization of the dnmt3a DNA methyltransferase and its functional implications. Prog. Mol. Biol. Transl. Sci. 117, 445\u2013464 (2013).","journal-title":"Prog. Mol. Biol. Transl. Sci."},{"key":"1704_CR43","doi-asserted-by":"publisher","first-page":"16966","DOI":"10.1074\/jbc.RA119.010126","volume":"294","author":"TV Nguyen","year":"2019","unstructured":"Nguyen, T. V. et al. The R882H DNMT3A hot spot mutation stabilizes the formation of large DNMT3A oligomers with low DNA methyltransferase activity. J. Biol. Chem. 294, 16966\u201316977 (2019).","journal-title":"J. Biol. Chem."},{"key":"1704_CR44","doi-asserted-by":"publisher","first-page":"1350","DOI":"10.1126\/science.6262918","volume":"212","author":"M Ehrlich","year":"1981","unstructured":"Ehrlich, M. & Wang, R. Y. 5-Methylcytosine in eukaryotic DNA. Science 212, 1350\u20131357 (1981).","journal-title":"Science"},{"key":"1704_CR45","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1038\/s41588-018-0073-4","volume":"50","author":"W Zhou","year":"2018","unstructured":"Zhou, W. et al. DNA methylation loss in late-replicating domains is linked to mitotic cell division. Nat. Genet. 50, 591\u2013602 (2018).","journal-title":"Nat. Genet."},{"key":"1704_CR46","doi-asserted-by":"publisher","first-page":"902","DOI":"10.1002\/jcb.20447","volume":"95","author":"ZX Chen","year":"2005","unstructured":"Chen, Z. X., Mann, J. R., Hsieh, C. L., Riggs, A. D. & Chedin, F. Physical and functional interactions between the human DNMT3L protein and members of the de novo methyltransferase family. J. Cell Biochem. 95, 902\u2013917 (2005).","journal-title":"J. Cell Biochem."},{"key":"1704_CR47","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-022-03119-z","volume":"5","author":"A Brohm","year":"2022","unstructured":"Brohm, A. et al. Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3. Commun. Biol. 5, 192 (2022).","journal-title":"Commun. Biol."},{"key":"1704_CR48","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1101\/gr.183368.114","volume":"25","author":"FD Lay","year":"2015","unstructured":"Lay, F. D. et al. The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Res. 25, 467\u2013477 (2015).","journal-title":"Genome Res."},{"key":"1704_CR49","doi-asserted-by":"publisher","first-page":"5279","DOI":"10.1093\/nar\/gkp524","volume":"37","author":"K Bouazoune","year":"2009","unstructured":"Bouazoune, K., Miranda, T. B., Jones, P. A. & Kingston, R. E. Analysis of individual remodeled nucleosomes reveals decreased histone\u2013DNA contacts created by hSWI\/SNF. Nucleic Acids Res. 37, 5279\u20135294 (2009).","journal-title":"Nucleic Acids Res."},{"key":"1704_CR50","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1038\/nmeth1139","volume":"5","author":"B Kastner","year":"2008","unstructured":"Kastner, B. et al. GraFix: sample preparation for single-particle electron cryomicroscopy. Nat. Methods 5, 53\u201355 (2008).","journal-title":"Nat. Methods"},{"key":"1704_CR51","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/S0076-6879(10)81005-5","volume":"481","author":"H Stark","year":"2010","unstructured":"Stark, H. GraFix: stabilization of fragile macromolecular complexes for single particle cryo-EM. Methods Enzymol. 481, 109\u2013126 (2010).","journal-title":"Methods Enzymol."},{"key":"1704_CR52","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1016\/j.jsb.2005.07.007","volume":"152","author":"DN Mastronarde","year":"2005","unstructured":"Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36\u201351 (2005).","journal-title":"J. Struct. Biol."},{"key":"1704_CR53","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-021-02399-1","volume":"4","author":"R Sanchez-Garcia","year":"2021","unstructured":"Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 4, 874 (2021).","journal-title":"Commun. Biol."},{"key":"1704_CR54","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","volume":"596","author":"J Jumper","year":"2021","unstructured":"Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583\u2013589 (2021).","journal-title":"Nature"},{"key":"1704_CR55","doi-asserted-by":"publisher","unstructured":"Evans R. et al. Protein complex prediction with AlphaFold-Multimer. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2021.10.04.463034 (2022).","DOI":"10.1101\/2021.10.04.463034"},{"key":"1704_CR56","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":"1704_CR57","doi-asserted-by":"publisher","first-page":"2126","DOI":"10.1107\/S0907444904019158","volume":"60","author":"P Emsley","year":"2004","unstructured":"Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126\u20132132 (2004).","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"1704_CR58","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1107\/S0907444909052925","volume":"66","author":"PD Adams","year":"2010","unstructured":"Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213\u2013221 (2010).","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"1704_CR59","doi-asserted-by":"publisher","first-page":"11626","DOI":"10.1093\/nar\/gkae584","volume":"52","author":"R Chadda","year":"2024","unstructured":"Chadda, R. et al. Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation. Nucleic Acids Res. 52, 11626\u201311640 (2024).","journal-title":"Nucleic Acids Res."},{"key":"1704_CR60","volume":"46","author":"W Zhou","year":"2018","unstructured":"Zhou, W., Triche, T. J. Jr., Laird, P. W. & Shen, H. SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions. Nucleic Acids Res. 46, e123 (2018).","journal-title":"Nucleic Acids Res."},{"key":"1704_CR61","doi-asserted-by":"publisher","first-page":"13733","DOI":"10.1093\/nar\/gkae1105","volume":"52","author":"RL Tiedemann","year":"2024","unstructured":"Tiedemann, R. L. et al. UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation. Nucleic Acids Res. 52, 13733\u201313756 (2024).","journal-title":"Nucleic Acids Res."}],"container-title":["Nature Structural &amp; Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41594-025-01704-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41594-025-01704-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41594-025-01704-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T17:04:53Z","timestamp":1768928693000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41594-025-01704-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,31]]},"references-count":61,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1]]}},"alternative-id":["1704"],"URL":"https:\/\/doi.org\/10.1038\/s41594-025-01704-4","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.06.10.658647","asserted-by":"object"}]},"ISSN":["1545-9993","1545-9985"],"issn-type":[{"value":"1545-9993","type":"print"},{"value":"1545-9985","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,31]]},"assertion":[{"value":"29 May 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 October 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 October 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"P.A.J. is a paid consultant for Zymo Research. The other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}