{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:57:48Z","timestamp":1792789068061,"version":"4.5.0"},"reference-count":45,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Canadian Institutes of Health Research","award":["CIHR 426213"],"award-info":[{"award-number":["CIHR 426213"]}],"id":[{"id":"https:\/\/ror.org\/01gavpb45","id-type":"ROR","asserted-by":"crossref"}]},{"award":["CIHR 426213"],"award-info":[{"award-number":["CIHR 426213"]}],"id":[{"id":"https:\/\/ror.org\/01gavpb45","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Memorial University Faculty of Science Start-Up"},{"name":"National Institute of General Medical Sciences","award":["1R24GM154186"],"award-info":[{"award-number":["1R24GM154186"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"crossref"}]},{"award":["1R24GM154186"],"award-info":[{"award-number":["1R24GM154186"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cells"],"abstract":"<jats:p>Nucleosomes integrate diverse histone variants to organize chromatin and coordinate genome maintenance. In plants, the structural interplay between replication-associated histones and DNA damage-responsive histone variants remains poorly understood. Here, we determine cryogenic electron microscopy structures of an Arabidopsis thaliana (At) nucleosome containing the replication-associated histones H2B.6 and H3.1 together with the DNA damage-responsive variant H2AXa. The mononucleosome structure, resolved at 2.73 \u00c5, preserves the canonical nucleosome architecture. Unexpectedly, the reconstituted mononucleosomes formed defined higher-order assemblies in the absence of linker DNA or chemical crosslinking. Two distinct nucleosome\u2013nucleosome arrangements, parallel and right offset, were identified. The right offset closely resembles the human counterpart, whereas the parallel arrangement exhibits slight displacement of H2B structural elements at the inter-nucleosomal interface. Together these structures reveal how a distinct histone composition preserves the canonical nucleosome architecture while supporting multiple defined modes of nucleosome packing, providing structural insights into conserved and divergent features of H2AX-containing chromatin organization across plants and animals.<\/jats:p>","DOI":"10.3390\/cells15191795","type":"journal-article","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T08:19:08Z","timestamp":1790842748000},"page":"1795","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Molecular Architecture of the H2AX-Containing Nucleosome from Arabidopsis"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1727-9269","authenticated-orcid":false,"given":"Rashmi","family":"Panigrahi","sequence":"first","affiliation":[{"name":"Department of Human Biosciences, Memorial University of Newfoundland, St John\u2019s, NL A1C 5S7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"project-administration","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]},{"given":"Ross","family":"Edwards","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-1391-7824","authenticated-orcid":false,"given":"Nathaniel","family":"Agbagba","sequence":"additional","affiliation":[{"name":"Department of Human Biosciences, Memorial University of Newfoundland, St John\u2019s, NL A1C 5S7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2733-7052","authenticated-orcid":false,"given":"Mark","family":"Glover","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,10,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.mrrev.2008.06.004","article-title":"Genotoxic stress in plants: Shedding light on DNA damage, repair and DNA repair helicases","volume":"681","author":"Tuteja","year":"2009","journal-title":"Mutat. Res."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1338","DOI":"10.3390\/biology2041338","article-title":"DNA Damage Response in Plants: Conserved and Variable Response Compared to Animals","volume":"2","author":"Yoshiyama","year":"2013","journal-title":"Biology"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1111\/j.1469-8137.2011.03926.x","article-title":"Repairing breaks in the plant genome: The importance of keeping it together","volume":"192","author":"Waterworth","year":"2011","journal-title":"New Phytol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1016\/j.dnarep.2008.11.012","article-title":"Rapid repair of DNA double strand breaks in Arabidopsis thaliana is dependent on proteins involved in chromosome structure maintenance","volume":"8","author":"Kozak","year":"2009","journal-title":"DNA Repair"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1016\/j.molcel.2017.04.012","article-title":"Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1","volume":"66","author":"Bednar","year":"2017","journal-title":"Mol. Cell"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"19390","DOI":"10.1073\/pnas.1314905110","article-title":"Structural insights into the histone H1-nucleosome complex","volume":"110","author":"Zhou","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_7","first-page":"2080","article-title":"A specialized histone H1 variant is required for adaptive responses to complex abiotic stress and related DNA methylation in Arabidopsis","volume":"169","author":"Rutowicz","year":"2015","journal-title":"Plant Physiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1387","DOI":"10.1042\/BST20253036","article-title":"Chromatin insulators in gene regulation and 3D genome organization","volume":"53","author":"Sultana","year":"2025","journal-title":"Biochem. Soc. Trans."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"102266","DOI":"10.1016\/j.pbi.2022.102266","article-title":"Deposition and eviction of histone variants define functional chromatin states in plants","volume":"69","author":"Probst","year":"2022","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Nunez-Vazquez, R., Desvoyes, B., and Gutierrez, C. (2022). Histone variants and modifications during abiotic stress response. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.984702"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Wu, X., Zhang, X., Huang, B., Han, J., and Fang, H. (2023). Advances in biological functions and mechanisms of histone variants in plants. Front. Genet., 14.","DOI":"10.3389\/fgene.2023.1229782"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1042\/BCJ20200066","article-title":"Structural insights into DNA double-strand break signaling","volume":"478","author":"Panigrahi","year":"2021","journal-title":"Biochem. J."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"gkaf1028","DOI":"10.1093\/nar\/gkaf1028","article-title":"Structural insights into \u03b3H2Ax containing nucleosomes","volume":"53","author":"Panigrahi","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Kumar, K.R.R. (2023). Lost in the bloom: DNA-PKcs in green plants. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1231678"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Guo, P., Wang, T.-J., Wang, S., Peng, X., Kim, D.H., and Liu, Y. (2024). Arabidopsis Histone Variant H2A.X Functions in the DNA Damage-Coupling Abscisic Acid Signaling Pathway. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25168940"},{"key":"ref_16","first-page":"9","article-title":"Histone H2AX and the small RNA pathway modulate both non-homologous end-joining and homologous recombination in plants","volume":"783","author":"Qi","year":"2016","journal-title":"Mutat. Res. Mol. Mech. Mutagen."},{"key":"ref_17","first-page":"3","article-title":"Preparation of nucleosome core particle from recombinant histones","volume":"304","author":"Luger","year":"1999","journal-title":"Elsevier"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nmeth.4169","article-title":"cryoSPARC: Algorithms for rapid unsupervised cryo-EM structure determination","volume":"14","author":"Punjani","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera? A visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1107\/S0907444910007493","article-title":"Features and development of Coot","volume":"66","author":"Emsley","year":"2010","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1107\/S0907444909052925","article-title":"PHENIX: A comprehensive Python-based system for macromolecular structure solution","volume":"66","author":"Adams","year":"2010","journal-title":"Acta Crystallogr. Sect. D. Biol. Crystallogr."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1107\/S2059798318002425","article-title":"ISOLDE: A physically realistic environment for model building into low-resolution electron-density maps","volume":"74","author":"Croll","year":"2018","journal-title":"Acta Crystallogr. Sect. D. Struct. Biol."},{"key":"ref_23","unstructured":"DeLano, W. (2002). The PyMOL Molecular Graphics System, DeLano Scientific."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1038\/nmeth.2727","article-title":"Quantifying the local resolution of cryo-EM density maps","volume":"11","author":"Kucukelbir","year":"2013","journal-title":"Nat. Methods"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Roy, S. (2014). Maintenance of genome stability in plants: Repairing DNA double strand breaks and chromatin structure stability. Front. Plant Sci., 5.","DOI":"10.3389\/fpls.2014.00487"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"a010140","DOI":"10.1101\/cshperspect.a010140","article-title":"Regulating DNA Replication in Plants","volume":"4","author":"Sanchez","year":"2012","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Manova, V., and Gruszka, D. (2015). DNA damage and repair in plants\u2014From models to crops. Front. Plant Sci., 6.","DOI":"10.3389\/fpls.2015.00885"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Jiang, D., Borg, M., Lorkovi\u0107, Z.J., Montgomery, S.A., Osakabe, A., Yelagandula, R., Axelsson, E., and Berger, F. (2020). The evolution and functional divergence of the histone H2B family in plants. PLoS Genet., 16.","DOI":"10.1371\/journal.pgen.1008964"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1111\/nph.15248","article-title":"Replication-coupled histone H3.1 deposition determines nucleosome composition and heterochromatin dynamics during Arabidopsis seedling development","volume":"221","author":"Benoit","year":"2018","journal-title":"New Phytol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1016\/j.jare.2024.12.001","article-title":"Genome-wide profiling and functional study of short N-terminal H2B variants in Arabidopsis","volume":"75","author":"Yao","year":"2024","journal-title":"J. Adv. Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"8665","DOI":"10.1093\/nar\/gky768","article-title":"Replication-dependent histone isoforms: A new source of complexity in chromatin structure and function","volume":"46","author":"Singh","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1048","DOI":"10.1038\/s41586-022-05236-5","article-title":"Columnar structure of human telomeric chromatin","volume":"609","author":"Soman","year":"2022","journal-title":"Nature"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41594-022-00768-w","article-title":"Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory","volume":"29","author":"Dombrowski","year":"2022","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/s42003-023-05694-1","article-title":"Genome-wide mapping and cryo-EM structural analyses of the overlapping tri-nucleosome composed of hexasome-hexasome-octasome moieties","volume":"7","author":"Nishimura","year":"2024","journal-title":"Commun. Biol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1126\/science.1251413","article-title":"Cryo-EM Study of the Chromatin Fiber Reveals a Double Helix Twisted by Tetranucleosomal Units","volume":"344","author":"Song","year":"2014","journal-title":"Science"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"902","DOI":"10.1016\/j.molcel.2018.09.027","article-title":"Structure of an H1-Bound 6-Nucleosome Array Reveals an Untwisted Two-Start Chromatin Fiber Conformation","volume":"72","author":"Menoni","year":"2018","journal-title":"Mol. Cell"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"169774","DOI":"10.1016\/j.jmb.2026.169774","article-title":"Histone Surface Exposure Drives Nucleosome Stacking Diversity Through DNA Engagement in Trans","volume":"438","author":"Mu","year":"2026","journal-title":"J. Mol. Biol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1038\/s41594-022-00758-y","article-title":"CENP-N promotes the compaction of centromeric chromatin","volume":"29","author":"Zhou","year":"2022","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"7046","DOI":"10.1038\/s41598-018-25429-1","article-title":"Cryo-EM of nucleosome core particle interactions in trans","volume":"8","author":"Bilokapic","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"11379","DOI":"10.1093\/nar\/gkab907","article-title":"Structural basis of chromatin regulation by histone variant H2A.Z","volume":"49","author":"Lewis","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_41","first-page":"e48913","article-title":"CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail","volume":"20","year":"2019","journal-title":"Embo Rep."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1093\/jb\/mvad069","article-title":"Cryo-EM and biochemical analyses of the nucleosome containing the human histone H3 variant H3.8","volume":"174","author":"Hirai","year":"2023","journal-title":"J. Biochem."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Jung, H., Sokolova, V., Lee, G., Stevens, V.R., and Tan, D. (2024). Structural and Biochemical Characterization of the Nucleosome Containing Variants H3.3 and H2A.Z. Epigenomes, 8.","DOI":"10.20944\/preprints202403.1829.v1"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"gkaf825","DOI":"10.1093\/nar\/gkaf825","article-title":"H2B.W2, a spermatocyte-specific histone variant, disrupts nucleosome stability, and reduces chromatin compaction","volume":"53","author":"Nguyen","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.1016\/j.jmb.2017.03.016","article-title":"Regulation of Nucleosome Stacking and Chromatin Compaction by the Histone H4 N-Terminal Tail\u2013H2A Acidic Patch Interaction","volume":"429","author":"Chen","year":"2017","journal-title":"J. Mol. Biol."}],"container-title":["Cells"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4409\/15\/19\/1795\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T04:10:22Z","timestamp":1791951022000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4409\/15\/19\/1795"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,1]]},"references-count":45,"journal-issue":{"issue":"19","published-online":{"date-parts":[[2026,10]]}},"alternative-id":["cells15191795"],"URL":"https:\/\/doi.org\/10.3390\/cells15191795","relation":{},"ISSN":["2073-4409"],"issn-type":[{"value":"2073-4409","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,1]]}}}