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Although the structures of reconstituted CENP-A nucleosomes have provided important insights, how this epigenetic mark is structurally organized within native chromatin remains incompletely understood. Here, we combine cryogenic electron microscopy with chromatin immunoprecipitation (ChIP-CryoEM) to determine the structures of human CENP-A nucleosomes isolated directly from cells without crosslinking or stabilizing agents. We resolved two distinct cellular CENP-A nucleosome structures: a homotypic CENP-A nucleosome and a heterotypic CENP-A\/H3 nucleosome, which have been proposed to represent centromeric and ectopic nucleosomes, respectively. Both cellular CENP-A nucleosomes assemble as histone octamers and wrap DNA in a left-handed superhelix, supporting an octameric model proposed for native CENP-A chromatin. In addition, the hallmark CENP-A-specific structural features previously characterized in vitro, including the shortened CENP-A N-terminal \u03b1-helix and the distinctive RG loop, are preserved in cellular CENP-A nucleosomes. These findings define the structural organization of CENP-A nucleosomes in cellular chromatin.<\/jats:p>","DOI":"10.1038\/s42003-026-10946-x","type":"journal-article","created":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T09:04:40Z","timestamp":1790672680000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Cryo-EM structures of CENP-A nucleosomes isolated from human cells"],"prefix":"10.1038","volume":"9","author":[{"given":"Eisho","family":"Tanida","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5678-4049","authenticated-orcid":false,"given":"Suguru","family":"Hatazawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takumi","family":"Oishi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuki","family":"Kobayashi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mitsuo","family":"Ogasawara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-6260-9952","authenticated-orcid":false,"given":"Marta A.","family":"Jaskiewicz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-1420-4549","authenticated-orcid":false,"given":"Akihito","family":"Harada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-5606-721X","authenticated-orcid":false,"given":"Takeru","family":"Fujii","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6440-9954","authenticated-orcid":false,"given":"Yasuyuki","family":"Ohkawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6265-4830","authenticated-orcid":false,"given":"Yoshimasa","family":"Takizawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7412-3722","authenticated-orcid":false,"given":"Hitoshi","family":"Kurumizaka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,29]]},"reference":[{"key":"10946_CR1","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/j.tcb.2005.12.008","volume":"16","author":"CW Carroll","year":"2006","unstructured":"Carroll, C. 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