{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T18:47:14Z","timestamp":1791917234126,"version":"4.3.4"},"reference-count":0,"publisher":"Cold Spring Harbor Laboratory","funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["25-71-20017"],"award-info":[{"award-number":["25-71-20017"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union's Horizon 2020 research and innovation program","award":["849029"],"award-info":[{"award-number":["849029"]}]},{"name":"David and Inez Myers foundation"},{"DOI":"10.13039\/501100003977","name":"the Israeli Science Foundation","doi-asserted-by":"publisher","award":["422\/23"],"award-info":[{"award-number":["422\/23"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genome Res."],"accepted":{"date-parts":[[2026,9,17]]},"abstract":"<jats:p>\n                    Chromatin structure is essential for gene regulation and genome stability, as neurons must preserve their 3D genome organization throughout life. This structure gradually deteriorates with aging and is further disrupted in neurodegenerative diseases. To investigate whether aging and neurodegeneration share early chromatin changes or diverge, we perform Hi-C on cortical neurons from adult, aged, and brain-specific\n                    <jats:italic>SIRT6<\/jats:italic>\n                    -knockout (S6-KO) mice and compare them to the previously published Hi-C data sets from a CK-p25 Alzheimer's disease model stratified by \u03b3H2AX levels. All models show early features such as weakened interactions between chromosomes in expanded nuclei, A- to B-compartment shifts, and loss of architectural loops. However, aged neurons retain TAD prominence, short-range interactions, and enhancer\u2013promoter loops, whereas pathological models showed reduced TAD prominence, shorter loops, and disorganized A\u2013B mixing. These changes correlate with increased DNA damage. Our findings suggest that aging represents a \u201cprimed\u201d state, in which chromatin regulation begins to erode, but further stressors like DNA damage are associated with progression toward neurodegenerative breakdown.\n                  <\/jats:p>","DOI":"10.1101\/gr.281732.125","type":"journal-article","created":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T18:10:24Z","timestamp":1791915024000},"source":"Crossref","is-referenced-by-count":0,"title":["The divergent 3D genome landscapes of aging and neurodegenerative mouse models"],"prefix":"10.1101","author":[{"given":"Ekaterina","family":"Kashuk","sequence":"first","affiliation":[{"name":"Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitrii","family":"Smirnov","sequence":"additional","affiliation":[{"name":"Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia;"},{"name":"Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel;"},{"name":"The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel;"},{"name":"Central University, Moscow 123056, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ekaterina","family":"Eremenko","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel;"},{"name":"The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra","family":"Tsitrina","sequence":"additional","affiliation":[{"name":"Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitrii","family":"Kriukov","sequence":"additional","affiliation":[{"name":"Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anastasia","family":"Golova","sequence":"additional","affiliation":[{"name":"Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shai","family":"Kaluski-Kopatch","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel;"},{"name":"The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6188-9139","authenticated-orcid":false,"given":"Ekaterina","family":"Khrameeva","sequence":"additional","affiliation":[{"name":"Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1465-0130","authenticated-orcid":false,"given":"Debra","family":"Toiber","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel;"},{"name":"The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel;"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"246","published-online":{"date-parts":[[2026,10,13]]},"container-title":["Genome Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/gr.281732.125","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T18:10:24Z","timestamp":1791915024000},"score":1,"resource":{"primary":{"URL":"http:\/\/genome.cshlp.org\/lookup\/doi\/10.1101\/gr.281732.125"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,13]]},"references-count":0,"alternative-id":["10.1101\/gr.281732.125"],"URL":"https:\/\/doi.org\/10.1101\/gr.281732.125","relation":{},"ISSN":["1088-9051","1549-5469"],"issn-type":[{"value":"1088-9051","type":"print"},{"value":"1549-5469","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,13]]}}}