{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T16:04:44Z","timestamp":1791821084167,"version":"4.3.4"},"reference-count":96,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,3,22]],"date-time":"2024-03-22T00:00:00Z","timestamp":1711065600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,3,22]],"date-time":"2024-03-22T00:00:00Z","timestamp":1711065600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["EFMA-1830961"],"award-info":[{"award-number":["EFMA-1830961"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["EFMA-1830969"],"award-info":[{"award-number":["EFMA-1830969"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["NSF DBI-2021795"],"award-info":[{"award-number":["NSF DBI-2021795"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["NSF PHY-2019745"],"award-info":[{"award-number":["NSF PHY-2019745"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01CA228272"],"award-info":[{"award-number":["R01CA228272"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U54 CA268084"],"award-info":[{"award-number":["U54 CA268084"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["5 UM1 HG012649"],"award-info":[{"award-number":["5 UM1 HG012649"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["UM1HG009375"],"award-info":[{"award-number":["UM1HG009375"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U54CA261694"],"award-info":[{"award-number":["U54CA261694"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["T32AI083216"],"award-info":[{"award-number":["T32AI083216"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP21H0419"],"award-info":[{"award-number":["JP21H0419"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000928","name":"Welch Foundation","doi-asserted-by":"publisher","award":["Q-1866"],"award-info":[{"award-number":["Q-1866"]}],"id":[{"id":"10.13039\/100000928","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001234","name":"Robert and Janice McNair Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001234","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001742","name":"United States-Israel Binational Science Foundation","doi-asserted-by":"publisher","award":["2019276"],"award-info":[{"award-number":["2019276"]}],"id":[{"id":"10.13039\/501100001742","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["RM1HG011016-01A1"],"award-info":[{"award-number":["RM1HG011016-01A1"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008258","name":"Hyundai Hope On Wheels","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008258","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100002039","name":"CURE Childhood Cancer","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100002039","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Genome Biol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>B-type lamins are critical nuclear envelope proteins that interact with the three-dimensional genomic architecture. However, identifying the direct roles of B-lamins on dynamic genome organization has been challenging as their joint depletion severely impacts cell viability. To overcome this, we engineered mammalian cells to rapidly and completely degrade endogenous B-type lamins using Auxin-inducible degron technology.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Using live-cell Dual Partial Wave Spectroscopic (Dual-PWS) microscopy, Stochastic Optical Reconstruction Microscopy (STORM), in situ Hi-C, CRISPR-Sirius, and fluorescence in situ hybridization (FISH), we demonstrate that lamin B1 and lamin B2 are critical structural components of the nuclear periphery that create a repressive compartment for peripheral-associated genes. Lamin B1 and lamin B2 depletion minimally alters higher-order chromatin folding but disrupts cell morphology, significantly increases chromatin mobility, redistributes both constitutive and facultative heterochromatin, and induces differential gene expression both within and near lamin-associated domain (LAD) boundaries. Critically, we demonstrate that chromatin territories expand as upregulated genes within LADs radially shift inwards. Our results indicate that the mechanism of action of B-type lamins comes from their role in constraining chromatin motion and spatial positioning of gene-specific loci, heterochromatin, and chromatin domains.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our findings suggest that, while B-type lamin degradation does not significantly change genome topology, it has major implications for three-dimensional chromatin conformation at the single-cell level both at the lamina-associated periphery and the non-LAD-associated nuclear interior with concomitant genome-wide transcriptional changes. This raises intriguing questions about the individual and overlapping roles of lamin B1 and lamin B2 in cellular function and disease.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13059-024-03212-y","type":"journal-article","created":{"date-parts":[[2024,3,22]],"date-time":"2024-03-22T05:02:32Z","timestamp":1711083752000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":40,"title":["Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism"],"prefix":"10.1186","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3520-835X","authenticated-orcid":false,"given":"Emily M.","family":"Pujadas Liwag","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaolong","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Acosta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucas M.","family":"Carter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiekun","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luay M.","family":"Almassalha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Surbhi","family":"Jain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ali","family":"Daneshkhah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suhas S. P.","family":"Rao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fidan","family":"Seker-Polat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyle L.","family":"MacQuarrie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joe","family":"Ibarra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vasundhara","family":"Agrawal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erez Lieberman","family":"Aiden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masato T.","family":"Kanemaki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vadim","family":"Backman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mazhar","family":"Adli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,3,22]]},"reference":[{"issue":"29","key":"3212_CR1","doi-asserted-by":"publisher","first-page":"E6697","DOI":"10.1073\/pnas.1717730115","volume":"115","author":"J Nuebler","year":"2018","unstructured":"Nuebler J, Fudenberg G, Imakaev M, Abdennur N, Mirny LA. Chromatin organization by an interplay of loop extrusion and compartmental segregation. Proc Natl Acad Sci. 2018;115(29):E6697\u2013706. https:\/\/doi.org\/10.1073\/pnas.1717730115.","journal-title":"Proc Natl Acad Sci"},{"issue":"7","key":"3212_CR2","doi-asserted-by":"publisher","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","volume":"159","author":"SS Rao","year":"2014","unstructured":"Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159(7):1665\u201380. https:\/\/doi.org\/10.1016\/j.cell.2014.11.021.","journal-title":"Cell"},{"key":"3212_CR3","doi-asserted-by":"publisher","first-page":"e63976","DOI":"10.7554\/eLife.63976","volume":"10","author":"G Bajpai","year":"2021","unstructured":"Bajpai G, Pavlov DA, Lorber D, Volk T, Safran S. Mesoscale phase separation of chromatin in the nucleus. ELife. 2021;10:e63976 (Physics of Living Systems).","journal-title":"ELife"},{"issue":"22","key":"3212_CR4","doi-asserted-by":"publisher","first-page":"5005","DOI":"10.1016\/j.bpj.2021.10.012","volume":"120","author":"R Laghmach","year":"2021","unstructured":"Laghmach R, Di Pierro M, Potoyan DA. The interplay of chromatin phase separation and lamina interactions in nuclear organization. Biophys J. 2021;120(22):5005\u201317.","journal-title":"Biophys J"},{"key":"3212_CR5","doi-asserted-by":"publisher","first-page":"136","DOI":"10.3390\/cells8020136","volume":"2","author":"YY Shevelyov","year":"2019","unstructured":"Shevelyov YY, Ulianov SV. The nuclear lamina as an organizer of chromosome architecture. Cells. 2019;2:136. https:\/\/doi.org\/10.3390\/cells8020136.","journal-title":"Cells"},{"key":"3212_CR6","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1007\/s13238-020-00794-8","volume":"13","author":"L Chang","year":"2022","unstructured":"Chang L, Li M, Shao S, Li C, Ai S, Xue B, et al. Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells. Protein Cell. 2022;13:258\u201380.","journal-title":"Protein Cell"},{"issue":"14","key":"3212_CR7","doi-asserted-by":"publisher","first-page":"2243","DOI":"10.1242\/jcs.202192","volume":"130","author":"YA Miroshnikova","year":"2017","unstructured":"Miroshnikova YA, Nava MM, Wickstr\u00f6m SA. Emerging roles of mechanical forces in chromatin regulation. J Cell Sci. 2017;130(14):2243\u201350. https:\/\/doi.org\/10.1242\/jcs.202192.","journal-title":"J Cell Sci"},{"key":"3212_CR8","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1016\/j.cell.2020.09.014","volume":"183","author":"T Misteli","year":"2020","unstructured":"Misteli T. The self-organizing genome: principles of genome architecture and function. Cell. 2020;183:28\u201345.","journal-title":"Cell"},{"key":"3212_CR9","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/j.ceb.2020.02.016","volume":"64","author":"K Maeshima","year":"2020","unstructured":"Maeshima K, Tamura S, Hansen JC, Itoh Y. Fluid-like chromatin: Toward understanding the real chromatin organization present in the cell. Curr Opin Cell Biol. 2020;64:77\u201389.","journal-title":"Curr Opin Cell Biol"},{"issue":"5","key":"3212_CR10","doi-asserted-by":"publisher","first-page":"802","DOI":"10.1016\/j.molcel.2018.05.017","volume":"71","author":"X Zheng","year":"2018","unstructured":"Zheng X, Hu J, Yue S, Kristiani L, Kim M, Sauria M, et al. Lamins organize the global three-dimensional genome from the nuclear periphery. Mol Cell. 2018;71(5):802\u201315.","journal-title":"Mol Cell"},{"key":"3212_CR11","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1016\/j.sbi.2020.06.017","volume":"64","author":"R Tenga","year":"2020","unstructured":"Tenga R, Medalia O. Structure and unique mechanical aspects of nuclear lamin filaments. Curr Opin Struct Biol. 2020;64:152\u20139.","journal-title":"Curr Opin Struct Biol"},{"key":"3212_CR12","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/s12860-019-0192-5","volume":"20","author":"D Ranade","year":"2019","unstructured":"Ranade D, Pradhan R, Jayakrishnan M, Hegde S, Sengupta K. Lamin A\/C and Emerin depletion impacts chromatin organization and dynamics in the interphase nucleus. BMC Mol Cell Biol. 2019;20:11.","journal-title":"BMC Mol Cell Biol"},{"issue":"8","key":"3212_CR13","doi-asserted-by":"publisher","first-page":"1884","DOI":"10.3390\/cells9081884","volume":"9","author":"M Stiekema","year":"2020","unstructured":"Stiekema M, van Zandvoort MAMJ, Ramaekers FCS, Broers JLV. Structural and mechanical aberrations of the nuclear lamina in disease. Cells. 2020;9(8):1884.","journal-title":"Cells"},{"key":"3212_CR14","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1007\/s00018-021-04084-2","volume":"79","author":"C Evangelisti","year":"2022","unstructured":"Evangelisti C, Rusciano I, Mongiorgi S, Ramazzotti G, Lattanzi G, Manzoli L, et al. The wide and growing range of lamin B-related diseases: from laminopathies to cancer. Cell Mol Life Sci. 2022;79:126.","journal-title":"Cell Mol Life Sci"},{"issue":"10","key":"3212_CR15","doi-asserted-by":"publisher","first-page":"4307","DOI":"10.1073\/pnas.1810070116","volume":"116","author":"B Nmezi","year":"2019","unstructured":"Nmezi B, Xu J, Fu R, Armiger Travis J, Rodriguez-Bey G, Powell Juliana S, et al. Concentric organization of A- and B-type lamins predicts their distinct roles in the spatial organization and stability of the nuclear lamina. PNAS. 2019;116(10):4307\u201315.","journal-title":"PNAS"},{"key":"3212_CR16","doi-asserted-by":"publisher","first-page":"3420","DOI":"10.1038\/s41467-018-05912-z","volume":"9","author":"L Pascual-Reguant","year":"2018","unstructured":"Pascual-Reguant L, Blanco E, Galan S, Le Dily F, Cuartero Y, Serra-Bardenys G, et al. Lamin B1 mapping reveals the existence of dynamic and functional euchromatin lamin B1 domains. Nat Commun. 2018;9:3420.","journal-title":"Nat Commun"},{"key":"3212_CR17","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1038\/s41586-019-1275-3","volume":"570","author":"M Falk","year":"2019","unstructured":"Falk M, Feodorova Y, Naumova N, Imakaev M, Lajoie BR, Leonhardt H, et al. Heterochromatin drives compartmentalization of inverted and conventional nuclei. Nature. 2019;570:395\u20139.","journal-title":"Nature"},{"issue":"3","key":"3212_CR18","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1016\/j.cell.2013.01.009","volume":"152","author":"I Solovei","year":"2013","unstructured":"Solovei I, Wang AS, Thanisch K, Schmidt CS, Krebs S, Zwerger M, et al. LBR and lamin A\/C sequentially tether peripheral heterochromatin and inversely regulate differentiation. Cell. 2013;152(3):584\u201398. https:\/\/doi.org\/10.1016\/j.cell.2013.01.009.","journal-title":"Cell"},{"key":"3212_CR19","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1016\/j.ceb.2020.11.006","volume":"70","author":"PMJ Rullens","year":"2021","unstructured":"Rullens PMJ, Kind J. Attach and stretch: Emerging roles for genome\u2013lamina contacts in shaping the 3D genome. Curr Opin Cell Biol. 2021;70:51\u20137.","journal-title":"Curr Opin Cell Biol"},{"issue":"4","key":"3212_CR20","doi-asserted-by":"publisher","first-page":"287","DOI":"10.4161\/nucl.29615","volume":"5","author":"JM Lee","year":"2014","unstructured":"Lee JM, Jung H-J, Fong LG, Young SG. Do lamin B1 and lamin B2 have redundant functions? Nucleus. 2014;5(4):287\u201392.","journal-title":"Nucleus."},{"issue":"24","key":"3212_CR21","doi-asserted-by":"publisher","first-page":"3409","DOI":"10.1101\/gad.1735208","volume":"22","author":"T Shimi","year":"2008","unstructured":"Shimi T, Pfleghaar K, Kojima S, Pack CG, Solovei I, Goldman AE, et al. The A- and B-type nuclear lamin networks: microdomains involved in chromatin organization and transcription. Genes Dev. 2008;22(24):3409\u201321. https:\/\/doi.org\/10.1101\/gad.1735208.","journal-title":"Genes Dev"},{"key":"3212_CR22","doi-asserted-by":"publisher","first-page":"e103159","DOI":"10.15252\/embj.2019103159","volume":"39","author":"L Brueckner","year":"2020","unstructured":"Brueckner L, Zhao PA, van Schaik T, Leemans C, Sima J, Peric-Hupkes D, et al. Local rewiring of genome\u2013nuclear lamina interactions by transcription. The EMBO Journal. 2020;39:e103159.","journal-title":"The EMBO Journal"},{"issue":"5","key":"3212_CR23","doi-asserted-by":"publisher","first-page":"780","DOI":"10.1016\/j.cell.2017.04.022","volume":"169","author":"B van Steensel","year":"2017","unstructured":"van Steensel B, Belmont AS. Lamina-associated domains: links with chromosome architecture, heterochromatin, and gene repression. Cell. 2017;169(5):780\u201391.","journal-title":"Cell"},{"key":"3212_CR24","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1186\/s13059-020-02003-5","volume":"21","author":"N Briand","year":"2020","unstructured":"Briand N, Collas P. Lamina-associated domains: peripheral matters and internal affairs. Genome Biol. 2020;21:85. https:\/\/doi.org\/10.1186\/s13059-020-02003-5.","journal-title":"Genome Biol"},{"issue":"5950","key":"3212_CR25","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1126\/science.1181369","volume":"326","author":"E Lieberman-Aiden","year":"2009","unstructured":"Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326(5950):289\u201393. https:\/\/doi.org\/10.1126\/science.1181369.","journal-title":"Science"},{"key":"3212_CR26","doi-asserted-by":"publisher","first-page":"948","DOI":"10.1038\/nature06947","volume":"453","author":"L Guelen","year":"2008","unstructured":"Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature. 2008;453:948\u201351.","journal-title":"Nature"},{"issue":"11","key":"3212_CR27","doi-asserted-by":"publisher","first-page":"e15013","DOI":"10.1371\/journal.pone.0015013","volume":"5","author":"JG van Bemmel","year":"2010","unstructured":"van Bemmel JG, Pagie L, Braunschweig U, Brugman W, Meuleman W, Kerkhoven RM, et al. The insulator protein SU(HW) fine-tunes nuclear lamina interactions of the Drosophila genome. PLoS One. 2010;5(11):e15013. https:\/\/doi.org\/10.1371\/journal.pone.0015013.","journal-title":"PLoS One"},{"issue":"7","key":"3212_CR28","doi-asserted-by":"publisher","first-page":"1772-1784.e13","DOI":"10.1016\/j.cell.2020.11.027","volume":"183","author":"H Strickfaden","year":"2020","unstructured":"Strickfaden H, Tolsma TO, Sharma A, Underhill DA, Hansen JC, Hendzel MJ. Condensed chromatin behaves like a solid on the mesoscale in vitro and in living cells. Cell. 2020;183(7):1772-1784.e13.","journal-title":"Cell"},{"key":"3212_CR29","doi-asserted-by":"publisher","first-page":"12198","DOI":"10.1038\/s41598-022-16028-2","volume":"12","author":"Y Li","year":"2022","unstructured":"Li Y, Agrawal V, Virk RKA, Roth E, Li WS, Eshein A, et al. Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM). Sci Rep. 2022;12:12198.","journal-title":"Sci Rep"},{"issue":"6349","key":"3212_CR30","doi-asserted-by":"publisher","first-page":"eaag0025","DOI":"10.1126\/science.aag0025","volume":"357","author":"HD Ou","year":"2017","unstructured":"Ou HD, Phan S, Deerinck TJ, Thor A, Ellisman MH, O\u2019Shea CC. ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science. 2017;357(6349):eaag0025.","journal-title":"Science"},{"issue":"12","key":"3212_CR31","doi-asserted-by":"publisher","first-page":"917","DOI":"10.1038\/nmeth.1401","volume":"6","author":"K Nishimura","year":"2009","unstructured":"Nishimura K, Fukagawa T, Takisawa H, Kakimoto T, Kanemaki M. An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nat Methods. 2009;6(12):917\u201322. https:\/\/doi.org\/10.1038\/nmeth.1401.","journal-title":"Nat Methods"},{"issue":"1","key":"3212_CR32","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1016\/j.celrep.2016.03.001","volume":"15","author":"T Natsume","year":"2016","unstructured":"Natsume T, Kiyomitsu T, Saga Y, Kanemaki MT. Rapid Protein Depletion in Human Cells by Auxin-Inducible Degron Tagging with Short Homology Donors. Cell Rep. 2016;15(1):210\u20138. https:\/\/doi.org\/10.1016\/j.celrep.2016.03.001.","journal-title":"Cell Rep"},{"key":"3212_CR33","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1016\/j.ymeth.2019.04.010","volume":"164\u2013165","author":"A Yesbolatova","year":"2019","unstructured":"Yesbolatova A, Natsume T, Hayashi KI, Kanemaki MT. Generation of conditional auxin-inducible degron (AID) cells and tight control of degron-fused proteins using the degradation inhibitor auxinole. Methods. 2019;164\u2013165:73\u201380. https:\/\/doi.org\/10.1016\/j.ymeth.2019.04.010.","journal-title":"Methods"},{"key":"3212_CR34","doi-asserted-by":"publisher","unstructured":"Itzhak DN, Tyanova S, Cox J, Borner GH. Global, quantitative and dynamic mapping of protein subcellular localization. Elife. 2016;5:e16950. https:\/\/doi.org\/10.7554\/eLife.16950","DOI":"10.7554\/eLife.16950"},{"issue":"20","key":"3212_CR35","doi-asserted-by":"publisher","first-page":"3381","DOI":"10.1242\/jcs.089110","volume":"124","author":"M-C Hung","year":"2011","unstructured":"Hung M-C, Link W. Protein localization in disease and therapy. J Cell Sci. 2011;124(20):3381\u201392. https:\/\/doi.org\/10.1242\/jcs.089110.","journal-title":"J Cell Sci"},{"key":"3212_CR36","doi-asserted-by":"publisher","first-page":"e16950","DOI":"10.7554\/eLife.16950","volume":"5","author":"DN Itzhak","year":"2016","unstructured":"Itzhak DN, Tyanova S, Cox J, Borner GHH. Global, quantitative and dynamic mapping of protein subcellular localization. ELife. 2016;5:e16950.","journal-title":"ELife"},{"issue":"2","key":"3212_CR37","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1007\/s10616-012-9481-y","volume":"65","author":"AP Demchenko","year":"2013","unstructured":"Demchenko AP. Beyond annexin V: fluorescence response of cellular membranes to apoptosis. Cytotechnology. 2013;65(2):157\u201372.","journal-title":"Cytotechnology"},{"key":"3212_CR38","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1186\/s13059-015-0741-y","volume":"16","author":"J-P Fortin","year":"2015","unstructured":"Fortin J-P, Hansen KD. Reconstructing A\/B compartments as revealed by Hi-C using long-range correlations in epigenetic data. Genome Biol. 2015;16:180.","journal-title":"Genome Biol"},{"key":"3212_CR39","doi-asserted-by":"publisher","unstructured":"Li Y, Eshein A, Virk RKA, Eid A, Wu W, Frederick J, et al. Nanoscale Chromatin Imaging and Analysis (nano-ChIA) platform bridges 4-D chromatin organization with molecular function. bioRxiv. 2020. https:\/\/doi.org\/10.1101\/2020.01.26.920363.","DOI":"10.1101\/2020.01.26.920363"},{"key":"3212_CR40","doi-asserted-by":"publisher","first-page":"734","DOI":"10.3390\/genes6030734","volume":"6","author":"V Ea","year":"2015","unstructured":"Ea V, Baudement M-O, Lesne A, Forn\u00e9 T. Contribution of topological domains and Loop formation to 3D chromatin organization. Genes. 2015;6:734\u201350. https:\/\/doi.org\/10.3390\/genes6030734.","journal-title":"Genes"},{"issue":"20 Pt A","key":"3212_CR41","doi-asserted-by":"publisher","first-page":"2877","DOI":"10.1016\/j.febslet.2015.08.044","volume":"589","author":"J Dekker","year":"2015","unstructured":"Dekker J, Heard E. Structural and functional diversity of Topologically Associating Domains. FEBS Lett. 2015;589(20 Pt A):2877\u201384. https:\/\/doi.org\/10.1016\/j.febslet.2015.08.044.","journal-title":"FEBS Lett"},{"key":"3212_CR42","doi-asserted-by":"publisher","first-page":"4721","DOI":"10.1038\/s41598-022-08602-5","volume":"12","author":"JT Sanders","year":"2022","unstructured":"Sanders JT, Golloshi R, Das P, Xu Y, Terry PH, Nash DG, et al. Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling. Sci Rep. 2022;12:4721.","journal-title":"Sci Rep"},{"issue":"7","key":"3212_CR43","doi-asserted-by":"publisher","first-page":"e70","DOI":"10.1093\/nar\/gkv1505","volume":"44","author":"H Shin","year":"2016","unstructured":"Shin H, Shi Y, Dai C, Tjong H, Gong K, Alber F, et al. TopDom: an efficient and deterministic method for identifying topological domains in genomes. Nucleic Acids Res. 2016;44(7):e70. https:\/\/doi.org\/10.1093\/nar\/gkv1505.","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"3212_CR44","doi-asserted-by":"publisher","first-page":"e50636","DOI":"10.15252\/embr.202050636","volume":"21","author":"T van Schaik","year":"2020","unstructured":"van Schaik T, Vos M, Peric-Hupkes D, Hn Celie P, van Steensel B. Cell cycle dynamics of lamina-associated DNA. EMBO Reports. 2020;21(11):e50636.","journal-title":"EMBO Reports"},{"key":"3212_CR45","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1038\/nature23884","volume":"549","author":"J Dekker","year":"2017","unstructured":"Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, et al. The 4D nucleome project. Nature. 2017;549:219\u201326.","journal-title":"Nature"},{"key":"3212_CR46","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1007\/978-1-4939-7680-5_19","volume":"1745","author":"S Gladstein","year":"2018","unstructured":"Gladstein S, Stawarz A, Almassalha LM, Cherkezyan L, Chandler JE, Zhou X, et al. Measuring nanoscale chromatin heterogeneity with partial wave spectroscopic microscopy. Methods Mol Biol. 2018;1745:337\u201360. https:\/\/doi.org\/10.1007\/978-1-4939-7680-5_19.","journal-title":"Methods Mol Biol"},{"issue":"15","key":"3212_CR47","doi-asserted-by":"publisher","first-page":"4290","DOI":"10.1364\/ol.39.004290","volume":"39","author":"L Cherkezyan","year":"2014","unstructured":"Cherkezyan L, Subramanian H, Backman V. What structural length scales can be detected by the spectral variance of a microscope image? Opt Lett. 2014;39(15):4290\u20133. https:\/\/doi.org\/10.1364\/ol.39.004290.","journal-title":"Opt Lett"},{"issue":"3","key":"3212_CR48","doi-asserted-by":"publisher","first-page":"30901","DOI":"10.1117\/1.jbo.22.3.030901","volume":"22","author":"L Cherkezyan","year":"2017","unstructured":"Cherkezyan L, Zhang D, Subramanian H, Capoglu I, Taflove A, Backman V. Review of interferometric spectroscopy of scattered light for the quantification of subdiffractional structure of biomaterials. J Biomed Opt. 2017;22(3):30901. https:\/\/doi.org\/10.1117\/1.jbo.22.3.030901.","journal-title":"J Biomed Opt"},{"key":"3212_CR49","doi-asserted-by":"publisher","first-page":"1652","DOI":"10.1038\/s41467-019-09717-6","volume":"10","author":"S Gladstein","year":"2019","unstructured":"Gladstein S, Almassalha LM, Cherkezyan L, Chandler JE, Eshein A, Eid A, et al. Multimodal interference-based imaging of nanoscale structure and macromolecular motion uncovers UV induced cellular paroxysm. Nat Commun. 2019;10:1652.","journal-title":"Nat Commun"},{"issue":"42","key":"3212_CR50","first-page":"E6372","volume":"113","author":"M Almassalha Luay","year":"2016","unstructured":"Almassalha Luay M, Bauer Greta M, Chandler John E, Gladstein S, Cherkezyan L, Stypula-Cyrus Y, et al. Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy. PNAS. 2016;113(42):E6372\u201381.","journal-title":"PNAS"},{"issue":"17","key":"3212_CR51","doi-asserted-by":"publisher","first-page":"4810","DOI":"10.1364\/OL.400231","volume":"45","author":"A Eid","year":"2020","unstructured":"Eid A, Eshein A, Li Y, Virk R, Van Derway D, Zhang D, et al. Characterizing chromatin packing scaling in whole nuclei using interferometric microscopy. Opt Lett. 2020;45(17):4810\u20133.","journal-title":"Opt Lett"},{"issue":"2","key":"3212_CR52","doi-asserted-by":"publisher","first-page":"eaax6232","DOI":"10.1126\/sciadv.aax6232","volume":"6","author":"RKA Virk","year":"2020","unstructured":"Virk RKA, Wu W, Almassalha LM, Bauer GM, Li Y, VanDerway D, et al. Disordered chromatin packing regulates phenotypic plasticity. Sci Adv. 2020;6(2):eaax6232. https:\/\/doi.org\/10.1126\/sciadv.aax6232.","journal-title":"Sci Adv"},{"issue":"4","key":"3212_CR53","doi-asserted-by":"publisher","first-page":"100865","DOI":"10.1016\/j.xpro.2021.100865","volume":"2","author":"L Martin","year":"2021","unstructured":"Martin L, Vicario C, Castells-Garc\u00eda \u00c1, Lakadamyali M, Neguembor MV, Cosma MP. A protocol to quantify chromatin compaction with confocal and super-resolution microscopy in cultured cells. STAR Protoc. 2021;2(4):100865.","journal-title":"STAR Protoc"},{"key":"3212_CR54","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1038\/s43586-021-00038-x","volume":"1","author":"M Lelek","year":"2021","unstructured":"Lelek M, Gyparaki MT, Beliu G, Schueder F, Griffi\u00e9 J, Manley S, et al. Single-molecule localization microscopy. Nat Rev Methods Primers. 2021;1:39.","journal-title":"Nat Rev Methods Primers"},{"key":"3212_CR55","doi-asserted-by":"publisher","first-page":"928","DOI":"10.1038\/s41592-018-0174-0","volume":"15","author":"H Ma","year":"2018","unstructured":"Ma H, Tu L-C, Naseri A, Chung Y-C, Grunwald D, Zhang S, et al. CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. Nat Methods. 2018;15:928\u201331.","journal-title":"Nat Methods"},{"issue":"3","key":"3212_CR56","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1093\/hmg\/10.3.211","volume":"10","author":"S Boyle","year":"2001","unstructured":"Boyle S, Gilchrist S, Bridger JM, Mahy NL, Ellis JA, Bickmore WA. The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum Mol Genet. 2001;10(3):211\u20139.","journal-title":"Hum Mol Genet"},{"key":"3212_CR57","doi-asserted-by":"publisher","first-page":"36819","DOI":"10.1038\/srep36819","volume":"6","author":"SN Fatakia","year":"2016","unstructured":"Fatakia SN, Mehta IS, Rao BJ. Systems-level chromosomal parameters represent a suprachromosomal basis for the non-random chromosomal arrangement in human interphase nuclei. Sci Rep. 2016;6:36819.","journal-title":"Sci Rep"},{"key":"3212_CR58","doi-asserted-by":"publisher","unstructured":"Federico C, Bruno F, Ragusa D, Clements CS, Brancato D, Henry MP, et al. Chromosomal Rearrangements and Altered Nuclear Organization: Recent Mechanistic Models in Cancer. Cancers (Basel). 2021;13(22). https:\/\/doi.org\/10.3390\/cancers13225860.","DOI":"10.3390\/cancers13225860"},{"issue":"6","key":"3212_CR59","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1083\/jcb.145.6.1119","volume":"145","author":"JA Croft","year":"1999","unstructured":"Croft JA, Bridger JM, Boyle S, Perry P, Teague P, Bickmore WA. Differences in the Localization and Morphology of Chromosomes in the Human Nucleus. J Cell Biol. 1999;145(6):1119\u201331.","journal-title":"J Cell Biol"},{"issue":"7","key":"3212_CR60","doi-asserted-by":"publisher","first-page":"e1602231","DOI":"10.1126\/sciadv.1602231","volume":"3","author":"B Chen","year":"2017","unstructured":"Chen B, Yusuf M, Hashimoto T, Estandarte Ana K, Thompson G, Robinson I. Three-dimensional positioning and structure of chromosomes in a human prophase nucleus. Sci Adv. 2017;3(7):e1602231.","journal-title":"Sci Adv"},{"issue":"2","key":"3212_CR61","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1016\/j.cels.2018.01.003","volume":"6","author":"S O'Hagan","year":"2018","unstructured":"O\u2019Hagan S, Wright Muelas M, Day PJ, Lundberg E, Kell DB. GeneGini: Assessment via the Gini Coefficient of Reference \u201cHousekeeping\u201d Genes and Diverse Human Transporter Expression Profiles. Cell Syst. 2018;6(2):230-44.e1. https:\/\/doi.org\/10.1016\/j.cels.2018.01.003.","journal-title":"Cell Syst"},{"issue":"3","key":"3212_CR62","doi-asserted-by":"publisher","first-page":"271","DOI":"10.3390\/cells8030271","volume":"8","author":"SJA Lochs","year":"2019","unstructured":"Lochs SJA, Kefalopoulou S, Kind J. Lamina associated domains and gene regulation in development and cancer. Cells. 2019;8(3):271.","journal-title":"Cells"},{"key":"3212_CR63","doi-asserted-by":"publisher","first-page":"702787","DOI":"10.3389\/fcell.2021.702787","volume":"9","author":"JJ Tena","year":"2021","unstructured":"Tena JJ, Santos-Pereira JM. Topologically associating domains and regulatory landscapes in development, evolution and disease. Front Cell Dev Biol. 2021;9:702787. https:\/\/doi.org\/10.3389\/fcell.2021.702787.","journal-title":"Front Cell Dev Biol"},{"issue":"8","key":"3212_CR64","doi-asserted-by":"publisher","first-page":"1272","DOI":"10.1038\/s41588-019-0462-3","volume":"51","author":"Y Ghavi-Helm","year":"2019","unstructured":"Ghavi-Helm Y, Jankowski A, Meiers S, Viales RR, Korbel JO, Furlong EEM. Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression. Nat Genet. 2019;51(8):1272\u201382. https:\/\/doi.org\/10.1038\/s41588-019-0462-3.","journal-title":"Nat Genet"},{"issue":"10","key":"3212_CR65","doi-asserted-by":"publisher","first-page":"e55","DOI":"10.1093\/nar\/gkad229","volume":"51","author":"M Heer","year":"2023","unstructured":"Heer M, Giudice L, Mengoni C, Giugno R, Rico D. Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers. Nucleic Acids Res. 2023;51(10):e55.","journal-title":"Nucleic Acids Res"},{"key":"3212_CR66","doi-asserted-by":"publisher","first-page":"1590","DOI":"10.1038\/s41467-018-03539-8","volume":"9","author":"R Almeida","year":"2018","unstructured":"Almeida R, Fern\u00e1ndez-Justel JM, Santa-Mar\u00eda C, Cadoret J-C, Cano-Aroca L, Lombra\u00f1a R, et al. Chromatin conformation regulates the coordination between DNA replication and transcription. Nat Commun. 2018;9:1590.","journal-title":"Nat Commun"},{"issue":"1","key":"3212_CR67","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1016\/j.cell.2013.02.028","volume":"153","author":"J Kind","year":"2013","unstructured":"Kind J, Pagie L, Ortabozkoyun H, Boyle S, de Vries SS, Janssen H, et al. Single-cell dynamics of genome-nuclear lamina interactions. Cell. 2013;153(1):178\u201392.","journal-title":"Cell"},{"issue":"12","key":"3212_CR68","doi-asserted-by":"publisher","first-page":"e1006617","DOI":"10.1371\/journal.pcbi.1006617","volume":"14","author":"L Liu","year":"2018","unstructured":"Liu L, Shi G, Thirumalai D, Hyeon C. Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci. PLoS Comput Biol. 2018;14(12):e1006617. https:\/\/doi.org\/10.1371\/journal.pcbi.1006617.","journal-title":"PLoS Comput Biol"},{"key":"3212_CR69","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/s13059-023-02849-5","volume":"24","author":"PP Shah","year":"2023","unstructured":"Shah PP, Keough KC, Gjoni K, Santini GT, Abdill RJ, Wickramasinghe NM, et al. An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. Genome Biol. 2023;24:16.","journal-title":"Genome Biol"},{"issue":"24","key":"3212_CR70","doi-asserted-by":"publisher","first-page":"2579","DOI":"10.1101\/gad.179515.111","volume":"25","author":"T Shimi","year":"2011","unstructured":"Shimi T, Butin-Israeli V, Adam SA, Hamanaka RB, Goldman AE, Lucas CA, et al. The role of nuclear lamin B1 in cell proliferation and senescence. Genes Dev. 2011;25(24):2579\u201393. https:\/\/doi.org\/10.1101\/gad.179515.111.","journal-title":"Genes Dev"},{"issue":"16","key":"3212_CR71","doi-asserted-by":"publisher","first-page":"1787","DOI":"10.1101\/gad.223834.113","volume":"27","author":"PP Shah","year":"2013","unstructured":"Shah PP, Donahue G, Otte GL, Capell BC, Nelson DM, Cao K, et al. Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape. Genes Dev. 2013;27(16):1787\u201399. https:\/\/doi.org\/10.1101\/gad.223834.113.","journal-title":"Genes Dev"},{"key":"3212_CR72","doi-asserted-by":"publisher","unstructured":"Shaban HA, Gasser SM. Dynamic 3D genome reorganization during senescence: defining cell states through chromatin. Cell Death Differ. 2023. https:\/\/doi.org\/10.1038\/s41418-023-01197-y.","DOI":"10.1038\/s41418-023-01197-y"},{"key":"3212_CR73","doi-asserted-by":"publisher","first-page":"6049","DOI":"10.1038\/s41467-020-19878-4","volume":"11","author":"I Olan","year":"2020","unstructured":"Olan I, Parry AJ, Schoenfelder S, Narita M, Ito Y, Chan ASL, et al. Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence. Nat Commun. 2020;11:6049.","journal-title":"Nat Commun"},{"key":"3212_CR74","doi-asserted-by":"publisher","first-page":"8044","DOI":"10.1038\/ncomms9044","volume":"6","author":"I Bronshtein","year":"2015","unstructured":"Bronshtein I, Kepten E, Kanter I, Berezin S, Lindner M, Redwood AB, et al. Loss of lamin A function increases chromatin dynamics in the nuclear interior. Nat Commun. 2015;6:8044.","journal-title":"Nat Commun"},{"key":"3212_CR75","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0074-7696(07)61001-8","volume":"261","author":"N Wagner","year":"2007","unstructured":"Wagner N, Krohne G. LEM-domain proteins: new insights into lamin-interacting proteins. Int Rev Cytol. 2007;261:1\u201346.","journal-title":"Int Rev Cytol"},{"key":"3212_CR76","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1016\/j.gde.2021.02.003","volume":"67","author":"VE Hoskins","year":"2021","unstructured":"Hoskins VE, Smith K, Reddy KL. The shifting shape of genomes: dynamics of heterochromatin interactions at the nuclear lamina. Curr Opin Genet Dev. 2021;67:163\u201373.","journal-title":"Curr Opin Genet Dev"},{"key":"3212_CR77","doi-asserted-by":"publisher","first-page":"116","DOI":"10.1038\/s41556-020-00630-5","volume":"23","author":"A Karoutas","year":"2021","unstructured":"Karoutas A, Akhtar A. Functional mechanisms and abnormalities of the nuclear lamina. Nat Cell Biol. 2021;23:116\u201326.","journal-title":"Nat Cell Biol"},{"key":"3212_CR78","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/s12575-019-0094-0","volume":"21","author":"O Oluwadare","year":"2019","unstructured":"Oluwadare O, Highsmith M, Cheng J. An overview of methods for reconstructing 3-D chromosome and genome structures from Hi-C data. Biol Proc Online. 2019;21:7.","journal-title":"Biol Proc Online"},{"issue":"2","key":"3212_CR79","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1016\/j.cels.2018.01.001","volume":"6","author":"JT Robinson","year":"2018","unstructured":"Robinson JT, Turner D, Durand NC, Thorvaldsd\u00f3ttir H, Mesirov JP, Aiden EL. Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data. Cell Systems. 2018;6(2):256\u20138.","journal-title":"Cell Systems"},{"issue":"5","key":"3212_CR80","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","volume":"26","author":"H Li","year":"2010","unstructured":"Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26(5):589\u201395. https:\/\/doi.org\/10.1093\/bioinformatics\/btp698.","journal-title":"Bioinformatics"},{"issue":"3","key":"3212_CR81","doi-asserted-by":"publisher","first-page":"1029","DOI":"10.1093\/imanum\/drs019","volume":"33","author":"PA Knight","year":"2012","unstructured":"Knight PA, Ruiz D. A fast algorithm for matrix balancing. IMA J Numer Anal. 2012;33(3):1029\u201347.","journal-title":"IMA J Numer Anal"},{"issue":"1","key":"3212_CR82","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1186\/s12859-021-04344-9","volume":"22","author":"DR Stirling","year":"2021","unstructured":"Stirling DR, Swain-Bowden MJ, Lucas AM, Carpenter AE, Cimini BA, Goodman A. Cell Profiler 4: improvements in speed, utility and usability. BMC Bioinformatics. 2021;22(1):433. https:\/\/doi.org\/10.1186\/s12859-021-04344-9.","journal-title":"BMC Bioinformatics"},{"issue":"7","key":"3212_CR83","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","volume":"9","author":"J Schindelin","year":"2012","unstructured":"Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9(7):676\u201382. https:\/\/doi.org\/10.1038\/nmeth.2019.","journal-title":"Nat Methods"},{"key":"3212_CR84","doi-asserted-by":"publisher","first-page":"2365","DOI":"10.1038\/s41467-022-29697-4","volume":"13","author":"SB Reiff","year":"2022","unstructured":"Reiff SB, Schroeder AJ, K\u0131rl\u0131 K, Cosolo A, Bakker C, Mercado L, et al. The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. Nat Commun. 2022;13:2365.","journal-title":"Nat Commun"},{"key":"3212_CR85","unstructured":"Pujadas E. NCBI Sequence Read Archive;2024. https:\/\/www.ncbi.nlm.nih.gov\/sra\/PRJNA1078503."},{"key":"3212_CR86","doi-asserted-by":"publisher","unstructured":"Pujadas EM, Wei X, Acosta N, Carter L, Yang J, Almassalha L, et al. Data from: Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion dependent mechanism\u00a0[Dataset]. Dryad; 2024. .https:\/\/doi.org\/10.5061\/dryad.bvq83bkh3.","DOI":"10.5061\/dryad.bvq83bkh3"},{"key":"3212_CR87","unstructured":"LucasMcNU, emilypujadas, Nicolas Acosta, & luaypurple. emilypujadas\/Lamin-Project: v.1.0.0 (v.1.0.0). Github; 2024. https:\/\/github.com\/emilypujadas\/Lamin-Project\/tree\/main."},{"key":"3212_CR88","doi-asserted-by":"publisher","unstructured":"LucasMcNU, emilypujadas, Acosta N, luaypurple. emilypujadas\/Lamin-Project: v.1.0.0 (v.1.0.0). Zenodo; 2024. https:\/\/doi.org\/10.5281\/zenodo.10680913.","DOI":"10.5281\/zenodo.10680913"},{"key":"3212_CR89","unstructured":"van Steensel B. DamID-seq on HCT116 cells. 4DN Data Portal; 2018. https:\/\/data.4dnucleome.org\/experiment-set-replicates\/4DNES24XA7U8\/."},{"key":"3212_CR90","doi-asserted-by":"publisher","unstructured":"Pujadas E. Western Blots for H3K27me3. figshare. Figure; 2024. https:\/\/doi.org\/10.6084\/m9.figshare.25246222.v2.","DOI":"10.6084\/m9.figshare.25246222.v2"},{"key":"3212_CR91","doi-asserted-by":"publisher","unstructured":"Pujadas E. Supplementary Figures. figshare. Figure; 2024. https:\/\/doi.org\/10.6084\/m9.figshare.25282123.v1","DOI":"10.6084\/m9.figshare.25282123.v1"},{"key":"3212_CR92","doi-asserted-by":"publisher","unstructured":"Pujadas E. STORM data. figshare. Figure; 2024. https:\/\/doi.org\/10.6084\/m9.figshare.25246747.v1","DOI":"10.6084\/m9.figshare.25246747.v1"},{"key":"3212_CR93","doi-asserted-by":"publisher","unstructured":"Pujadas E. FISH Experiments. figshare. Figure; 2024. https:\/\/doi.org\/10.6084\/m9.figshare.25246438.v1","DOI":"10.6084\/m9.figshare.25246438.v1"},{"key":"3212_CR94","doi-asserted-by":"publisher","unstructured":"Pujadas E. 2024. CRISPR-Sirius Confocal figshare Figure; 2024. https:\/\/doi.org\/10.6084\/m9.figshare.25246528.v2.","DOI":"10.6084\/m9.figshare.25246528.v2"},{"key":"3212_CR95","doi-asserted-by":"publisher","unstructured":"Pujadas E. Confocal H3K27me3 and H3K27ac. figshare. Figure; 2024. https:\/\/doi.org\/10.6084\/m9.figshare.25246618.v1","DOI":"10.6084\/m9.figshare.25246618.v1"},{"key":"3212_CR96","doi-asserted-by":"publisher","unstructured":"Pujadas E. Chromosome Paint Data. figshare. Figure; 2024. https:\/\/doi.org\/10.6084\/m9.figshare.25246288.v1","DOI":"10.6084\/m9.figshare.25246288.v1"}],"container-title":["Genome Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13059-024-03212-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13059-024-03212-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13059-024-03212-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,22]],"date-time":"2024-03-22T06:11:14Z","timestamp":1711087874000},"score":1,"resource":{"primary":{"URL":"https:\/\/genomebiology.biomedcentral.com\/articles\/10.1186\/s13059-024-03212-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,22]]},"references-count":96,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["3212"],"URL":"https:\/\/doi.org\/10.1186\/s13059-024-03212-y","relation":{},"ISSN":["1474-760X"],"issn-type":[{"value":"1474-760X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,3,22]]},"assertion":[{"value":"5 June 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 March 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 March 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"77"}}