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For: Miron E, Oldenkamp R, Brown JM, Pinto DMS, Xu CS, Faria AR, Shaban HA, Rhodes JDP, Innocent C, de Ornellas S, Hess HF, Buckle V, Schermelleh L. Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin. Sci Adv 2020;6:eaba8811. [PMID: 32967822 PMCID: PMC7531892 DOI: 10.1126/sciadv.aba8811] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 08/06/2020] [Indexed: 05/05/2023]
Number Cited by Other Article(s)
1
Vidi PA, Liu J, Bonin K, Bloom K. Closing the loops: chromatin loop dynamics after DNA damage. Nucleus 2025;16:2438633. [PMID: 39720924 DOI: 10.1080/19491034.2024.2438633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 11/29/2024] [Accepted: 11/30/2024] [Indexed: 12/26/2024]  Open
2
Delvaux de Fenffe CM, Govers J, Mattiroli F. Always on the Move: Overview on Chromatin Dynamics within Nuclear Processes. Biochemistry 2025;64:2138-2153. [PMID: 40312022 PMCID: PMC12096440 DOI: 10.1021/acs.biochem.5c00114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2025] [Revised: 04/04/2025] [Accepted: 04/08/2025] [Indexed: 05/03/2025]
3
Prakash K, Baddeley D, Eggeling C, Fiolka R, Heintzmann R, Manley S, Radenovic A, Shroff H, Smith C, Schermelleh L. Resolution in super-resolution microscopy - facts, artifacts, technological advancements and biological applications. J Cell Sci 2025;138:jcs263567. [PMID: 40421932 DOI: 10.1242/jcs.263567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2025]  Open
4
Zhou H, Hutchings J, Shiozaki M, Zhao X, Doolittle LK, Yang S, Yan R, Jean N, Riggi M, Yu Z, Villa E, Rosen MK. Quantitative spatial analysis of chromatin biomolecular condensates using cryoelectron tomography. Proc Natl Acad Sci U S A 2025;122:e2426449122. [PMID: 40327693 PMCID: PMC12088439 DOI: 10.1073/pnas.2426449122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Accepted: 03/31/2025] [Indexed: 05/08/2025]  Open
5
Paggi JM, Zhang B. Toward decoding the mechanisms that shape sub-megabase-scale genome organization. Curr Opin Struct Biol 2025;92:103062. [PMID: 40344741 DOI: 10.1016/j.sbi.2025.103062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2025] [Revised: 04/15/2025] [Accepted: 04/16/2025] [Indexed: 05/11/2025]
6
Chen JK, Liu T, Cai S, Ruan W, Ng CT, Shi J, Surana U, Gan L. Nanoscale analysis of human G1 and metaphase chromatin in situ. EMBO J 2025;44:2658-2694. [PMID: 40097852 PMCID: PMC12048539 DOI: 10.1038/s44318-025-00407-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 02/11/2025] [Accepted: 02/21/2025] [Indexed: 03/19/2025]  Open
7
Wang Y, Frederick J, Medina KI, Bartom ET, Almassalha LM, Zhang Y, Wodarcyk G, Huang H, Ye IC, Gong R, Dunton CL, Duval A, Gonzalez PC, Pritchard J, Carinato J, Topchu I, Li J, Ji Z, Adli M, Backman V, Matei D. Chromatin Organization Governs Transcriptional Response and Plasticity of Cancer Stem Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025;12:e2407426. [PMID: 40051293 PMCID: PMC12061297 DOI: 10.1002/advs.202407426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 12/16/2024] [Indexed: 03/09/2025]
8
Lin H, Seitz S, Tan Y, Lugagne JB, Wang L, Ding G, He H, Rauwolf TJ, Dunlop MJ, Connor JH, Porco JA, Tian L, Cheng JX. Label-free nanoscopy of cell metabolism by ultrasensitive reweighted visible stimulated Raman scattering. Nat Methods 2025;22:1040-1050. [PMID: 39820753 PMCID: PMC12074879 DOI: 10.1038/s41592-024-02575-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 11/26/2024] [Indexed: 01/19/2025]
9
Maeshima K. The shifting paradigm of chromatin structure: from the 30-nm chromatin fiber to liquid-like organization. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2025:pjab.101.020. [PMID: 40301047 DOI: 10.2183/pjab.101.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2025]
10
Patil S, Vicidomini G, Slenders E. Open-source 3D active sample stabilization for fluorescence microscopy. BIOPHYSICAL REPORTS 2025;5:100208. [PMID: 40254224 PMCID: PMC12124610 DOI: 10.1016/j.bpr.2025.100208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Revised: 03/27/2025] [Accepted: 04/09/2025] [Indexed: 04/22/2025]
11
Fujishiro S, Sasai M, Maeshima K. Chromatin domains in the cell: Phase separation and condensation. Curr Opin Struct Biol 2025;91:103006. [PMID: 39983411 DOI: 10.1016/j.sbi.2025.103006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2024] [Revised: 01/25/2025] [Accepted: 01/27/2025] [Indexed: 02/23/2025]
12
Minami K, Nakazato K, Ide S, Kaizu K, Higashi K, Tamura S, Toyoda A, Takahashi K, Kurokawa K, Maeshima K. Replication-dependent histone labeling dissects the physical properties of euchromatin/heterochromatin in living human cells. SCIENCE ADVANCES 2025;11:eadu8400. [PMID: 40153514 PMCID: PMC11952110 DOI: 10.1126/sciadv.adu8400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2024] [Accepted: 02/25/2025] [Indexed: 03/30/2025]
13
Oliveira RJ, Oliveira Junior AB, Contessoto VG, Onuchic JN. The synergy between compartmentalization and motorization in chromatin architecture. J Chem Phys 2025;162:114116. [PMID: 40105139 DOI: 10.1063/5.0239634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Accepted: 02/20/2025] [Indexed: 03/20/2025]  Open
14
Acosta N, Gong R, Su Y, Frederick J, Medina KI, Li WS, Mohammadian K, Almassalha L, Wang G, Backman V. Three-color single-molecule localization microscopy in chromatin. LIGHT, SCIENCE & APPLICATIONS 2025;14:123. [PMID: 40091134 PMCID: PMC11911409 DOI: 10.1038/s41377-025-01786-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 02/09/2025] [Accepted: 02/12/2025] [Indexed: 03/19/2025]
15
Uckelmann M, Levina V, Taveneau C, Ng XH, Pandey V, Martinez J, Mendiratta S, Houx J, Boudes M, Venugopal H, Trépout S, Fulcher AJ, Zhang Q, Flanigan S, Li M, Sierecki E, Gambin Y, Das PP, Bell O, de Marco A, Davidovich C. Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates. Nat Struct Mol Biol 2025;32:520-530. [PMID: 39815045 PMCID: PMC11919719 DOI: 10.1038/s41594-024-01457-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 11/21/2024] [Indexed: 01/18/2025]
16
Lokesh NR, Pownall ME. Microscopy methods for the in vivo study of nanoscale nuclear organization. Biochem Soc Trans 2025;53:BST20240629. [PMID: 39898979 DOI: 10.1042/bst20240629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Revised: 12/23/2024] [Accepted: 01/06/2025] [Indexed: 02/04/2025]
17
Fillot T, Mazza D. Rethinking chromatin accessibility: from compaction to dynamic interactions. Curr Opin Genet Dev 2025;90:102299. [PMID: 39705880 PMCID: PMC11793080 DOI: 10.1016/j.gde.2024.102299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 12/02/2024] [Accepted: 12/03/2024] [Indexed: 12/23/2024]
18
Pujadas Liwag EM, Acosta N, Almassalha LM, Su Y(P, Gong R, Kanemaki MT, Stephens AD, Backman V. Nuclear blebs are associated with destabilized chromatin-packing domains. J Cell Sci 2025;138:jcs262161. [PMID: 39878045 PMCID: PMC11883274 DOI: 10.1242/jcs.262161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 12/24/2024] [Indexed: 01/31/2025]  Open
19
Li WS, Carter LM, Almassalha LM, Gong R, Pujadas-Liwag EM, Kuo T, MacQuarrie KL, Carignano M, Dunton C, Dravid V, Kanemaki MT, Szleifer I, Backman V. Mature chromatin packing domains persist after RAD21 depletion in 3D. SCIENCE ADVANCES 2025;11:eadp0855. [PMID: 39854464 PMCID: PMC11759041 DOI: 10.1126/sciadv.adp0855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 12/20/2024] [Indexed: 01/26/2025]
20
Wagh K, Stavreva DA, Hager GL. Transcription dynamics and genome organization in the mammalian nucleus: Recent advances. Mol Cell 2025;85:208-224. [PMID: 39413793 PMCID: PMC11741928 DOI: 10.1016/j.molcel.2024.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/31/2024] [Accepted: 09/19/2024] [Indexed: 10/18/2024]
21
Almassalha LM, Carignano M, Liwag EP, Li WS, Gong R, Acosta N, Dunton CL, Gonzalez PC, Carter LM, Kakkaramadam R, Kröger M, MacQuarrie KL, Frederick J, Ye IC, Su P, Kuo T, Medina KI, Pritchard JA, Skol A, Nap R, Kanemaki M, Dravid V, Szleifer I, Backman V. Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system. SCIENCE ADVANCES 2025;11:eadq6652. [PMID: 39792661 PMCID: PMC11721585 DOI: 10.1126/sciadv.adq6652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 12/04/2024] [Indexed: 01/12/2025]
22
Shaban HA, Gasser SM. Dynamic 3D genome reorganization during senescence: defining cell states through chromatin. Cell Death Differ 2025;32:9-15. [PMID: 37596440 PMCID: PMC11748698 DOI: 10.1038/s41418-023-01197-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/20/2023]  Open
23
Valades-Cruz CA, Barth R, Abdellah M, Shaban HA. Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D. Nat Protoc 2025;20:163-179. [PMID: 39198619 DOI: 10.1038/s41596-024-01038-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/22/2024] [Indexed: 09/01/2024]
24
Wang Z, Wang B, Niu D, Yin C, Bi Y, Cattoglio C, Loh KM, Lavis LD, Ge H, Deng W. Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells. Nat Struct Mol Biol 2025;32:125-136. [PMID: 39367253 DOI: 10.1038/s41594-024-01385-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/07/2024] [Indexed: 10/06/2024]
25
Chen L, Maristany MJ, Farr SE, Luo J, Gibson BA, Doolittle LK, Espinosa JR, Huertas J, Redding S, Collepardo-Guevara R, Rosen MK. Nucleosome Spacing Can Fine-Tune Higher Order Chromatin Assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.23.627571. [PMID: 39763792 PMCID: PMC11703229 DOI: 10.1101/2024.12.23.627571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2025]
26
Bairamukov VY, Ankudinov AV, Kovalev RA, Pantina RA, Grigoriev SV, Varfolomeeva EY. Chromatin condensed domains revealed by AFM, and their transformation in mechanically deformed normal and malignant cell nuclei. Biochem Biophys Res Commun 2024;736:150861. [PMID: 39461009 DOI: 10.1016/j.bbrc.2024.150861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Accepted: 10/18/2024] [Indexed: 10/28/2024]
27
Frederick J, Virk RKA, Ye IC, Almassalha LM, Wodarcyk GM, VanDerway D, Gonzalez PC, Nap RJ, Agrawal V, Anthony NM, Carinato J, Li WS, Dunton CL, Medina KI, Kakkaramadam R, Jain S, Shahabi S, Ameer G, Szleifer IG, Backman V. Leveraging chromatin packing domains to target chemoevasion in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.14.623612. [PMID: 39605341 PMCID: PMC11601449 DOI: 10.1101/2024.11.14.623612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
28
Gupta R, Goswami Y, Yuan L, Roy B, Pereiro E, Shivashankar GV. Correlative light and soft X-ray tomography of in situ mesoscale heterochromatin structure in intact cells. Sci Rep 2024;14:27706. [PMID: 39532928 PMCID: PMC11557596 DOI: 10.1038/s41598-024-77361-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 10/22/2024] [Indexed: 11/16/2024]  Open
29
Popenko V, Spirin P, Prassolov V, Leonova O. Chromomeres, Topologically Associating Domains and Structural Organization of Chromatin Bodies in Somatic Nuclei (Macronuclei) of Ciliates. FRONT BIOSCI-LANDMRK 2024;29:378. [PMID: 39614448 DOI: 10.31083/j.fbl2911378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 09/25/2024] [Accepted: 10/09/2024] [Indexed: 12/01/2024]
30
Maarouf A, Iqbal F, Sanaullah S, Locatelli M, Atanasiu AT, Kolbin D, Hommais C, Mühlemann JK, Bonin K, Bloom K, Liu J, Vidi PA. RAD51 regulates eukaryotic chromatin motions in the absence of DNA damage. Mol Biol Cell 2024;35:ar136. [PMID: 39292916 PMCID: PMC11617103 DOI: 10.1091/mbc.e24-04-0188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 08/12/2024] [Accepted: 09/13/2024] [Indexed: 09/20/2024]  Open
31
Cremer C, Schock F, Failla AV, Birk U. Modulated illumination microscopy: Application perspectives in nuclear nanostructure analysis. J Microsc 2024;296:121-128. [PMID: 38618985 DOI: 10.1111/jmi.13297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 02/26/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024]
32
Lacen A, Lee HT. Tracing the Chromatin: From 3C to Live-Cell Imaging. CHEMICAL & BIOMEDICAL IMAGING 2024;2:659-682. [PMID: 39483638 PMCID: PMC11523001 DOI: 10.1021/cbmi.4c00033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 11/03/2024]
33
Dasgupta N, Arnold R, Equey A, Gandhi A, Adams PD. The role of the dynamic epigenetic landscape in senescence: orchestrating SASP expression. NPJ AGING 2024;10:48. [PMID: 39448585 PMCID: PMC11502686 DOI: 10.1038/s41514-024-00172-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 09/24/2024] [Indexed: 10/26/2024]
34
Chu FY, Clavijo AS, Lee S, Zidovska A. Transcription-dependent mobility of single genes and genome-wide motions in live human cells. Nat Commun 2024;15:8879. [PMID: 39438437 PMCID: PMC11496510 DOI: 10.1038/s41467-024-51149-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/31/2024] [Indexed: 10/25/2024]  Open
35
Carignano MA, Kroeger M, Almassalha LM, Agrawal V, Li WS, Pujadas-Liwag EM, Nap RJ, Backman V, Szleifer I. Local volume concentration, packing domains, and scaling properties of chromatin. eLife 2024;13:RP97604. [PMID: 39331520 PMCID: PMC11434620 DOI: 10.7554/elife.97604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2024]  Open
36
Labade AS, Chiang ZD, Comenho C, Reginato PL, Payne AC, Earl AS, Shrestha R, Duarte FM, Habibi E, Zhang R, Church GM, Boyden ES, Chen F, Buenrostro JD. Expansion in situ genome sequencing links nuclear abnormalities to hotspots of aberrant euchromatin repression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.24.614614. [PMID: 39386718 PMCID: PMC11463693 DOI: 10.1101/2024.09.24.614614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
37
Naas J, Nies G, Li H, Stoldt S, Schmitzer B, Jakobs S, Munk A. MultiMatch: geometry-informed colocalization in multi-color super-resolution microscopy. Commun Biol 2024;7:1139. [PMID: 39271907 PMCID: PMC11399439 DOI: 10.1038/s42003-024-06772-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024]  Open
38
Iida S, Ide S, Tamura S, Sasai M, Tani T, Goto T, Shribak M, Maeshima K. Orientation-independent-DIC imaging reveals that a transient rise in depletion attraction contributes to mitotic chromosome condensation. Proc Natl Acad Sci U S A 2024;121:e2403153121. [PMID: 39190347 PMCID: PMC11388287 DOI: 10.1073/pnas.2403153121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/19/2024] [Indexed: 08/28/2024]  Open
39
Yang SH, Zeng YZ, Jia XZ, Gu YW, Wood C, Yang RS, Yang JS, Yang WJ. Activated dormant stem cells recover spermatogenesis in chemoradiotherapy-induced infertility. Cell Rep 2024;43:114582. [PMID: 39096488 DOI: 10.1016/j.celrep.2024.114582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 03/23/2024] [Accepted: 07/18/2024] [Indexed: 08/05/2024]  Open
40
Hibino K, Sakai Y, Tamura S, Takagi M, Minami K, Natsume T, Shimazoe MA, Kanemaki MT, Imamoto N, Maeshima K. Single-nucleosome imaging unveils that condensins and nucleosome-nucleosome interactions differentially constrain chromatin to organize mitotic chromosomes. Nat Commun 2024;15:7152. [PMID: 39169041 PMCID: PMC11339268 DOI: 10.1038/s41467-024-51454-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/08/2024] [Indexed: 08/23/2024]  Open
41
Rahman F, Augoustides V, Tyler E, Daugird TA, Arthur C, Legant WR. Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.27.605159. [PMID: 39211261 PMCID: PMC11360932 DOI: 10.1101/2024.07.27.605159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
42
Uckelmann M, Levina V, Taveneau C, Ng XH, Pandey V, Martinez J, Mendiratta S, Houx J, Boudes M, Venugopal H, Trépout S, Zhang Q, Flanigan S, Li M, Sierecki E, Gambin Y, Das PP, Bell O, de Marco A, Davidovich C. Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.08.539931. [PMID: 38405976 PMCID: PMC10888862 DOI: 10.1101/2023.05.08.539931] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
43
Pabba MK, Meyer J, Celikay K, Schermelleh L, Rohr K, Cardoso MC. DNA choreography: correlating mobility and organization of DNA across different resolutions from loops to chromosomes. Histochem Cell Biol 2024;162:109-131. [PMID: 38758428 PMCID: PMC11227476 DOI: 10.1007/s00418-024-02285-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2024] [Indexed: 05/18/2024]
44
Presman DM, Benítez B, Lafuente AL, Vázquez Lareu A. Chromatin structure and dynamics: one nucleosome at a time. Histochem Cell Biol 2024;162:79-90. [PMID: 38607419 DOI: 10.1007/s00418-024-02281-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2024] [Indexed: 04/13/2024]
45
Semeigazin A, Iida S, Minami K, Tamura S, Ide S, Higashi K, Toyoda A, Kurokawa K, Maeshima K. Behaviors of nucleosomes with mutant histone H4s in euchromatic domains of living human cells. Histochem Cell Biol 2024;162:23-40. [PMID: 38743310 DOI: 10.1007/s00418-024-02293-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2024] [Indexed: 05/16/2024]
46
Salari H, Fourel G, Jost D. Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization. Nat Commun 2024;15:5393. [PMID: 38918438 PMCID: PMC11199603 DOI: 10.1038/s41467-024-49727-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 06/17/2024] [Indexed: 06/27/2024]  Open
47
Hsiao YT, Liao IH, Wu BK, Chu HPC, Hsieh CL. Probing chromatin condensation dynamics in live cells using interferometric scattering correlation spectroscopy. Commun Biol 2024;7:763. [PMID: 38914653 PMCID: PMC11196589 DOI: 10.1038/s42003-024-06457-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 06/14/2024] [Indexed: 06/26/2024]  Open
48
Carignano M, Kröger M, Almassalha LM, Agrawal V, Li WS, Pujadas-Liwag EM, Nap RJ, Backman V, Szleifer I. Local Volume Concentration, Packing Domains and Scaling Properties of Chromatin. ARXIV 2024:arXiv:2310.02257v3. [PMID: 38495560 PMCID: PMC10942481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
49
Shim AR, Frederick J, Pujadas EM, Kuo T, Ye IC, Pritchard JA, Dunton CL, Gonzalez PC, Acosta N, Jain S, Anthony NM, Almassalha LM, Szleifer I, Backman V. Formamide denaturation of double-stranded DNA for fluorescence in situ hybridization (FISH) distorts nanoscale chromatin structure. PLoS One 2024;19:e0301000. [PMID: 38805476 PMCID: PMC11132451 DOI: 10.1371/journal.pone.0301000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/10/2024] [Indexed: 05/30/2024]  Open
50
Kant A, Guo Z, Vinayak V, Neguembor MV, Li WS, Agrawal V, Pujadas E, Almassalha L, Backman V, Lakadamyali M, Cosma MP, Shenoy VB. Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization. Nat Commun 2024;15:4338. [PMID: 38773126 PMCID: PMC11109243 DOI: 10.1038/s41467-024-48698-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/06/2024] [Indexed: 05/23/2024]  Open
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