Rowley MJ, Corces VG (2018) Organizational principles of 3D genome architecture. Nat Rev Genet 19:789–800. https://doi.org/10.1038/s41576-018-0060-8
Article CAS PubMed Google Scholar
Misteli T (2020) The self-organizing genome: principles of genome architecture and function. Cell 183:28–45. https://doi.org/10.1016/j.cell.2020.09.014
Article CAS PubMed PubMed Central Google Scholar
Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251–260. https://doi.org/10.1038/38444
Article CAS PubMed Google Scholar
Ricci MA, Manzo C, García-Parajo MF, Lakadamyali M, Cosma MP (2015) Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo. Cell 160:1145–1158. https://doi.org/10.1016/j.cell.2015.01.054
Article CAS PubMed Google Scholar
Lakadamyali M, Cosma MP (2020) Visualizing the genome in high resolution challenges our textbook understanding. Nat Methods 17:371–379. https://doi.org/10.1038/s41592-020-0758-3
Article CAS PubMed Google Scholar
Mohanta TK, Mishra AK, Al-Harrasi A (2021) The 3D genome: from structure to function. Int J Mol Sci 22:11585. https://doi.org/10.3390/ijms222111585
Article CAS PubMed PubMed Central Google Scholar
Pedrotti S, Castiglioni I, Perez-Estrada C, Zhao L, Chen JP, Crosetto N, Bienko M (2024) Emerging methods and applications in 3D genomics. Curr Opin Cell Biol 90:102409. https://doi.org/10.1016/j.ceb.2024.102409
Article CAS PubMed Google Scholar
Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EGY, Huang PYH, Welboren W-J, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KDSA, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RKM, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung W-K, Liu ET, Wei C-L, Cheung E, Ruan Y (2009) An oestrogen-receptor-α-bound human chromatin interactome. Nature 462:58–64. https://doi.org/10.1038/nature08497
Article CAS PubMed PubMed Central Google Scholar
Lieberman-Aiden E, Van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–293. https://doi.org/10.1126/science.1181369
Article CAS PubMed PubMed Central Google Scholar
Krietenstein N, Abraham S, Venev SV, Abdennur N, Gibcus J, Hsieh T-HS, Parsi KM, Yang L, Maehr R, Mirny LA, Dekker J, Rando OJ (2020) Ultrastructural details of mammalian chromosome architecture. Mol Cell 78:554–565e7. https://doi.org/10.1016/j.molcel.2020.03.003
Article CAS PubMed PubMed Central Google Scholar
Quinodoz SA, Ollikainen N, Tabak B, Palla A, Schmidt JM, Detmar E, Lai MM, Shishkin AA, Bhat P, Takei Y, Trinh V, Aznauryan E, Russell P, Cheng C, Jovanovic M, Chow A, Cai L, McDonel P, Garber M, Guttman M (2018) Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus. Cell 174:744-757e24. https://doi.org/10.1016/j.cell.2018.05.024
Article CAS PubMed PubMed Central Google Scholar
Beagrie RA, Scialdone A, Schueler M, Kraemer DCA, Chotalia M, Xie SQ, Barbieri M, de Santiago I, Lavitas L-M, Branco MR, Fraser J, Dostie J, Game L, Dillon N, Edwards PAW, Nicodemi M, Pombo A (2017) Complex multi-enhancer contacts captured by genome architecture mapping (GAM). Nature 543:519–524. https://doi.org/10.1038/nature21411
Article CAS PubMed PubMed Central Google Scholar
Quinodoz SA, Bhat P, Chovanec P, Jachowicz JW, Ollikainen N, Detmar E, Soehalim E, Guttman M (2022) SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding. Nat Protoc 17:36–75. https://doi.org/10.1038/s41596-021-00633-y
Article CAS PubMed PubMed Central Google Scholar
Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, Fraser P (2013) Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502:59–64. https://doi.org/10.1038/nature12593
Article CAS PubMed Google Scholar
Nagano T, Lubling Y, Yaffe E, Wingett SW, Dean W, Tanay A, Fraser P (2015) Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell. Nat Protoc 10:1986–2003. https://doi.org/10.1038/nprot.2015.127
Article CAS PubMed Google Scholar
Cosma MP, Neguembor MV (2023) The magic of unraveling genome architecture and function. Cell Rep 42:112361. https://doi.org/10.1016/j.celrep.2023.112361
Article CAS PubMed Google Scholar
Sullivan BA (2020) A sampling of methods to study chromosome and genome structure and function. Chromosom Res 28:1–5. https://doi.org/10.1007/s10577-020-09629-y
Cosma MP (2025) The diffraction limit of light taken by storm. Nat Rev Mol Cell Biol. https://doi.org/10.1038/s41580-025-00856-x
Balzarotti F, Eilers Y, Gwosch KC, Gynnå AH, Westphal V, Stefani FD, Elf J, Hell SW (2017) Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes. Science 355:606–612. https://doi.org/10.1126/science.aak9913
Article CAS PubMed Google Scholar
Beliveau BJ, Boettiger AN, Avendaño MS, Jungmann R, McCole RB, Joyce EF, Kim-Kiselak C, Bantignies F, Fonseka CY, Erceg J, Hannan MA, Hoang HG, Colognori D, Lee JT, Shih WM, Yin P, Zhuang X, Wu C (2015) Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using oligopaint FISH probes. Nat Commun 6:7147. https://doi.org/10.1038/ncomms8147
Article CAS PubMed Google Scholar
Mateo LJ, Murphy SE, Hafner A, Cinquini IS, Walker CA, Boettiger AN (2019) Visualizing DNA folding and RNA in embryos at single-cell resolution. Nature 568:49–54. https://doi.org/10.1038/s41586-019-1035-4
Article CAS PubMed PubMed Central Google Scholar
Simon F, Weiss LE, van Teeffelen S (2024) A guide to single-particle tracking. Nat Rev Methods Primer 4:1–19. https://doi.org/10.1038/s43586-024-00341-3
Boland MA, Lightley JPE, Garcia E, Kumar S, Dunsby C, Flaxman S, Neil MAA, French PMW, Cohen EAK (2025) Model-free machine learning-based 3D single molecule localisation microscopy. J Microsc. https://doi.org/10.1111/jmi.13420
Article PubMed PubMed Central Google Scholar
Yang KD, Belyaeva A, Venkatachalapathy S, Damodaran K, Katcoff A, Radhakrishnan A, Shivashankar GV, Uhler C (2021) Multi-domain translation between single-cell imaging and sequencing data using autoencoders. Nat Commun 12:31. https://doi.org/10.1038/s41467-020-20249-2
Article CAS PubMed PubMed Central Google Scholar
Severin Y, Hale BD, Mena J, Goslings D, Frey BM, Snijder B (2022) Multiplexed high-throughput immune cell imaging reveals molecular health-associated phenotypes. Sci Adv 8:eabn5631. https://doi.org/10.1126/sciadv.abn5631
Article CAS PubMed PubMed Central Google Scholar
Severin Y, Festl Y, Benoit TM, Wegmann R, Hale BD, Roiss M, Kienzler A-K, Pabst T, Scharl M, Sunagawa S, Manz MG, Müller AMS, Snijder B (2024) The cellular hierarchy of acute myeloid leukemia informs personalized treatment. bioRxiv https://doi.org/10.1101/2024.07.24.243107
Soelistyo CJ, Lowe AR (2024) Discovering interpretable models of scientific image data with deep learning. In: 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW). IEEE, Seattle, WA, USA, pp 6884–6893
Venkatachalapathy S, Jokhun DS, Andhari M, Shivashankar GV (2021) Single cell imaging-based chromatin biomarkers for tumor progression. Sci Rep 11:23041.
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