Bauman JG, Wiegant J, Borst P, van Duijn P (1980) A new method for fluorescence microscopical localization of specific DNA sequences by in situ hybridization of fluorochromelabelled RNA. Exp Cell Res 128:485–490

Article  CAS  PubMed  Google Scholar 

Beel AJ, Azubel M, Mattei PJ, Kornberg RD (2021) Structure of mitotic chromosomes. Mol Cell 81(4369–76):e3

Google Scholar 

Beliveau BJ, Joyce EF, Apostolopoulos N, Yilmaz F, Fonseka CY, McCole RB, Chang Y, Li JB, Senaratne TN, Williams BR, Rouillard JM, Wu CT (2012) Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proc Natl Acad Sci USA 109:21301–21306

Article  CAS  PubMed  PubMed Central  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, Chao-ting Wu (2015) Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nat Commun 6:7147

Article  CAS  PubMed  Google Scholar 

Bintu B, Mateo LJ, Su JH, Sinnott-Armstrong NA, Parker M, Kinrot S, Yamaya K, Boettiger AN, Zhuang X (2018) Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science. https://doi.org/10.1126/science.aau1783

Article  PubMed  PubMed Central  Google Scholar 

Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu CT, Zhuang X (2016) Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature 529:418–422

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bond C, Santiago-Ruiz AN, Tang Q, Lakadamyali M (2022) Technological advances in super-resolution microscopy to study cellular processes. Mol Cell 82:315–332

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brown JM, De Ornellas S, Parisi E, Schermelleh L, Buckle VJ (2022) RASER-FISH: non-denaturing fluorescence in situ hybridization for preservation of three-dimensional interphase chromatin structure. Nat Protoc 17:1306–1331

Article  CAS  PubMed  Google Scholar 

Cai S, Bock D, Pilhofer M, Gan L (2018) The in situ structures of mono-, di-, and trinucleosomes in human heterochromatin. Mol Biol Cell 29:2450–2457

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cardozo Gizzi AM, Cattoni DI, Fiche JB, Espinola SM, Gurgo J, Messina O, Houbron C, Ogiyama Y, Papadopoulos GL, Cavalli G, Lagha M, Nollmann M (2019) Microscopy-based chromosome conformation capture enables simultaneous visualization of genome organization and transcription in intact organisms. Mol Cell 74(212–22):e5

Google Scholar 

Castells Garcia A, EEd Daoui IGI, Gonzalez Almela E, Vicario C, Ottestrom J, Lakadamyali M, Cosma MP (2022) Super resolution microscopy reveals how elongating RNA polymerase II and nascent RNA interact with nucleosome clutches. Nucleic Acids Res. https://doi.org/10.1093/nar/gkab1215

Article  PubMed  Google Scholar 

Cattoni DI, Cardozo Gizzi AM, Georgieva M, Di Stefano M, Valeri A, Chamousset D, Houbron C, Dejardin S, Fiche JB, Gonzalez I, Chang JM, Sexton T, Marti-Renom MA, Bantignies F, Cavalli G, Nollmann M (2017) Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions. Nat Commun 8:1753

Article  PubMed  PubMed Central  Google Scholar 

Chambeyron S, Bickmore WA (2004) Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev 18:1119–1130

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chaudhary N, Nho SH, Cho H, Gantumur N, Ra JS, Myung K, Kim H (2020) Background-suppressed live visualization of genomic loci with an improved CRISPR system based on a split fluorophore. Genome Res 30:1306–1316

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B (2013) Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155:1479–1491

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen KH, Boettiger AN, Moffitt JR, Wang S, Zhuang X (2015) RNA imaging spatially resolved, highly multiplexed RNA profiling in single cells. Science. https://doi.org/10.1126/science.aaa6090

Article  PubMed  PubMed Central  Google Scholar 

Chen LF, Long HK, Park M, Swigut T, Boettiger AN, Wysocka J (2023) Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus. Mol Cell 83(1446–61):e6

Google Scholar 

Chieco P, Derenzini M (1999) The Feulgen reaction 75 years on. Histochem Cell Biol 111:345–358

Article  CAS  PubMed  Google Scholar 

Cremer T, Cremer M (2010) Chromosome territories. Cold Spring Harb Perspect Biol 2:a003889

Article  PubMed  PubMed Central  Google Scholar 

de Wit E, Nora EP (2023) New insights into genome folding by loop extrusion from inducible degron technologies. Nat Rev Genet 24:73–85

Article  PubMed  Google Scholar 

Espinola SM, Götz M, Bellec M, Messina O, Fiche J-B, Houbron C, Dejean M, Reim I, Cardozo AM, Gizzi ML, Nollmann M (2021) Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early drosophila development. Nat Genet 53:477–486

Article  CAS  PubMed  Google Scholar 

Finn EH, Misteli T (2021) A high-throughput DNA FISH protocol to visualize genome regions in human cells. STAR Protoc 2:100741

Article  CAS  PubMed  PubMed Central  Google Scholar 

Finn EH, Pegoraro G, Brandao HB, Valton AL, Oomen ME, Dekker J, Mirny L, Misteli T (2019) Extensive heterogeneity and intrinsic variation in spatial genome organization. Cell 176(1502–15):e10

Google Scholar 

Finn E, Misteli T, Pegoraro G (2022) High-throughput DNA FISH (hiFISH). Methods Mol Biol 2532:245–274

Article  CAS  PubMed  PubMed Central  Google Scholar 

Flors C (2013) Super-resolution fluorescence imaging of directly labelled DNA: from microscopy standards to living cells. J Microsc 251:1–4

Article  CAS  PubMed  Google Scholar 

Flors C, Ravarani CN, Dryden DT (2009) Super-resolution imaging of DNA labelled with intercalating dyes. ChemPhysChem 10:2201–2204

Article  CAS  PubMed  Google Scholar 

Franklin RE, Gosling RG (1953) Molecular configuration in sodium thymonucleate. Nature 171:740–741

Article  CAS  PubMed  Google Scholar 

Gall JG, Pardue ML (1969) Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc Natl Acad Sci U S A 63:378–383

Article  CAS  PubMed  PubMed Central  Google Scholar 

Germier T, Audibert S, Kocanova S, Lane D, Bystricky K (2018) Real-time imaging of specific genomic loci in eukaryotic cells using the ANCHOR DNA labelling system. Methods 142:16–23

Article  PubMed  Google Scholar 

Gomes CJ, Harman MW, Centuori SM, Wolgemuth CW, Martinez JD (2018) Measuring DNA content in live cells by fluorescence microscopy. Cell Div 13:6

Article  PubMed  PubMed Central  Google Scholar 

Hafner A, Park M, Berger SE, Murphy SE, Nora EP, Boettiger AN (2023) Loop stacking organizes genome folding from TADs to chromosomes. Mol Cell 83(1377–92):e6

Google Scholar 

Heo S-J, Thakur S, Chen X, Loebel C, Xia B, McBeath R, Burdick JA, Shenoy VB, Mauck RL, Lakadamyali M (2023) Aberrant c