Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms

Cardozo Gizzi, Andrés M., Cattoni, Diego I., Fiche, Jean-Bernard, Espinola, Sergio M., Gurgo, Julian, Messina, Olivier, Houbron, Christophe, Ogiyama, Yuki, Papadopoulos, Giorgio L., Cavalli, Giacomo, Lagha, Mounia, Nollmann, Marcelo·2019·Molecular Cell

Cited by (270)

Items 101–200 of 270

  1. The Impact of Space and Time on the Functional Output of the Genome
    Marcelo Nollmann, Isma Bennabi, Markus Götz, Thomas Gregor · 2021 · Cold Spring Harbor Perspectives in Biology
  2. 3D genome organisation in Drosophila
    C. Moretti, Isabelle Stévant, Yad Ghavi-Helm · 2019 · Briefings in Functional Genomics
  3. Physical mechanisms of chromatin spatial organization
    Andrea M. Chiariello, Simona Bianco, Andrea Esposito, Luca Fiorillo, Mattia Conte, Ehsan Irani, Francesco Musella, Alex Abraham, Antonella Prisco, Mario Nicodemi · 2021 · FEBS Journal
  4. Multi-Scale Organization of the Drosophila melanogaster Genome
    Samantha C. Peterson, Kaylah B. Samuelson, Stacey L. Hanlon · 2021 · Genes
  5. Interchromosomal interaction of homologous Stat92E alleles regulates transcriptional switch during stem-cell differentiation
    Matthew Antel, Romir Raj, Madona Y. G. Masoud, Ziwei Pan, Sheng Li, Barbara G. Mellone, Mayu Inaba · 2022 · Nature Communications
  6. Advances in Spatial Omics Technologies
    Tianxiao Hui, Jian Zhou, Muchen Yao, Ying Xie, Hu Zeng · 2025 · Small Methods
  7. Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics
    Véra Pancaldi · 2021 · Frontiers in Bioinformatics
  8. Mitotic chromosome organization: General rules meet species-specific variability
    Tomáš Beseda, Petr Cápal, Ivona Kubalová, Veit Schubert, Jaroslav Doležel, Hana Šimková · 2020 · Computational and Structural Biotechnology Journal
  9. The scales, mechanisms, and dynamics of the genome architecture
    Ludvig Lizana, Yuri B. Schwartz · 2024 · Science Advances
  10. Understanding transcription across scales: From base pairs to chromosomes
    Seychelle M. Vos · 2021 · Molecular Cell
  11. Chromatin Organization and Function in Drosophila
    Palmira Llorens‐Giralt, Carlos Camilleri‐Robles, Montserrat Corominas, Paula Climent‐Cantó · 2021 · Cells
  12. Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila
    Markus Götz, Olivier Messina, Sergio Espínola, Jean-Bernard Fiche, Marcelo Nöllmann · 2022 · Nature Communications
  13. A PRE loop at the dac locus acts as a topological chromatin structure that restricts and specifies enhancer–promoter communication
    Sandrine Denaud, Marion Bardou, Giorgio Lucio Papadopoulos, Stefan Grob, Marco Di Stefano, Gonzalo Sabarís, Marcelo Nöllmann, Bernd Schuettengruber, Giacomo Cavalli · 2024 · Nature Structural & Molecular Biology
  14. Enhancers: A Focus on Synthetic Biology and Correlated Gene Expression
    Christopher H. Bohrer, Nadezda A. Fursova, Daniel R. Larson · 2024 · ACS Synthetic Biology
  15. Tn5-FISH, a novel cytogenetic method to image chromatin interactions with sub-kilobase resolution
    Jing Niu, Xu Zhang, Guipeng Li, Pixi Yan, Yan Qing, Dai Qionghai, Jin Dayong, Xiaohua Shen, Jichang Wang, Zhang Michael Q. et al. · 2020 · Journal of genetics and genomics/Journal of Genetics and Genomics
  16. Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures
    Xian Feng Hao, Jyotsana J. Parmar, Benoît Lelandais, Andrey I. Aristov, Wei Ouyang, Christian Weber, Christophe Zimmer · 2021 · Genome biology
  17. Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging
    Franziska Barho, Jean-Bernard Fiche, Marion Bardou, Olivier Messina, Alexandre Martinière, Christophe Houbron, Marcelo Nöllmann · 2022 · Open Research Europe
  18. Multiplexed Sequential DNA FISH in Caenorhabditis elegans Embryos
    Ahilya N. Sawh, Susan E. Mango · 2020 · STAR Protocols
  19. Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging
    Sabaté, Thomas, Lelandais, Benoît, Bertrand, Edouard, Zimmer, Christophe · 2023 · Nucleic Acids Research
  20. Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ
    Beckwith, K. S., Ødegård-Fougner, Ø., Morero, N. R., Barton, C., Schueder, F., Tang, W., Alexander, S., Peters, J- M., Jungmann, R., Birney, E. et al. · 2025 · Nature Communications
  21. Polymer models are a versatile tool to study chromatin 3D organization
    Andrea Esposito, Simona Bianco, Luca Fiorillo, Mattia Conte, Alex Abraham, Francesco Musella, Mario Nicodemi, Antonella Prisco, Andrea M. Chiariello · 2021 · Biochemical Society Transactions
  22. An open source 16-channel fluidics system for automating sequential fluorescent in situ hybridization (FISH)-based imaging
    Zhaojie Deng, Brian J. Beliveau · 2022 · HardwareX
  23. Multiplexed chromatin imaging reveals predominantly pairwise long-range coordination between Drosophila Polycomb genes
    Julian Gurgo, Jean‐Charles Walter, Jean-Bernard Fiche, Christophe Houbron, Marie Schaeffer, Giacomo Cavalli, Frédéric Bantignies, Marcelo Nöllmann · 2024 · Cell Reports
  24. Formamide denaturation of double-stranded DNA for fluorescence in situ hybridization (FISH) distorts nanoscale chromatin structure
    Anne R. Shim, Jane Frederick, Emily M. Pujadas-Liwag, Tiffany Kuo, I Chae Ye, Joshua A. Pritchard, Cody L. Dunton, Paola Carrillo Gonzalez, Nicolas Acosta, Surbhi Jain et al. · 2024 · PLoS ONE
  25. Robust and efficient gene regulation through localized nuclear microenvironments
    Albert Tsai, Rafael Galupa, Justin Crocker · 2020 · Development
  26. The two waves in single-cell 3D genomics
    Sergey V. Ulianov, Sergey V. Razin · 2021 · Seminars in Cell and Developmental Biology
  27. FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains
    Antonina Maslova, Alla Krasikova · 2021 · Frontiers in Cell and Developmental Biology
  28. TADs or no TADS: Lessons From Single-cell Imaging of Chromosome Architecture
    Andrés M. Cardozo Gizzi, Diego Ignacio Cattoni, Marcelo Nöllmann · 2020 · Journal of Molecular Biology
  29. 3D genomics and its applications in precision medicine
    Meng-Jie Chen, Xingyu Liu, Qing-You Liu, D. Shi, Hui Li · 2023 · Cellular & Molecular Biology Letters
  30. Reprogramming of three-dimensional chromatin organization in the early embryo
    Alexandra Theis, Melissa M. Harrison · 2023 · Current Opinion in Structural Biology
  31. Visualising three-dimensional genome organisation in two dimensions
    Elizabeth Ing‐Simmons, Juan M. Vaquerizas · 2019 · Development
  32. Dynamic and equilibrium properties of finite-size polymer models of chromosome folding
    Mattia Conte, Luca Fiorillo, Carlo Annunziatella, Andrea Esposito, Francesco Musella, Alex Abraham, Simona Bianco, Andrea M. Chiariello · 2021 · Physical review. E
  33. A Shift in Paradigms: Spatial Genomics Approaches to Reveal Single-Cell Principles of Genome Organization
    Andrés M. Cardozo Gizzi · 2021 · Frontiers in Genetics
  34. Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells
    Tianming Zhou, Ruochi Zhang, Deyong Jia, Raymond T. Doty, Adam D. Munday, Daniel Gao, Li Xin, Janis L. Abkowitz, Zhijun Duan, Jian Ma · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  35. Chromatin insulators in gene regulation and 3D genome organization
    Hina Sultana, Rohit Kunar, A. Gregory Matera · 2025 · Biochemical Society Transactions
  36. The Drosophila embryo as a tabula rasa for the epigenome
    Kami Ahmad, Steven Henikoff · 2022 · Faculty Reviews
  37. Image-based 3D genomics through chromatin tracing
    Yang, Tianqi, Wang, Siyuan · 2024 · Nature Reviews Methods Primers
  38. Unveiling the Machinery behind Chromosome Folding by Polymer Physics Modeling
    Mattia Conte, Andrea Esposito, Francesca Vercellone, Alex Abraham, Simona Bianco · 2023 · International Journal of Molecular Sciences
  39. Epigenetic inheritance and gene expression regulation in early Drosophila embryos
    Filippo Ciabrelli, Nazerke Atinbayeva, Attilio Pane, Nicola Iovino · 2024 · EMBO Reports
  40. Revisiting the organization of Polycomb-repressed domains: 3D chromatin models from Hi-C compared with super-resolution imaging
    Lei Liu, Changbong Hyeon · 2020 · Nucleic Acids Research
  41. Integrative approaches to study enhancer–promoter communication
    Mach, Pia, Giorgetti, Luca · 2023 · Current Opinion in Genetics & Development
  42. pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging
    Xavier Devos, Jean-Bernard Fiche, Marion Bardou, Olivier Messina, Christophe Houbron, Julian Gurgo, Marie Schaeffer, Markus Götz, Thomas Walter, Florian Mueller et al. · 2024 · Genome biology
  43. The N-terminus of Stag1 is required to repress the 2C program by maintaining rRNA expression and nucleolar integrity
    Dubravka Pezić, Samuel Weeks, Wazeer Varsally, Pooran Singh Dewari, Steven M. Pollard, Miguel Ramos Branco, Suzana Hadjur · 2023 · Stem Cell Reports
  44. Recent advances in methodologies of epigenomics
    Hiroaki Ohishi, Wan Kin Au Yeung · 2025 · Epigenomics
  45. Novel orthogonal methods to uncover the complexity and diversity of nuclear architecture
    Sjoerd J. D. Tjalsma, Wouter L. de Laat · 2020 · Current Opinion in Genetics & Development
  46. Genome-wide tracing to decipher nuclear organization
    Victoria Flores, Irene Farabella, Guy Nir · 2023 · Current Opinion in Cell Biology
  47. SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data
    Lindsay Lee, Hongyu Yu, Bojing Blair Jia, Adam Jussila, Chenxu Zhu, Jiawen Carmen Chen, Liangqi Xie, Antonina Hafner, Shreya V. Mishra, Duan Dennis Wang et al. · 2023 · Nature Communications
  48. Multiple allelic configurations govern long-range Shh enhancer-promoter communication in the embryonic forebrain
    Jailynn Harke, Jeewon R Lee, Son C. Nguyen, Arian Arab, Staci M. Rakowiecki, Siewert Hugelier, Christina Paliou, Antonella Rauseo, Rebecca Yunker, Ke Xu et al. · 2024 · Molecular Cell
  49. Unveiling the role of chromosome structure morphology on gene function through chromosome conformation analysis
    Yuxiang Zhan, Aslı Yıldırım, Lorenzo Boninsegna, Frank Alber · 2025 · Genome biology
  50. Redefining enhancer action: Insights from structural, genomic, and single-molecule perspectives
    David Llères, Andrés M. Cardozo Gizzi, Marcelo Nöllmann · 2025 · Current Opinion in Cell Biology
  51. Erythroid Cell Research: 3D Chromatin, Transcription Factors and Beyond
    Charlotte Andrieu‐Soler, Éric Soler · 2022 · International Journal of Molecular Sciences
  52. Kinetic organization of the genome revealed by ultra-resolution, multiscale live imaging
    Joo Lee, Liangfu Chen, Simon Gaudin, Kavvya Gupta, Andrew J. Spakowitz, Alistair Nicol Boettiger · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  53. Zooming in on chromosome dynamics
    John K. Eykelenboom, Tomoyuki U Tanaka · 2020 · Cell Cycle
  54. The hierarchical packing of euchromatin domains can be described as multiplicative cascades
    Amra Noa, Hui-Shun Kuan, Vera Aschmann, Vasily Zaburdaev, Lennart Hilbert · 2021 · PLoS Computational Biology
  55. Simultaneous Epigenetic Perturbation and Genome Imaging Reveal Distinct Roles of H3K9me3 in Chromatin Architecture and Transcription
    Ying Feng, Yao Wang, Xiangnan Wang, Xiaohui He, Yang Chen, Ardalan Naseri, Thoru Pederson, Jing Zheng, Shaojie Zhang, Xiao Xiao et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  56. Quantitative multiplexed imaging of chromatin ultrastructure with Decode-PAINT
    Hiroshi M. Sasaki, Jocelyn Y. Kishi, Chao-ting Wu, Brian J. Beliveau, Peng Yin · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  57. Super-resolving chromatin in its own terms: Recent approaches to portray genomic organization
    Manuel Fernández, Maria Pia Cosma, Maria Victoria Neguembor · 2025 · Current Opinion in Structural Biology
  58. Microfluidics in biomedical research and its application in orthopedics: a perspective review
    Hemalatha Kanniyappan, Mareeswari Paramasivan, Vanaja Narayanaswamy, Rucha Konety, Govindaraj Perumal, Yang Lin, Ravindra V. Badhe, Mathew T. Mathew · 2025 · Microfluidics and Nanofluidics
  59. Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternal C. elegans chromosomes
    Silvia Gutnik, Jia Emil You, Ahilya N. Sawh, Aude Andriollo, Susan E. Mango · 2024 · Genome biology
  60. The 3D Genome in Brain Development: An Exploration of Molecular Mechanisms and Experimental Methods
    Samir Rahman, Panos Roussos · 2024 · Neuroscience Insights
  61. Dissecting the cosegregation probability from genome architecture mapping
    Lei Liu, Xinmeng Cao, Bokai Zhang, Changbong Hyeon · 2022 · Biophysical Journal
  62. The magic of unraveling genome architecture and function
    Maria Pia Cosma, Maria Victoria Neguembor · 2023 · Cell Reports
  63. From feulgen to modern methods: marking a century of DNA imaging advances
    Melike Lakadamyali · 2024 · Histochemistry and Cell Biology
  64. Generation of densely labeled oligonucleotides for the detection of small genomic elements
    Clemens Steinek, Miguel Guirao‐Ortiz, Gabriela Stumberger, Annika J. Tölke, David Hörl, Thomas Carell, Hartmann Harz, Heinrich Leonhardt · 2024 · Cell Reports Methods
  65. Polycomb repression of Hox genes involves spatial feedback but not domain compaction or demixing
    Sedona E. Murphy, Alistair Nicol Boettiger · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  66. A Multiscale Perspective on Chromatin Architecture through Polymer Physics
    Francesca Vercellone, Andrea M. Chiariello, Andrea Esposito, Mattia Conte, Alex Abraham, Andrea Fontana, Florinda Di Pierno, Fabrizio Tafuri, Sougata Guha, Sumanta Kundu et al. · 2024 · Physiology
  67. Microscopy methods to visualize nuclear organization in biomechanical studies
    Hannah Hyun-Sook Kim, Melike Lakadamyali · 2024 · Current Opinion in Biomedical Engineering
  68. Spectral-based detection of chromatin loops in multiplexed super-resolution FISH data
    Michaël Liefsoens, Timothy Földes, Maria Barbi · 2024 · Nature Communications
  69. Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations
    Mattia Conte, Alex Abraham, Andrea Esposito, Liyan Yang, Johan Harmen Gibcus, Krishna Mohan Parsi, Francesca Vercellone, Andrea Fontana, Florinda Di Pierno, Job Dekker et al. · 2024 · International Journal of Molecular Sciences
  70. Cis-regulatory hubs: a new 3D model of complex disease genetics with an application to schizophrenia
    Loïc Mangnier, Charles Joly-Beauparlant, Arnaud Droit, Steve Bilodeau, Alexandre Bureau · 2022 · Life Science Alliance
  71. Weak Transcription Factor Clustering at Binding Sites can Facilitate Information Transfer from Molecular Signals
    Tamara Mijatović, Aimée R. Kok, Merlijn Brüggen, Jos W. Zwanikken, Marianne Bauer · 2025 · PRX Life
  72. Detecting higher-order chromosome interactions by polymer modeling
    Mattia Conte, Simona Bianco, Andrea Esposito, Alex Abraham, Sougata Guha, Francesca Vercellone, Andrea Fontana, Florinda Di Pierno · 2025 · The European Physical Journal Plus
  73. The MVPs (masterful versatile players): Chromatin factors as pivotal mediators between 3D genome organization and the response to environment
    Chloé Dias Lopes, Xiaoning He, Federico Ariel, Leonardo I. Pereyra-Bistraín, Moussa Benhamed · 2024 · Current Opinion in Plant Biology
  74. Shedding Structured Light on Molecular Immunity: The Past, Present and Future of Immune Cell Super Resolution Microscopy
    Timothy M. Johanson, Christine R. Keenan, Rhys S. Allan · 2021 · Frontiers in Immunology
  75. The 3D genome landscape: Diverse chromosomal interactions and their functional implications
    Katherine Fleck, Romir Raj, Jelena Erceg · 2022 · Frontiers in Cell and Developmental Biology
  76. From insects to mammals: regulation of genome architecture in neural development
    Tanguy Lucas, Minoree Kohwi · 2019 · Current Opinion in Neurobiology
  77. Transcriptional clusters follow a conserved condensation-dispersal sequence during stem cell differentiation
    Tim Klingberg, Irina Wachter, Agnieszka Pancholi, Yomna Gohar, Priya Kumar, Marcel Sobucki, Elisa Kämmer, Süheyla Eroğlu-Kayıkçı, Sylvia Erhardt, Carmelo Ferrai et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  78. Hi-M: A Multiplex Oligopaint FISH Method to Capture Chromatin Conformations In Situ and Accompanying Open-Source Acquisition Software
    Jean-Bernard Fiche, Marie Schaeffer, Christophe Houbron, Christel Elkhoury Youhanna, Olivier Messina, Franziska Barho, Marcelo Nöllmann · 2024 · Methods in molecular biology
  79. Role of Chromatin Looping Factors in Leukemia
    Shira G. Glushakow-Smith, Zuzana Tóthová · 2025 · Annual Review of Pathology Mechanisms of Disease
  80. 3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells
    Federica Marasca, Alice Cortesi, Lara Manganaro, Beatrice Bodega · 2020 · Journal of Visualized Experiments
  81. Fly Me to the Micron: Microtechnologies for Drosophila Research
    Utku M. Sönmez, Nolan Frey, Philip R. LeDuc, Jonathan S. Minden · 2024 · Annual Review of Biomedical Engineering
  82. Inferring interphase chromosomal structure from multiplexed fluorescence in situ hybridization data: A unified picture from human and mouse cells
    Loucif Remini, Midas Segers, Andrea Parmeggiani, Enrico Carlon · 2025 · The Journal of Chemical Physics
  83. Structure and Function in Drosophila Chromosomes: Visualizing Topological Domains
    Daniel R. Larson · 2019 · Molecular Cell
  84. How chromosome topologies get their shape: views from proximity ligation and microscopy methods
    Yike Huang, Roel Neijts, Wouter L. de Laat · 2020 · FEBS Letters
  85. Physics-Based Polymer Models to Probe Chromosome Structure in Single Molecules
    Mattia Conte, Andrea M. Chiariello, Simona Bianco, Andrea Esposito, Alex Abraham, Mario Nicodemi · 2023 · Methods in molecular biology
  86. Theoretical Principles of Enhancer-Promoter Communication in Transcriptional Bursting
    Zihao Wang, Zhenquan Zhang, Songhao Luo, Tianshou Zhou, Jiajun Zhang · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  87. Single-allele chromatin folding is organized by recurrent motifs that are reweighted across cell types and states
    Olivier Messina, Jean-Bernard Fiche, Gautham Ganesh, Christel Elkhoury Youhanna, Yasmine Kemkem, Alexandre Mesnager, Jorge P. Ferrer, Adrian Villalba, Raphaël Scharfmann, İldem Akerman et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  88. Assessing the Polymer Coil-Globule State from the Very First Spectral Modes
    Timothy Földes, Antony Lesage, Maria Barbi · 2021 · Physical Review Letters
  89. Toward a comprehensive view of gene architecture during transcription
    Marcus A. Woodworth, Melike Lakadamyali · 2024 · Current Opinion in Genetics & Development
  90. SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data
    Hongyu Yu, Daiqing Wu, Shreya V. Mishra, Guning Shen, Huaigu Sun, Ming Hu, Yun Li · 2024 · Communications Biology
  91. Single-molecule Tracking and Kinetic Analysis in Living Cells and Multicellular Organisms
    J. Christof M. Gebhardt · 2025 · Journal of Molecular Biology
  92. Regulatory roles of three-dimensional structures of chromatin domains
    Kelly Yichen Li, Qin Cao, Savio Ho-Chit Chow, Chiara Nicoletti, Prem Puri, Huating Wang, Danny Leung, Kevin Yuk-Lap Yip · 2025 · Genome biology
  93. A methodology to reduce the localization error in multi-loci microscopy provides new insights into enhancer biology
    Christopher H. Bohrer, Daniel R. Larson · 2025 · PLoS Computational Biology
  94. bacto_tracker: a method for single-cell tracking of M. xanthus in dense and multispecies colonies
    Sara Rombouts, Jean-Bernard Fiche, Tâm Mignot, Marcelo Nöllmann · 2022 · Open Research Europe
  95. FISH Omics Format: a standard enabling FAIR chromatin tracing data sharing across repositories
    Rahi Navelkar, Andrea Cosolo, Iago Maceda Porto, Bogdan Bintu, Yubao Cheng, Vincent Gardeux, Silvia Gutnik, Taihei Fujimori, Antonina Hafner, Atishay Jay et al. · 2025 · PubMed
  96. Single-cell mapping of cell-type specific chromatin architecture in the central nervous system
    Letian Zhang, Marek Bartošovič · 2024 · Current Opinion in Structural Biology
  97. Epigenomic Sequencing Technologies
    Jocelyn Chen, Tina Keshavarzian, Mathieu Lupien · 2024 · Royal Society of Chemistry eBooks
  98. A guide to studying 3D genome structure and dynamics in the kidney
    Brian J. Beliveau, Shreeram Akilesh · 2024 · Nature Reviews Nephrology
  99. Microscopy methods for the in vivo study of nanoscale nuclear organization
    Nidhi Rani Lokesh, Mark E. Pownall · 2025 · Biochemical Society Transactions
  100. Emergent domain segregation in self-interacting polymers explains chromosome 3D conformations in single human cells
    Mattia Conte, Simona Bianco, Sougata Guha, Andrea M. Chiariello, Andrea Esposito, Alex Abraham, Sumanta Kundu, Francesca Vercellone, Andrea Fontana, Florinda Di Pierno et al. · 2026 · Physical review. E