Heterochromatin drives compartmentalization of inverted and conventional nuclei

Falk, Martin, Feodorova, Yana, Naumova, Natalia, Imakaev, Maxim, Lajoie, Bryan R., Leonhardt, Heinrich, Joffe, Boris, Dekker, Job +3 more·2019·Nature

Cited by (676)

Items 201–300 of 676

  1. Genome-wide variability in recombination activity is associated with meiotic chromatin organization
    Xiaofan Jin, G. Fudenberg, K. Pollard · 2021 · bioRxiv
  2. SAFB restricts contact domain boundaries associated with L1 chimeric transcription
    Yaqiang Hong, Luyao Bie, Tao Zhang, Xiaohan Yan, Guangpu Jin, Zhuo Chen, Yang Wang, Xiufeng Li, Gaofeng Pei, Yongyan Zhang et al. · 2024 · Molecular Cell
  3. Nuclear envelope assembly and dynamics during development
    Bernhard Hampoelz, Janina Baumbach · 2022 · Seminars in Cell and Developmental Biology
  4. Every gene everywhere all at once: High-precision measurement of 3D chromosome architecture with single-cell Hi-C
    Yi Chi, Jenny Shi, Dong Xing, Longzhi Tan · 2022 · Frontiers in Molecular Biosciences
  5. Multilevel view on chromatin architecture alterations in cancer
    M. Gridina, V. Fishman · 2022 · Frontiers in Genetics
  6. Multivalent binding proteins can drive collapse and reswelling of chromatin in confinement
    Sougata Guha, Mithun Kumar Mitra · 2022 · Soft Matter
  7. Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin
    Javier Arpòn, Kaori Sakai, Valérie Gaudin, Philippe Andrey · 2021 · Scientific Reports
  8. Alteration of active and repressive histone marks during adipogenic differentiation of porcine mesenchymal stem cells
    Joanna Stachecka, Pawel Antoni Kolodziejski, Magdalena Noak, Izabela Szczerbal · 2021 · Scientific Reports
  9. Cell Cycle Regulation of the Pdx1 Transcription Factor in Developing Pancreas and Insulin-Producing β-Cells
    Xiaodong Zhu, Alexis U. Oguh, Morgan A. Gingerich, Scott A. Soleimanpour, Doris A. Stoffers, MAUREEN A. GANNON · 2021 · Diabetes
  10. Chromatin Structure and Dynamics: Focus on Neuronal Differentiation and Pathological Implication
    Sophie Nothof, Frédérique Magdinier, Julien Van‐Gils · 2022 · Genes
  11. Nuclear organization by satellite DNA, SAF-A/hnRNPU and matrix attachment regions
    OI Podgornaya · 2022 · Seminars in Cell and Developmental Biology
  12. A GC-centered view of 3D genome organization
    Britta A. M. Bouwman, Nicola Crosetto, Magda Bienko · 2023 · Current Opinion in Genetics & Development
  13. Chemical-induced phase transition and global conformational reorganization of chromatin
    Tengfei Wang, Shuxiang Shi, Yuanyuan Shi, Peipei Jiang, Ganlu Hu, Qinying Ye, Zhan Shi, Ke‐Xin Yu, Chenguang Wang, Guoping Fan et al. · 2023 · Nature Communications
  14. TULIPs decorate the three-dimensional genome of PFA ependymoma
    Michael J.G. Johnston, John J. Y. Lee, Bo Hu, Ana Nikolić, Elham Hasheminasabgorji, Audrey Baguette, Seungil Paik, Haifen Chen, Sachin A. Kumar, Carol C. L. Chen et al. · 2024 · Cell
  15. Chromatin Compaction Leads to a Preference for Peripheral Heterochromatin
    Quinn MacPherson, Bruno Gabriel Beltran, Andrew J. Spakowitz · 2020 · Biophysical Journal
  16. MeCP2 and Major Satellite Forward RNA Cooperate for Pericentric Heterochromatin Organization
    Salvatore Fioriniello, Eva Csukonyi, Domenico Marano, Arianna Brancaccio, Michele Madonna, Carmela Zarrillo, Alessia Romano, Federico Marracino, Maria Rosaria Matarazzo, Maurizio D’Esposito et al. · 2020 · Stem Cell Reports
  17. Vimentin binds to G-quadruplex repeats found at telomeres and gene promoters
    Silvia Ceschi, Michele Berselli, Marta Cozzaglio, M. Giantin, S. Toppo, B. Spolaore, C. Sissi · 2021 · bioRxiv
  18. Uncovering the Principles of Genome Folding by 3D Chromatin Modeling
    Aslı Yıldırım, Lorenzo Boninsegna, Yuxiang Zhan, Frank Alber · 2021 · Cold Spring Harbor Perspectives in Biology
  19. Decoding the organization, dynamics, and function of the 4D genome.
    Erin L. Aboelnour, B. Bonev · 2021 · Developmental Cell
  20. Phosphorylation-dependent mitotic SUMOylation drives nuclear envelope–chromatin interactions
    Christopher P. Ptak, Natasha O. Saik, Ashwini Premashankar, Diego L. Lapetina, John D. Aitchison, Ben Montpetit, Richard W. Wozniak · 2021 · The Journal of Cell Biology
  21. Phase Separation-Mediated Chromatin Organization and Dynamics: From Imaging-Based Quantitative Characterizations to Functional Implications
    Woei Shyuan Ng, Hendrik Sielaff, Ziqing Zhao · 2022 · International Journal of Molecular Sciences
  22. Heterochromatic 3D genome organization is directed by HP1a- and H3K9-dependent and independent mechanisms
    Alexis V. Stutzman, Christina A. Hill, Robin L. Armstrong, Riya Gohil, Robert J. Duronio, Jill M. Dowen, Daniel J. McKay · 2024 · Molecular Cell
  23. Dynamics of nuclear architecture during early embryonic development and lessons from liveimaging
    Federico Pecori, Maria‐Elena Torres‐Padilla · 2023 · Developmental Cell
  24. Mature chromatin packing domains persist after RAD21 depletion in 3D
    Wing Shun Li, Lucas M. Carter, Luay Matthew Almassalha, Ruyi Gong, Emily M. Pujadas-Liwag, Tiffany Kuo, Kyle L. MacQuarrie, Marcelo A. Carignano, Cody L. Dunton, Vinayak P. Dravid et al. · 2025 · Science Advances
  25. Chromatin Alterations in Neurological Disorders and Strategies of (Epi)Genome Rescue
    Marcin Janowski, Małgorzata Milewska, Payman Zare, Aleksandra Pękowska · 2021 · Pharmaceuticals
  26. Cell cycle dynamics and developmental dynamics of the 3D genome: toward linking the two timescales
    Hisashi Miura, Ichiro Hiratani · 2022 · Current Opinion in Genetics & Development
  27. Phase Separation: Direct and Indirect Driving Force for High-Order Chromatin Organization
    Xiaoli Li, Ziyang An, Wenqing Zhang, Feifei Li · 2023 · Genes
  28. Long interspersed nuclear element 1 and B1/Alu repeats blueprint genome compartmentalization
    Siyang Li, Xiaohua Shen · 2023 · Current Opinion in Genetics & Development
  29. Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin
    Igor S. Tolokh, Nicholas Allen Kinney, Igor V. Sharakhov, Alexey V. Onufriev · 2023 · Epigenetics & Chromatin
  30. Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus
    Ali Göktuğ Attar, Jarosław Paturej, Edward J. Banigan, Aykut Erbaş · 2024 · Nucleus
  31. Genome organization via loop extrusion, insights from polymer physics models
    Surya K. Ghosh, Daniel Jost · 2019 · Briefings in Functional Genomics
  32. Endogenous topoisomerase II-mediated DNA breaks drive thymic cancer predisposition linked to ATM deficiency
    Alejandro Álvarez-Quilón, José Terrón-Bautista, Irene Delgado‐Sainz, Almudena Serrano-Benítez, Rocío Romero‐Granados, Pedro Manuel Martínez‐García, Silvia Jimeno-González, Cristina Bernal‐Lozano, Cristina Quintero, Lourdes Garcia‐Quintanilla et al. · 2020 · Nature Communications
  33. Probe-free optical chromatin deformation and measurement of differential mechanical properties in the nucleus
    Benjamin Seelbinder, Susan Wagner, Manavi Jain, Elena Erben, Sergei Klykov, Iliya Dimitrov Stoev, Venkat Raghavan Krishnaswamy, Moritz Kreysing · 2023 · eLife
  34. HP1 loses its chromatin clustering and phase separation function across evolution
    Sanâa Bensaha, Dominika Lewandowska, Fernando Muzzopappa, Stephanie Hutin, Mark D. Tully, Michela Anfossi, Florence M. Cammas, Christophe Normand, Fabian Erdel · 2025 · Nature Communications
  35. The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate
    Harold C. Marin, Charlie Allen, Eric Simental, Eric W. Martin, Barbara Panning, Bassem Al‐Sady, Abigail L. Buchwalter · 2025 · Nature Cell Biology
  36. Revealing the biophysics of lamina-associated domain formation by integrating theoretical modeling and high-resolution imaging
    Monika Dhankhar, Zixian Guo, Aayush Kant, Ramin Basir, Rohit Joshi, Vinayak Vinayak, Su‐Jin Heo, Robert L. Mauck, Melike Lakadamyali, Vivek B. Shenoy · 2025 · Nature Communications
  37. Protect-seq: genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin
    George Spracklin, Sriharsa Pradhan · 2019 · Nucleic Acids Research
  38. The genome organization of Neurospora crassa at high resolution uncovers principles of fungal chromosome topology
    Sara Rodríguez, Ashley W. Scadden, Andrew T. Reckard, Yulia Shtanko, Clayton Hull-Crew, Andrew D. Klocko · 2022 · G3 Genes Genomes Genetics
  39. Function of Nuclear Pore Complexes in Regulation of Plant Defense Signaling
    Xi Wu, Junyou Han, Changkui Guo · 2022 · International Journal of Molecular Sciences
  40. Drosophila insulator proteins exhibit in vivo liquid–liquid phase separation properties
    Bright Amankwaa, T. Schoborg, M. Labrador · 2022 · Life Science Alliance
  41. Loops and the activity of loop extrusion factors constrain chromatin dynamics
    Mary Lou P. Bailey, I. Surovtsev, Jessica F. Williams, Hao Yan, Tianyu Yuan, Kevin C. Li, Katherine Duseau, S. Mochrie, M. King · 2020 · bioRxiv
  42. Transcriptional machinery as an architect of genome structure
    Nadezda A. Fursova, Daniel R. Larson · 2024 · Current Opinion in Structural Biology
  43. Polymer models for the mechanisms of chromatin 3D folding: review and perspective
    Rui Zhou, Yi Qin Gao · 2020 · Physical Chemistry Chemical Physics
  44. Chromatin domains in the cell: Phase separation and condensation
    Shin Fujishiro, Masaki Sasai, Kazuhiro Maeshima · 2025 · Current Opinion in Structural Biology
  45. LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis
    Renard TM Lewis, Virginia Sinigiani, Noura Maziak, Krisztián Koós, Cristiana Bersaglieri, Ivo Zemp, Caroline Ashiono, Constance Ciaudo, Péter Horváth, Juan M. Vaquerizas et al. · 2026 · Nature Cell Biology
  46. Chromatin structure changes during various processes from a DNA sequence view.
    Hui Quan, Ying Yang, Sirui Liu, Hao Tian, Yue Xue, Yi-Qin Gao · 2019 · Current Opinion in Structural Biology
  47. How enzymatic activity is involved in chromatin organization
    Rakesh Das, Takahiro Sakaue, G. V. Shivashankar, Jacques Prost, Tetsuya Hiraiwa · 2022 · eLife
  48. Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction
    Greg Schuette, Xinqiang Ding, Bin Zhang · 2023 · Biophysical Journal
  49. Attraction and disruption: how loop extrusion and compartmentalisation shape the nuclear genome
    Mikhail D. Magnitov, Elzo de Wit · 2024 · Current Opinion in Genetics & Development
  50. Spandrels of the cell nucleus
    Irina V. Solovei, Leonid A. Mirny · 2024 · Current Opinion in Cell Biology
  51. RNA gradients: Shapers of 3D genome architecture
    Britta A. M. Bouwman, Nicola Crosetto, Magda Bienko · 2022 · Current Opinion in Cell Biology
  52. 3DGenBench: a web-server to benchmark computational models for 3D Genomics
    Polina S. Belokopytova, Emil Viesná, Mateusz Chiliński, Yifeng Qi, Hossein Salari, Marco Di Stefano, Andrea Esposito, Mattia Conte, Andrea M. Chiariello, Vladimir B. Teif et al. · 2022 · Nucleic Acids Research
  53. Circadian PERIOD proteins regulate TC-DSB repair through anchoring to the nuclear envelope
    Benjamin Le Bozec, Laure Guitton-Sert, Sarah Collins, Anne-Laure Finoux, Charlotte Payrault, Emmanuelle Guillou, Marion Aguirrebengoa, Vanessa Dougados, Virginie Jouffret, Jessica Frison et al. · 2025 · Molecular Cell
  54. Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish
    Stefan Redl, António Miguel de Jesus Domingues, Edoardo Caspani, Stefanie Möckel, Willi Salvenmoser, María Méndez-Lago, René F. Ketting · 2020 · Development
  55. Chromatin Organization and Function in Drosophila
    Palmira Llorens‐Giralt, Carlos Camilleri‐Robles, Montserrat Corominas, Paula Climent‐Cantó · 2021 · Cells
  56. Phospho-Tau and Chromatin Landscapes in Early and Late Alzheimer’s Disease
    Laura Gil, Sandra Aurora Niño, Carmen Guerrero, María Esther Jiménez-Capdeville · 2021 · International Journal of Molecular Sciences
  57. β-actin mediated H3K27ac changes demonstrate the link between compartment switching and enhancer-dependent transcriptional regulation
    Syed Raza Mahmood, Nadine Hosny El Said, Kristin C. Gunsalus, Piergiorgio Percipalle · 2023 · Genome biology
  58. Epigenetic dynamics of aging and cancer development: current concepts from studies mapping aging and cancer epigenomes
    Shilpa Bisht, Yiqing Mao, Hariharan Easwaran · 2024 · Current Opinion in Oncology
  59. The scales, mechanisms, and dynamics of the genome architecture
    Ludvig Lizana, Yuri B. Schwartz · 2024 · Science Advances
  60. Genetic–epigenetic interplay in the determination of plant 3D genome organization
    Xiaoning He, Chloé Dias Lopes, Leonardo I. Pereyra-Bistraín, Ying Huang, Jing An, Rim Brik‐Chaouche, Hugo Zalzalé, Qingyi Wang, Xing Ma, Javier Antúnez-Sánchez et al. · 2024 · Nucleic Acids Research
  61. Double-strand breaks in motion: implications for chromosomal rearrangement
    Thomas E. Wilson, Sham Sunder · 2019 · Current Genetics
  62. The “Genomic Code”: DNA Pervasively Moulds Chromatin Structures Leaving no Room for “Junk”
    G. Bernardi · 2021 · Life
  63. Interplay between regulatory elements and chromatin topology in cellular lineage determination.
    Vallari Shukla, A. Cetnarowska, Mette Hyldahl, S. Mandrup · 2022 · Trends in Genetics
  64. Genome anchoring to nuclear landmarks drives functional compartmentalization of the nuclear space
    Antoine Canat, Adeline Veillet, Amandine Bonnet, Pierre Therizols · 2020 · Briefings in Functional Genomics
  65. Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into genome architecture and regulation
    Ni Huang, Wei Qiang Seow, Alex Appert, Dong Yan, Przemysław Stempor, Julie Ahringer · 2021 · Genome Research
  66. 3D Genome Organization: Causes and Consequences for DNA Damage and Repair
    Ànnia Carré Simon, Emmanuelle Fabre · 2021 · Genes
  67. Pentad: a tool for distance-dependent analysis of Hi-C interactions within and between chromatin compartments
    Mikhail D. Magnitov, Azat K Garaev, Alexander Tyakht, Sergey V. Ulianov, Sergey V. Razin · 2022 · BMC Bioinformatics
  68. Nuclear Actin Dynamics in Gene Expression, DNA Repair, and Cancer
    Yuanjian Huang, Shengzhe Zhang, Jae‐Il Park · 2022 · Results and problems in cell differentiation
  69. Phase transitions in heterochromatin organization
    Fabian Erdel · 2023 · Current Opinion in Structural Biology
  70. Interphase chromatin biophysics and mechanics: new perspectives and open questions
    Antoine Coulon · 2024 · Current Opinion in Genetics & Development
  71. Interactions between the genome and the nuclear lamina are multivalent and cooperative
    Lise Dauban, M Eder, Marcel de Haas, Vinícius H. Franceschini-Santos, J. Omar Yáñez-Cuna, Moreno Martinovic, Tom van Schaik, Christ Leemans, Hans Teunissen, Koen Rademaker et al. · 2025 · Nature Structural & Molecular Biology
  72. The Genomic Code: A Pervasive Encoding/Molding of Chromatin Structures and a Solution of the “Non‐Coding DNA” Mystery
    Giorgio Bernardi · 2019 · BioEssays
  73. Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains
    Kiran Kumari, J. Ravi Prakash, Ranjith Padinhateeri · 2022 · Biophysical Journal
  74. Progressive Domain Segregation in Early Embryonic Development and Underlying Correlation to Genetic and Epigenetic Changes
    Hui Quan, Hao Tian, Sirui Liu, Yue Xue, Yu Zhang, Wei Xie, Yi Qin Gao · 2021 · Cells
  75. Are the processes of DNA replication and DNA repair reading a common structural chromatin unit?
    Stefania Mamberti, M. Cristina Cardoso · 2020 · Nucleus
  76. Three-dimensional chromatin organization in brain function and dysfunction
    Dileep, Vishnu, Tsai, Li-Huei · 2021 · Current Opinion in Neurobiology
  77. Peripheral heterochromatin tethering is required for chromatin-based nuclear mechanical response
    Ali Göktuğ Attar, Jarosław Paturej, Ozan S. Sarıyer, Edward J. Banigan, Aykut Erbaş · 2025 · Nucleic Acids Research
  78. Mechanistic drivers of chromatin organization into compartments
    Hannah L. Harris, M. Jordan Rowley · 2024 · Current Opinion in Genetics & Development
  79. Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus
    Martin Girard, Mónica Olvera de la Cruz, John F. Marko, Aykut Erbaş · 2024 · Physical review. E
  80. Chromatin protein complexes involved in gene repression in lamina-associated domains
    Stefano Giustino Manzo, Abdelghani Mazouzi, Christ Leemans, Tom van Schaik, Nadia Neyazi, Marjon S. van Ruiten, Benjamin D. Rowland, Thijn R. Brummelkamp, Bas van Steensel · 2024 · The EMBO Journal
  81. Chromatin Landscaping At Mitotic Exit Orchestrates Genome Function
    Muhammad Shoaib, Nidhi Nair, Claus Storgaard Sørensen · 2020 · Frontiers in Genetics
  82. A Cohesin Traffic Pattern Genetically Linked to Gene Regulation
    Anne-Laure Valton, Job Dekker, Sergey V. Venev, Barbara Mair, Eraj Shafiq Khokhar, Athma A. Pai, Jason Moffat · 2021 · HAL
  83. Computational characterization of domain‐segregated 3D chromatin structure and segmented DNA methylation status in carcinogenesis
    Yue Xue, Ying Yang, Hao Tian, Hui Quan, Sirui Liu, Ling Zhang, Lu Yang, Haichuan Zhu, Hong Wu, Yi Qin Gao · 2021 · Molecular Oncology
  84. A cohesin traffic pattern genetically linked to gene regulation
    Anne-Laure Valton, Sergey V. Venev, Barbara Mair, Eraj Shafiq Khokhar, Amy H. Y. Tong, Matej Ušaj, Katherine S. K. Chan, Athma A. Pai, Jason Moffat, Job Dekker · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  85. Theoretical modelling of liquid–liquid phase separation: from particle-based to field-based simulation
    Linge Li, Hou Zhonghuai · 2022 · Biophysics Reports
  86. Consistencies and contradictions in different polymer models of chromatin architecture
    Amanda Souza Câmara, Martin Mascher · 2023 · Computational and Structural Biotechnology Journal
  87. Differential contributions of nuclear lamina association and genome compartmentalization to gene regulation
    Priyojit Das, Rebeca San Martin, Rachel Patton McCord · 2023 · Nucleus
  88. Melts of nonconcatenated rings in spherical confinement
    Stanard Mebwe Pachong, Iurii Chubak, Kurt Kremer, Jan Smrek · 2020 · The Journal of Chemical Physics
  89. TAD cliques predict key features of chromatin organization
    Tharvesh M. Liyakat Ali, Annaël Brunet, Philippe Collas, Jonas Paulsen · 2021 · BMC Genomics
  90. Physical constraints in polymer modeling of chromatin associations with the nuclear periphery at kilobase scale
    Annaël Brunet, Nicolas Destainville, Philippe Collas · 2021 · Nucleus
  91. Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies
    Laurianne Scourzic, Eralda Salataj, Effie Apostolou · 2021 · Frontiers in Immunology
  92. New insights into the functional role of retrotransposon dynamics in mammalian somatic cells
    Arianna Mangiavacchi, Peng Liu, Francesco Della Valle, Valerio Orlando · 2021 · Cellular and Molecular Life Sciences
  93. Comparison of genome architecture at two stages of male germline cell differentiation inDrosophila
    Artem A. Ilyin, Anna D. Kononkova, Anastasia Golova, Viktor V. Shloma, Oxana M. Olenkina, Valentina V. Nenasheva, Yuri A. Abramov, Alexei A. Kotov, Daniil A. Maksimov, Petr P. Laktionov et al. · 2022 · Nucleic Acids Research
  94. Architectural proteins for the formation and maintenance of the 3D genome
    Mengfan Li, Jingbo Gan, Yuao Sun, Zihan Xu, Junsheng Yang, Yujie Sun, Cheng Li · 2020 · Science China Life Sciences
  95. Single-cell nascent transcription reveals sparse genome usage and plasticity
    Shaoqian Ma, Yantao Hong, Junhan Chen, Jingzhao Xu, Xiaohua Shen · 2025 · Cell
  96. Shifting landscapes: the role of 3D genomic organizations in gene regulatory strategies
    Jenks Hehmeyer, François Spitz, Heather Q. Marlow · 2023 · Current Opinion in Genetics & Development
  97. DNA-protamine condensates under low salt conditions: molecular dynamics simulation with a simple coarse-grained model focusing on electrostatic interactions
    Yun Hee Jang, Éric Raspaud, Yves Lansac · 2023 · Nanoscale Advances
  98. Motorized chain models of the ideal chromosome
    Zhiyu Cao, Peter Guy Wolynes · 2024 · Proceedings of the National Academy of Sciences
  99. A Molecular View into the Structure and Dynamics of Phase-Separated Chromatin
    Andrew Golembeski, Joshua P. Lequieu · 2024 · The Journal of Physical Chemistry B
  100. Sequence Ontology terminology for gene regulation
    David Sant, Michael S. Sinclair, Chris Mungall, Stefan Schulz, Daniel R. Zerbino, Ruth C. Lovering, Colin Logie, Karen L Eilbeck · 2021 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms