Long-Range Chromatin Interactions

Dekker, Job, Misteli, Tom·2015·Cold Spring Harbor Perspectives in Biology

Cited by (255)

Items 101–200 of 255

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    Carmen Adriaens, Leonid Serebryannyy, Marina Feric, Andria Schibler, Karen J. Meaburn, Nard Kubben, Paweł Trzaskoma, Sigal Shachar, Sandra Vidak, Elizabeth H. Finn et al. · 2018 · Histochemistry and Cell Biology
  3. Integrating Long-Range Regulatory Interactions to Predict Gene Expression Using Graph Convolutional Networks
    Jeremy Bigness, Xavier Loinaz, Shalin S. Patel, Erica Larschan, Ritambhara Singh · 2022 · Journal of Computational Biology
  4. Polymer models of the hierarchical folding of the Hox-B chromosomal locus
    Carlo Annunziatella, Andrea M. Chiariello, Simona Bianco, Mario Nicodemi · 2016 · Physical review. E
  5. The LINC Complex Inhibits Excessive Chromatin Repression
    Daria Amiad Pavlov, C. P. Unnikannan, Dana Lorber, Gaurav Bajpai, Tsviya Olender, Elizabeth Stoops, Adriana Reuveny, Samuel A. Safran, Talila Volk · 2023 · Cells
  6. The Yeast Genomes in Three Dimensions: Mechanisms and Functions
    Ken-ichi Noma · 2017 · Annual Review of Genetics
  7. Multivalent binding proteins can drive collapse and reswelling of chromatin in confinement
    Sougata Guha, Mithun Kumar Mitra · 2022 · Soft Matter
  8. The Necessity of Chromatin: A View in Perspective
    Vincenzo Pirrotta · 2016 · Cold Spring Harbor Perspectives in Biology
  9. The importance of the nuclear positioning of the PPARG gene for its expression during porcine in vitro adipogenesis
    Joanna Stachecka, Joanna Nowacka‐Woszuk, Pawel Antoni Kolodziejski, Izabela Szczerbal · 2019 · Chromosome Research
  10. Programmed DNA elimination in the parasitic nematode Ascaris
    Brandon Estrem, Jianbin Wang · 2023 · PLoS Pathogens
  11. HMGNs: The enhancer charmers
    Alexia Martínez de Paz, Juan Ausió · 2015 · BioEssays
  12. Investigating the Interplay between Sister Chromatid Cohesion and Homolog Pairing in Drosophila Nuclei
    Tharanga Niroshini Senaratne, Eric F. Joyce, Son C. Nguyen, Chao-ting Wu · 2016 · PLoS Genetics
  13. Topology of Folded Molecular Chains: From Single Biomolecules to Engineered Origami
    Barbara Scalvini, Vahid Sheikhhassani, Jaie C. Woodard, Jana Aupič, Remus Thei Dame, Roman Jerala, Alireza Mashaghi · 2020 · Trends in Chemistry
  14. Cohesin prevents cross-domain gene coactivation
    Peng Dong, Shu Zhang, Valentina Gandin, Liangqi Xie, Lihua Wang, Andrew L. Lemire, Wenhong Li, Hideo Otsuna, Takashi Kawase, Arthur D. Lander et al. · 2024 · Nature Genetics
  15. Clusters of lineage-specific genes are anchored by ZNF274 in repressive perinucleolar compartments
    Martina Begnis, Julien Duc, Sandra Eloise Offner, Delphine Grün, Shaoline Sheppard, Olga Rosspopoff, Didier Trono · 2024 · Science Advances
  16. Choreographing the Double Strand Break Response: Ubiquitin and SUMO Control of Nuclear Architecture
    Shane M. Harding, Roger A. Greenberg · 2016 · Frontiers in Genetics
  17. 3D genomic regulation of lncRNA and Xist in X chromosome
    Furong Yan, Xiangdong Wang, Yiming Zeng · 2018 · Seminars in Cell and Developmental Biology
  18. Female-to-male sex reversal associated with unique Xp21.2 deletion disrupting genomic regulatory architecture of the dosage-sensitive sex reversal region
    Pankaj Dangle, María Sol Touzón, Miguel Reyes‐Múgica, Selma Feldman Witchel, Aleksandar Rajkovic, Francis X. Schneck, Svetlana A. Yatsenko · 2017 · Journal of Medical Genetics
  19. Alterations in 3D chromatin organization contribute to tumorigenesis of EGFR-amplified glioblastoma
    Qi Yang, Nian Jiang, Han Zou, Xuning Fan, Tao Liu, Xi Huang, S. Wanggou, Xuejun Li · 2022 · Computational and Structural Biotechnology Journal
  20. Multi-Scale Organization of the Drosophila melanogaster Genome
    Samantha C. Peterson, Kaylah B. Samuelson, Stacey L. Hanlon · 2021 · Genes
  21. A Final Frontier in Environment-Genome Interactions? Integrated, Multi-Omic Approaches to Predictions of Non-Communicable Disease Risk
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  22. Nuclear filaments: role in chromosomal positioning and gene expression
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  23. Genome-wide methylome and chromatin interactome identify abnormal enhancer to be risk factor of breast cancer
    Yuan Wang, Dapeng Hao, Jingjing Li, Li Wang, Lijun Di · 2017 · Oncotarget
  24. Evolution of 3D Chromatin Folding
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  25. 4C-seq characterization of Drosophila BEAF binding regions provides evidence for highly variable long-distance interactions between active chromatin
    Shraddha Shrestha, Dong‐Ha Oh, J. Keller McKowen, Maheshi Dassanayake, Craig M. Hart · 2018 · PLoS ONE
  26. Topoisomerase VI participates in an insulator-like function that prevents H3K9me2 spreading
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  27. Reorganization of 3D chromatin architecture in doxorubicin-resistant breast cancer cells
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  28. 10q26 – The enigma in age-related macular degeneration
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  29. Establishment of chromatin architecture interplays with embryo hypertranscription
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  30. Mapping catalytically engaged TOP2B in neurons reveals the principles of topoisomerase action within the genome
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  31. Physical modeling of nucleosome clustering in euchromatin resulting from interactions between epigenetic reader proteins
    Joseph G. Wakim, Andrew J. Spakowitz · 2024 · Proceedings of the National Academy of Sciences
  32. A genome disconnect
    Elizabeth H. Finn, Tom Misteli · 2019 · Nature Genetics
  33. Interplay between genome organization and epigenomic alterations of pericentromeric DNA in cancer
    Subhadip Kundu, M.D. Ray, Ashok Kumar Sharma · 2021 · Journal of genetics and genomics/Journal of Genetics and Genomics
  34. Membrane receptor MerTK is a newly identified transcriptional regulator that associates to chromatin as nanoclusters during human DC differentiation
    Kyra J. E. Borgman, Georgina Flórez‐Grau, Maria Aurelia Ricci, Carlo Manzo, Melike Lakadamyali, Alessandra Cambi, Daniel Benítez‐Ribas, Felix Campelo, M.F. Garcia Parajo · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  35. 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
  36. Single-cell DNA methylome and 3D genome atlas of human subcutaneous adipose tissue
    Zeyuan Johnson Chen, Sankha Subhra Das, Asha Kar, Seung Hyuk Lee, Kevin Daniel Abuhanna, Marcus Alvarez, Mihir G. Sukhatme, Zitian Wang, Kyla Z. Gelev, Matthew G. Heffel et al. · 2025 · Nature Genetics
  37. De novo identification of complex traits associated with asthma
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  38. Mb-level CpG and TFBS islands visualized by AI and their roles in the nuclear organization of the human genome
    Kennosuke Wada, Yoshiko Wada, Toshimichi Ikemura · 2020 · Genes & Genetic Systems
  39. DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks
    Wenduo Cheng, Zhenqiao Song, Yang Zhang, Shike Wang, Danqing Wang, Muyu Yang, Lei Li, Jian Ma · 2025 · Nature Communications
  40. Prediction of gene co-expression from chromatin contacts with graph attention network
    Ke Zhang, Chenxi Wang, Liping Sun, Jie Zheng · 2022 · Bioinformatics
  41. A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships
    Ruchi Lohia, Nathan Fox, Jesse A Gillis · 2022 · Genome biology
  42. Reshaping Chromatin Architecture around DNA Breaks
    Pierre Caron, Sophie E. Polo · 2019 · Trends in Biochemical Sciences
  43. Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics
    Gaurav Bajpai, Samuel A. Safran · 2023 · PLoS Computational Biology
  44. Systems-level chromosomal parameters represent a suprachromosomal basis for the non-random chromosomal arrangement in human interphase nuclei
    S. N. Fatakia, Ishita S. Mehta, Basuthkar Jagadeeshwar Rao · 2016 · Scientific Reports
  45. End resection and telomere healing of DNA double-strand breaks during nematode programmed DNA elimination
    Brandon Estrem, Richard E. Davis, Jianbin Wang · 2024 · Nucleic Acids Research
  46. 3D genomic organization in cancers
    Junting Wang, Huan Tao, Hao Li, Xiaochen Bo, Hebing Chen · 2023 · Quantitative Biology
  47. Rapid nucleus-scale reorganization of chromatin in neurons enables transcriptional adaptation for memory consolidation
    Manuel Peter, Dominik F. Aschauer, Renata Rose, Anne Sinning, Florian Groessl, Dominic Kargl, Klaus Kraitsy, Thomas Rainer Burkard, Heiko J. Luhmann, Wulf E. Haubensak et al. · 2021 · PLoS ONE
  48. Structural and mechanistic insight into DNA bending by antitumour calicheamicins
    Alberto Mills, Federico Gago · 2021 · Organic & Biomolecular Chemistry
  49. Cohesin and CTCF complexes mediate contacts in chromatin loops depending on nucleosome positions
    Aymen Attou, Tilo Zülske, Gero Wedemann · 2022 · Biophysical Journal
  50. Genome dynamics over evolutionary time: “C-value enigma” in light of chromosome structure
    Predrag Slijepčević · 2018 · Mutation Research/Genetic Toxicology and Environmental Mutagenesis
  51. Physiological aging in three dimensions
    Fei Ma, Ranjan Sen · 2025 · Trends in Cell Biology
  52. Twelve Years of Genome-Wide Association Studies of Human Protein N-Glycosylation
    Anna N. Timoshchuk, Sodbo Sharapov, Yurii S. Aulchenko · 2023 · Engineering
  53. Conformations, correlations, and instabilities of a flexible fiber in an active fluid
    Scott Weady, David B. Stein, Alexandra Zidovska, Michael Shelley · 2024 · Physical Review Fluids
  54. Controlling gene expression by DNA mechanics: emerging insights and challenges
    David Levens, Laura Baranello, Fedor Kouzine · 2016 · Biophysical Reviews
  55. Network-Based Methods and Other Approaches for Predicting lncRNA Functions and Disease Associations
    Rosario Michael Piro, Annalisa Marsico · 2019 · Methods in molecular biology
  56. Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ
    Ashley F. Tsue, Evan E. Kania, Diana Q. Lei, Rose Fields, Christopher D. McGann, Elliot A. Hershberg, Xinxian Deng, Maryanne Kihiu, Shao‐En Ong, Christine M. Distèche et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  57. AI for the collective analysis of a massive number of genome sequences: various examples from the small genome of pandemic SARS-CoV-2 to the human genome
    Toshimichi Ikemura, Yuki Iwasaki, Kennosuke Wada, Yoshiko Wada, Takashi Abe · 2021 · Genes & Genetic Systems
  58. Large-scale mapping of positional changes of hypoxia-responsive genes upon activation
    Koh Nakayama, Sigal Shachar, Elizabeth H. Finn, Hiroyuki Sato, Akihiro Hirakawa, Tom Misteli · 2022 · Molecular Biology of the Cell
  59. Multi-level genomic convergence of secondary aquatic adaptation in marine mammals
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  60. Exploring the interplay between enhancer–promoter interactions and transcription
    Ryan Kittle, Michal Levo · 2025 · Current Opinion in Genetics & Development
  61. The Non-random Location of Autosomal Genes That Participate in X Inactivation
    Barbara R. Migeon · 2019 · Frontiers in Cell and Developmental Biology
  62. Human Age Estimation from Gene Expression Data using Artificial Neural Networks
    Salman Mohamadi, Nasser M. Nasrabadi, Gianfranco Doretto, Donald Adjeroh · 2021 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  63. Chromosome Folding: Driver or Passenger of Epigenetic State?: Figure 1.
    Tom Sexton, Eitan Yaffe · 2015 · Cold Spring Harbor Perspectives in Biology
  64. Evaluation of chromatin mesoscale organization
    Dana Lorber, Talila Volk · 2022 · APL Bioengineering
  65. Epimutations and Their Effect on Chromatin Organization: Exciting Avenues for Cancer Treatment
    Asad Mohammad, Sudhakar Jha · 2022 · Cancers
  66. Genome organization: Tag it, move it, place it
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  67. Exploring chromatin conformation and gene co-expression through graph embedding
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  68. Reconstructing the blood metabolome and genotype using long-range chromatin interactions
    Tayaza Fadason, William S. Schierding, Nikolai Kolbenev, Jiamou Liu, John R. Ingram, Justin Martin O'Sullivan · 2020 · Metabolism Open
  69. Chromatin loop anchors predict transcript and exon usage
    Yu Zhang, Yichao Cai, Xavier Roca, Chee Keong Kwoh, Melissa J. Fullwood · 2021 · Briefings in Bioinformatics
  70. Micro-C XL: assaying chromosome conformation at length scales from the nucleosome to the entire genome
    Tsung-Han S. Hsieh, Geoffrey Fudenberg, Anton A. Goloborodko, Oliver J. Rando · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
  71. Interplay and Dynamics of Chromatin Architecture and DNA Damage Response: An Overview
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  72. Recursive Convolutional Neural Networks for Epigenomics
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  73. Conserved noncoding sequences correlate with distant gene contacts in Arabidopsis and Brassica
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  74. Transient crosslinking controls the condensate formation pathway within chromatin networks
    Zong-Pei Wu, Kerry Bloom, M. Gregory Forest, Xue‐Zheng Cao · 2024 · Physical review. E
  75. Insights into genome architecture deduced from the properties of short Lac repressor-mediated DNA loops
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  76. Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
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  77. Metabolic resilience is encoded in genome plasticity
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  83. 3D Genomics
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  84. Unified theory of human genome reveals a constrained spatial chromosomal arrangement in interphase nuclei
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  93. Learning induces persistent chromatin loops underlying robust gene expression during memory recall
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