A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Rao, Suhas S.P., Huntley, Miriam H., Durand, Neva C., Stamenova, Elena K., Bochkov, Ivan D., Robinson, James T., Sanborn, Adrian L., Machol, Ido, Omer, Arina D., Lander, Eric S., Aiden, Erez Lieberman·2014·Cell
DOI 10.1016/j.cell.2014.11.021

Cited by (228)

Items 201–228 of 228

  1. ‘Generating chromosome geometries in a minimal cell from cryo-electron tomograms and chromosome conformation capture maps’
    Gilbert, Benjamin R., Thornburg, Zane R., Lam, Vinson, Rashid, Fatema-Zahra M., Glass, John I., Villa, Elizabeth, Dame, Remus T., Luthey-Schulten, Zaida · 2021 · Frontiers in Molecular Biosciences
  2. Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA
    Nagy, Gergely, Czipa, Erik, Steiner, László, Nagy, Tibor, Pongor, Sándor, Nagy, László, Barta, Endre · 2016 · BMC Genomics
  3. Erosion of the Epigenetic Landscape and Loss of Cellular Identity as a Cause of Aging in Mammals
    Yang, Jae-Hyun, Griffin, Patrick T., Vera, Daniel L., Apostolides, John K., Hayano, Motoshi, Meer, Margarita V., Salfati, Elias L., Su, Qiao, Munding, Elizabeth M., Blanchette, Marco et al. · 2019
  4. Loop formation by SMC complexes: turning heads, bending elbows, and fixed anchors
    Sedeño Cacciatore, Ángela, Rowland, Benjamin D · 2019 · Current Opinion in Genetics & Development
  5. Spatial promoter–enhancer hubs in cancer: organization, regulation, and function
    Zhao, Jingru, Faryabi, Robert B. · 2023 · Trends in Cancer
  6. The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance
    Song, Wei, Sharan, Roded, Ovcharenko, Ivan · 2019 · Genome Biology
  7. Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function
    Narducci, Domenic N., Hansen, Anders S. · 2025 · Molecular Cell
  8. Mutant IDH : A Targetable Driver of Leukemic Phenotypes Linking Metabolism, Epigenetics and Transcriptional Regulation
    Garrett-Bakelman, Francine E, Melnick, Ari M · 2016 · Epigenomics
  9. RepliChrom: Interpretable machine learning predicts cancer‐associated enhancer‐promoter interactions using DNA replication timing
    Dao, Fuying, Lebeau, Benjamin, Ling, Crystal Chia Yin, Yang, Mi, Xie, Xueqin, Fullwood, Melissa Jane, Lin, Hao, Lyu, Hao · 2025 · iMeta
  10. Genome-wide absolute quantification of chromatin looping
    Jusuf, James M., Yang, Jin H., Toppen, Jack, Grosse-Holz, Simon, Gabriele, Michele, Mach, Pia, Flyamer, Ilya M., Zechner, Christoph, Giorgetti, Luca, Mirny, Leonid A. et al. · 2026 · Nature Structural & Molecular Biology
  11. Prioritization of Osteoporosis‐Associated Genome‐wide Association Study ( GWAS) Single‐Nucleotide Polymorphisms ( SNPs) Using Epigenomics and Transcriptomics
    Zhang, Xiao, Deng, Hong‐Wen, Shen, Hui, Ehrlich, Melanie · 2021 · JBMR Plus
  12. HiC-GNN: A Generalizable Model for 3D Chromosome Reconstruction Using Graph Convolutional Neural Networks
    Van Hovenga, Oluwadare, Oluwatosin, Kalita, Jugal · 2021
  13. Graph convolutional networks for epigenetic state prediction using both sequence and 3D genome data
    Lanchantin, Jack, Qi, Yanjun · 2020 · Bioinformatics
  14. Single-cell damagenome profiling unveils vulnerable genes and functional pathways in human genome toward DNA damage
    Zhu, Qiangyuan, Niu, Yichi, Gundry, Michael, Zong, Chenghang · 2021 · Science Advances
  15. BioMaster: Multi-agent System for Automated Bioinformatics Analysis Workflow
    Su, Houcheng, Long, Weicai, Zhang, Yanlin · 2025
  16. Chromatin accessibility dynamics of myogenesis at single cell resolution
    Pliner, Hannah A., Packer, Jonathan, McFaline-Figueroa, José L., Cusanovich, Darren A., Daza, Riza, Srivatsan, Sanjay, Qiu, Xiaojie, Jackson, Dana, Minkina, Anna, Adey, Andrew et al. · 2017
  17. Enhancer Function in the 3D Genome
    Razin, Sergey V., Ulianov, Sergey V., Iarovaia, Olga V. · 2023 · Genes
  18. Between form and function: the complexity of genome folding
    Oudelaar, A. Marieke, Hanssen, Lars L.P., Hardison, Ross C., Kassouf, Mira T., Hughes, Jim R., Higgs, Douglas R. · 2017 · Human Molecular Genetics
  19. Genomic properties of chromosomal bands are linked to evolutionary rearrangements and new centromere formation in primates
    Federico, Concetta, Pappalardo, Anna Maria, Ferrito, Venera, Tosi, Sabrina, Saccone, Salvatore · 2017 · Chromosome Research
  20. Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle
    Xia, Xiaoting, Wang, Fuwen, Luo, Xiaoyu, Li, Shuang, Lyu, Yang, Zheng, Yining, Ma, Zhijie, Qu, Kaixing, Song, Rende, Liu, Jianyong et al. · 2025 · Advanced Science
  21. 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
  22. Trait-associated noncoding variant regions affect TBX3 regulation and cardiac conduction
    van Weerd, Jan Hendrik, Mohan, Rajiv A, van Duijvenboden, Karel, Hooijkaas, Ingeborg B, Wakker, Vincent, Boukens, Bastiaan J, Barnett, Phil, Christoffels, Vincent M · 2020 · eLife
  23. The Chromatin Organization Close to SNP rs12913832, Involved in Eye Color Variation, Is Evolutionary Conserved in Vertebrates
    Brancato, Desiree, Bruno, Francesca, Coniglio, Elvira, Sturiale, Valentina, Saccone, Salvatore, Federico, Concetta · 2024 · International Journal of Molecular Sciences
  24. Evaluation of chromatin accessibility in prefrontal cortex of schizophrenia cases and controls
    Bryois, Julien, Garrett, Melanie E, Song, Lingyun, Safi, Alexias, Giusti-Rodriguez, Paola, Johnson, Graham D, Demur, Alfonso Buil, Fullard, John F, Roussos, Panos, Sklar, Pamela et al. · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  25. O-GlcNAcylation of FOXK1 orchestrates the E2F pathway and promotes oncogenesis
    Masclef, Louis, Ahmed, Oumaima, Iannantuono, Nicholas, Gagnon, Jessica, Gushul-Leclaire, Mila, Boulay, Karine, Estavoyer, Benjamin, Echbicheb, Mohamed, Poy, Marty, Ali Boubacar, Kalidou et al. · 2024
  26. Robertsonian Translocation between Human Chromosomes 21 and 22, Inherited across Three Generations, without Any Phenotypic Effect
    Federico, Concetta, Brancato, Desiree, Bruno, Francesca, Galvano, Daiana, Caruso, Mariella, Saccone, Salvatore · 2024 · Genes
  27. Epigenetic Rewiring of Enhancer–Promoter Interactions in Cancer: Mechanisms and Therapeutic Implications
    Choppavarapu, Lavanya, Nosirov, Bakhtiyor, Kahn, Michael, Jin, Victor X. · 2026 · Cancers
  28. Deep intronic NIPBL variants underlie unresolved Cornelia de Lange syndrome revealed by integrated epigenomic and transcriptomic analysis
    Rondeau, Sophie, Huber, Céline, Kerkhof, Jennifer, Sadikovic, Bekim, Cormier-Daire, Valérie · 2026 · European Journal of Human Genetics