The DOI matches its Crossref record; 120 of the 120 references it cites were found in a registry or an index.
The 4D nucleome project
Open accessPublished version of a preprint
Abstract
The 4D Nucleome Network aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes in space and time with the goal of gaining deeper mechanistic insights into how the nucleus is organized and functions. The project will develop and benchmark experimental and computational approaches for measuring genome conformation and nuclear organization, and investigate how these contribute to gene regulation and other genome functions. Validated experimental technologies will be combined with biophysical approaches to generate quantitative models of spatial genome organization in different biological states, both in cell populations and in single cells.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
““4D mapping” of chromatin interactions (i.e., brain regions across developmental time) is critical for understanding the functional relationships of regulatory regions to genes (Dekker et al., 2017)”
From Defining the genetic, genomic, cellular, and diagnostic architectures of psychiatric disorders (2019) · cites this paper as Dekker et al., 2017
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
Self-citationA 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212
Imaging Intracellular Fluorescent Proteins at Nanometer Resolution
Betzig, E., Patterson, G. H., Sougrat, R., Lindwasser, O. W., Olenych, S. G., Bonifacino, J. S., Davidson, M. W., Lippincott‐Schwartz, J., & Hess, H. F. (2006) · Science · doi:10.1126/science.1127344 · Cited by 8,941
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898
Self-citationSub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)
Rust, M., Bates, M., & Zhuang, X. (2006) · Nature Methods · doi:10.1038/nmeth929 · Cited by 7,823
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829
Self-citationIntegrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368
Self-citationSystematic Localization of Common Disease-Associated Variation in Regulatory DNA
Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716
Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy
Hess, S. T., Girirajan, T. P. K., & Mason, M. D. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.091116 · Cited by 3,684
Capturing Chromosome Conformation
Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652
Self-citationThe Transcriptional Landscape of the Mammalian Genome
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C. A., et al. (2005) · Science · doi:10.1126/science.1112014 · Cited by 3,492
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895
Self-citationChromosome territories, nuclear architecture and gene regulation in mammalian cells
Cremer, T. J., & Cremer, C. G. (2001) · Nature Reviews Genetics · doi:10.1038/35066075 · Cited by 2,423
Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions
Guelen, L., Pagie, L., Brasset, É., Meuleman, W. R. A., Faza, M. B., Talhout, W., Eussen, B. H. J., de Klein, A., Wessels, L. F. A., de Laat, W. L., et al. (2008) · Nature · doi:10.1038/nature06947 · Cited by 2,042
Formation of chromosomal domains by loop extrusion
Fudenberg, G., Imakaev, M., Lu, C., Goloborodko, A., Abdennur, N., & Mirny, L. A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.085 · Cited by 2,003
Self-citationDynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System
Chen, B., Gilbert, L. A., Cimini, B. A., Schnitzbauer, J., Zhang, W., Li, G., Park, J. S., Blackburn, E. H., Weissman, J. S., Qi, L. S., et al. (2013) · Cell · doi:10.1016/j.cell.2013.12.001 · Cited by 1,988
Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution
Chen, B., Legant, W. R., Wang, K., Shao, L., Milkie, D. E., Davidson, M. W., Janetopoulos, C., Wu, X., Hammer, J. A., Liu, Z. J., et al. (2014) · Science · doi:10.1126/science.1257998 · Cited by 1,947
An oestrogen-receptor-α-bound human chromatin interactome
Fullwood, M. J., Liu, M. H., Pan, Y. F., Liu, J., Han, X., Mohamed, Y. B., Orlov, Y. L., Velkov, S., Ho, A., Poh, H. M., et al. (2009) · Nature · doi:10.1038/nature08497 · Cited by 1,752
Sanborn, A. L., Rao, S. S. P., Huang, S.-C., Durand, N. C., Huntley, M. H., Jewett, A. I., Bochkov, I. D., Chinnappan, D., Cutkosky, A., Li, J., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518552112 · Cited by 1,730
Chromatin architecture reorganization during stem cell differentiation
Dixon, J. R., Jung, I., Selvaraj, S., Shen, Y., Antosiewicz-Bourget, J. E., Lee, A. Y., Ye, Z., Kim, A., Rajagopal, N., Xie, W., et al. (2015) · Nature · doi:10.1038/nature14222 · Cited by 1,646
Self-citationSingle-cell Hi-C reveals cell-to-cell variability in chromosome structure
Nagano, T., Lubling, Y., Stevens, T. J., Schoenfelder, S., Yaffe, E., Dean, W., Laue, E. D., Tanay, A., & Fraser, P. (2013) · Nature · doi:10.1038/nature12593 · Cited by 1,589
A general method to improve fluorophores for live-cell and single-molecule microscopy
Grimm, J. B., English, B. P., Chen, J., Slaughter, J. P., Zhang, Z., Revyakin, A. G., Patel, R. H., Macklin, J. J., Normanno, D., Singer, R. H., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3256 · Cited by 1,509
Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B., & de Laat, W. (2006) · Nature Genetics · doi:10.1038/ng1896 · Cited by 1,386
Looping and Interaction between Hypersensitive Sites in the Active β-globin Locus
Tolhuis, B., Palstra, R.-J., Splinter, E., Grosveld, F., & de Laat, W. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00781-5 · Cited by 1,344
Dostie, J., Richmond, T., Arnaout, R., Selzer, R. R., Lee, W. L., Honan, T., Rubio, E. D., Krumm, A., Lamb, J., Nusbaum, C., et al. (2006) · Genome Research · doi:10.1101/gr.5571506 · Cited by 1,237
Self-citationCRISPR/Cas9 in Genome Editing and Beyond
Wang, H., Russa, M. F. L., & Qi, L. S. (2016) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060815-014607 · Cited by 1,213
The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3
McHugh, C. A., Chen, C., Chow, A. Y., Surka, C., Tran, C., McDonel, P. E., Pandya‐Jones, A., Blanco, M. R., Burghard, C. P., Moradian, A., et al. (2015) · Nature · doi:10.1038/nature14443 · Cited by 1,139
Self-citationSystematic Discovery of Xist RNA Binding Proteins
Chu, C., Zhang, Q. C., da Rocha, S. T., Flynn, R. A., Bharadwaj, M. C., Calabrese, J. M., Magnuson, T., Heard, É., & Chang, H. Y. (2015) · Cell · doi:10.1016/j.cell.2015.03.025 · Cited by 1,100
The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome
Engreitz, J., Pandya‐Jones, A., McDonel, P. E., Shishkin, A., Sirokman, K., Surka, C., Kadri, S., Xing, J. C., Goren, A., Lander, E. S., et al. (2013) · Science · doi:10.1126/science.1237973 · Cited by 1,008
Self-citationSingle-cell in situ RNA profiling by sequential hybridization
Lubeck, E., Coskun, A. F., Zhiyentayev, T., Ahmad, M., & Cai, L. (2014) · Nature Methods · doi:10.1038/nmeth.2892 · Cited by 985
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
Tang, Z., Luo, O. J., Li, X., Zheng, M., Zhu, J. J., Szalaj, P., Trzaskoma, P., Magalska, A., Wlodarczyk, J., Ruszczycki, B., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.024 · Cited by 982
Organization of the mitotic chromosome
Naumova, N., Imakaev, M., Fudenberg, G., Zhan, Y., Lajoie, B. R., Mirny, L. A., & Dekker, J. (2013) · Science · doi:10.1126/science.1236083 · Cited by 976
Self-citationTopologically associating domains are stable units of replication-timing regulation
Pope, B. D., Ryba, T., Dileep, V., Yue, F., Wu, W.-S., Denas, O., Vera, D. L., Wang, Y., Hansen, R. S., Canfield, T. K., et al. (2014) · Nature · doi:10.1038/nature13986 · Cited by 953
Self-citationThe 3D Genome as Moderator of Chromosomal Communication
Dekker, J., & Mirny, L. (2016) · Cell · doi:10.1016/j.cell.2016.02.007 · Cited by 937
Self-citationChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells
Ou, H. D., Phan, S., Deerinck, T. J., Thor, A., Ellisman, M. H., & O’Shea, C. C. (2017) · Science · doi:10.1126/science.aag0025 · Cited by 887
Self-citationMapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C
Hsieh, T.-H. S., Weiner, A., Lajoie, B., Dekker, J., Friedman, N., & Rando, O. J. (2015) · Cell · doi:10.1016/j.cell.2015.05.048 · Cited by 788
Self-citationBiogenesis and function of nuclear bodies
Mao, Y. S., Zhang, B., & Spector, D. L. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.05.006 · Cited by 736
Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy
Martell, J. D., Deerinck, T. J., Sancak, Y., Poulos, T. L., Mootha, V. K., Sosinsky, G. E., Ellisman, M. H., & Ting, A. Y. (2012) · Nature Biotechnology · doi:10.1038/nbt.2375 · Cited by 722
Enhancer Control of Transcriptional Bursting
Fukaya, T., Lim, B., & Levine, M. (2016) · Cell · doi:10.1016/j.cell.2016.05.025 · Cited by 721
Robinett, C. C., Straight, A. F., Li, G., Willhelm, C., Sudlow, G., Murray, A. W., & Belmont, A. S. (1996) · The Journal of Cell Biology · doi:10.1083/jcb.135.6.1685 · Cited by 720
Self-citationQuantitative analysis of chromosome conformation capture assays (3C-qPCR)
Hagège, H., Klous, P., Braem, C., Splinter, E., Dekker, J., Cathala, G., de Laat, W., & Forné, T. (2007) · Nature Protocols · doi:10.1038/nprot.2007.243 · Cited by 720
Self-citationComplex multi-enhancer contacts captured by genome architecture mapping
Beagrie, R. A., Scialdone, A., Schueler, M., Kraemer, D. C. A., Chotalia, M., Xie, S. Q., Barbieri, M., de Santiago, I., Lavitas, L.-M., Branco, M. R., et al. (2017) · Nature · doi:10.1038/nature21411 · Cited by 715
Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture
Vietri Rudan, M., Barrington, C., Henderson, S., Ernst, C., Odom, D. T., Tanay, A., & Hadjur, S. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.02.004 · Cited by 680
CTCF Binding Polarity Determines Chromatin Looping
de Wit, E., Vos, E. S. M., Holwerda, S. J. B., Valdes-Quezada, C., Verstegen, M. J. A. M., Teunissen, H., Splinter, E., Wijchers, P. J., Krijger, P. H. L., & de Laat, W. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.09.023 · Cited by 641
Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase
van Steensel, B., & Henikoff, S. (2000) · Nature Biotechnology · doi:10.1038/74487 · Cited by 629
CTCF and cohesin regulate chromatin loop stability with distinct dynamics
Hansen, A. S., Pustova, I., Cattoglio, C., Tjian, R., & Darzacq, X. (2017) · eLife · doi:10.7554/elife.25776 · Cited by 613
Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells
Chen, J., Zhang, Z., Li, L., Chen, B.-C., Revyakin, A., Hajj, B., Legant, W., Dahan, M., Lionnet, T., Betzig, E., et al. (2014) · Cell · doi:10.1016/j.cell.2014.01.062 · Cited by 602
A genetically encoded photosensitizer
Bulina, M. E., Chudakov, D. M., Britanova, O. V., Yanushevich, Y. G., Staroverov, D. B., Chepurnykh, T. V., Merzlyak, E. M., Shkrob, M., Lukyanov, S., & Lukyanov, K. A. (2005) · Nature Biotechnology · doi:10.1038/nbt1175 · Cited by 597
Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression
Engreitz, J., Ollikainen, N., & Guttman, M. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.126 · Cited by 595
Self-citationGlobal Reorganization of Replication Domains During Embryonic Stem Cell Differentiation
Hiratani, I., Ryba, T., Itoh, M., Yokochi, T., Schwaiger, M., Chang, C., Lyou, Y., Townes, T. M., Schübeler, D., & Gilbert, D. M. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060245 · Cited by 576
Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations
Zhang, Y., McCord, R. P., Ho, Y.-J., Lajoie, B. R., Hildebrand, D. G., Simon, A. C., Becker, M. S., Alt, F. W., & Dekker, J. (2012) · Cell · doi:10.1016/j.cell.2012.02.002 · Cited by 572
Self-citationSequencing newly replicated DNA reveals widespread plasticity in human replication timing
Hansen, R. S., Thomas, S., Sandstrom, R. S., Canfield, T. K., Thurman, R. E., Weaver, M., Dorschner, M. O., Gartler, S. M., & Stamatoyannopoulos, J. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0912402107 · Cited by 556
Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F., & Chen, L. (2011) · Nature Biotechnology · doi:10.1038/nbt.2057 · Cited by 554
Massively multiplex single-cell Hi-C
Ramani, V., Deng, X., Qiu, R., Gunderson, K. L., Steemers, F. J., Distèche, C. M., Noble, W. S., Duan, Z., & Shendure, J. (2017) · Nature Methods · doi:10.1038/nmeth.4155 · Cited by 545
Self-citationEngreitz, J., Sirokman, K., McDonel, P. E., Shishkin, A. A., Surka, C., Russell, P. H., Grossman, S. R., Chow, A. Y., Guttman, M., & Lander, E. S. (2014) · Cell · doi:10.1016/j.cell.2014.08.018 · Cited by 514
Self-citationReal-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells
Cissé, I. I., Izeddin, I., Causse, S., Boudarène, L., Senecal, A., Mureşan, L., Dugast‐Darzacq, C., Hajj, B., Dahan, M., & Darzacq, X. (2013) · Science · doi:10.1126/science.1239053 · Cited by 507
The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery
Stunnenberg, H. G., Abrignani, S., Adams, D. J., de Almeida, M., Altucci, L., Amin, V. R., Amit, I., Antonarakis, S. E., Aparicio, S. A. J. R., Arima, T., et al. (2016) · Cell · doi:10.1016/j.cell.2016.11.007 · Cited by 485
Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow
Ma, H., Tu, L., Naseri, A., Huisman, M., Zhang, S., Grünwald, D., & Pederson, T. (2016) · Nature Biotechnology · doi:10.1038/nbt.3526 · Cited by 472
Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells
Kind, J., Pagie, L., de Vries, S., Nahidiazar, L., Dey, S. S., Bienko, M., Zhan, Y., Lajoie, B. R., de Graaf, C. A., Amendola, M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.08.040 · Cited by 467
Self-citationHughes, J. R., Roberts, N., McGowan, S., Hay, D., Giannoulatou, E., Lynch, M., De Gobbi, M., Taylor, S., Gibbons, R., & Higgs, D. R. (2014) · Nature Genetics · doi:10.1038/ng.2871 · Cited by 461
The genomic binding sites of a noncoding RNA
Simon, M. D., Wang, C. I., Kharchenko, P. V., West, J. A., Chapman, B., Alekseyenko, A. A., Borowsky, M. L., Kuroda, M. I., & Kingston, R. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1113536108 · Cited by 454
Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains
Jost, D., Carrivain, P., Cavalli, G., & Vaillant, C. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku698 · Cited by 445
Reactivation of developmentally silenced globin genes by forced chromatin looping
Deng, W., Rupon, J. W., Krivega, I., Breda, L., Motta, I., Jahn, K. S., Reik, A., Gregory, P. D., Rivella, S., Dean, A., et al. (2014) · Cell · doi:10.1016/j.cell.2014.05.050 · Cited by 443
Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging
Szymborska, A., de Marco, A., Daigle, N., Cordes, V. C., Briggs, J. A. G., & Ellenberg, J. (2013) · Science · doi:10.1126/science.1240672 · Cited by 434
Spatial proximity of translocation-prone gene loci in human lymphomas
Roix, J. J., McQueen, P. G., Munson, P. J., Parada, L. A., & Misteli, T. (2003) · Nature Genetics · doi:10.1038/ng1177 · Cited by 414
Multicolor CRISPR labeling of chromosomal loci in human cells
Ma, H., Naseri, A., Reyes‐Gutierrez, P., Wolfe, S. A., Zhang, S., & Pederson, T. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1420024112 · Cited by 413
Structural organization of the inactive X chromosome in the mouse
Giorgetti, L., Lajoie, B. R., Carter, A. C., Attia, M., Zhan, Y., Xu, J., Chen, C. J., Kaplan, N., Chang, H. Y., Heard, É., et al. (2016) · Nature · doi:10.1038/nature18589 · Cited by 410
Self-citationInitial Genomics of the Human Nucleolus
Németh, A., Conesa, A., Santoyo‐López, J., Medina, I., Montaner, D. A., Péterfia, B. F., Solovei, I. V., Cremer, T. J., Dopazo, J., & Längst, G. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000889 · Cited by 399
The Spatial Organization of the Human Genome
Bickmore, W. A. (2013) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-091212-153515 · Cited by 391
The second decade of 3C technologies: detailed insights into nuclear organizationPreprint
Denker, A., & de Laat, W. L. (2016) · Genes & Development · doi:10.1101/gad.281964.116 · Cited by 357
van Koningsbruggen, S., Gierliński, M., Schofield, P. G., Martin, D. M. A., Barton, G. J., Ariyürek, Y., den Dunnen, J. T., & Lamond, A. I. (2010) · Molecular Biology of the Cell · doi:10.1091/mbc.e10-06-0508 · Cited by 345
Chromatin Position Effects Assayed by Thousands of Reporters Integrated in Parallel
Akhtar, W., de Jong, J., Pindyurin, A. V., Pagie, L., Meuleman, W. R. A., de Ridder, J., Berns, A. J. M., Wessels, L. F. A., van Lohuizen, M., & van Steensel, B. (2013) · Cell · doi:10.1016/j.cell.2013.07.018 · Cited by 338
Izeddin, I., Récamier, V., Bosanac, L., Cissé, I. I., Boudarène, L., Dugast‐Darzacq, C., Proux, F., Bénichou, O., Voituriez, R., Bensaude, O., et al. (2014) · eLife · doi:10.7554/elife.02230 · Cited by 338
Detection of in vivo protein–DNA interactions using DamID in mammalian cells
Vogel, M. J., Peric‐Hupkes, D., & van Steensel, B. (2007) · Nature Protocols · doi:10.1038/nprot.2007.148 · Cited by 336
Single-molecule analysis of gene expression using two-color RNA labeling in live yeast
Hocine, S., Raymond, P., Zenklusen, D., Chao, J. A., & Singer, R. H. (2013) · Nature Methods · doi:10.1038/nmeth.2305 · Cited by 297
High-density three-dimensional localization microscopy across large volumes
Legant, W. R., Shao, L., Grimm, J. B., Brown, T. A., Milkie, D. E., Avants, B., Lavis, L. D., & Betzig, E. (2016) · Nature Methods · doi:10.1038/nmeth.3797 · Cited by 291
CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells
Deng, W., Shi, X., Tjian, R., Lionnet, T., & Singer, R. H. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1515692112 · Cited by 279
Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture
Darrow, E. M., Huntley, M. H., Dudchenko, O., Stamenova, E. K., Durand, N. C., Sun, Z., Huang, S.-C., Sanborn, A. L., Machol, I., Shamim, M., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1609643113 · Cited by 276
Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-CPreprint
Dryden, N. H., Broome, L. R., Dudbridge, F., Johnson, N., Orr, N., Schoenfelder, S., Nagano, T., Andrews, S., Wingett, S., Kozarewa, I., et al. (2014) · Genome Research · doi:10.1101/gr.175034.114 · Cited by 261
Live visualization of chromatin dynamics with fluorescent TALEs
Miyanari, Y., Ziegler-Birling, C., & Torres‐Padilla, M. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2680 · Cited by 260
4C Technology: Protocols and Data Analysis
van de Werken, H. J. G., de Vree, P. J. P., Splinter, E., Holwerda, S. J. B., Klous, P., de Wit, E., & de Laat, W. L. (2012) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-391938-0.00004-5 · Cited by 248
Lucas, J., Zhang, Y., Dudko, O. K., & Murre, C. (2014) · Cell · doi:10.1016/j.cell.2014.05.036 · Cited by 239
Splinter, E., de Wit, E., van de Werken, H. J. G., Klous, P., & de Laat, W. L. (2012) · Methods · doi:10.1016/j.ymeth.2012.04.009 · Cited by 228
CRISPR-Cas9 nuclear dynamics and target recognition in living cells
Ma, H., Tu, L., Naseri, A., Huisman, M., Zhang, S., Grünwald, D., & Pederson, T. (2016) · The Journal of Cell Biology · doi:10.1083/jcb.201604115 · Cited by 224
Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome
Hsieh, T.-H. S., Fudenberg, G., Goloborodko, A., & Rando, O. J. (2016) · Nature Methods · doi:10.1038/nmeth.4025 · Cited by 216
Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes
Ma, W., Ay, F., Lee, C., Gülsoy, G., Deng, X., Cook, S. M., Hesson, J., Cavanaugh, C., Ware, C. B., Krumm, A., et al. (2014) · Nature Methods · doi:10.1038/nmeth.3205 · Cited by 191
Self-citationAnalysis of long-range chromatin interactions using Chromosome Conformation Capture
Naumova, N., Smith, E. M., Zhan, Y., & Dekker, J. (2012) · Methods · doi:10.1016/j.ymeth.2012.07.022 · Cited by 183
Self-citationIdentification of Gene Positioning Factors Using High-Throughput Imaging Mapping
Shachar, S., Voss, T. C., Pegoraro, G., Sciascia, N., & Misteli, T. (2015) · Cell · doi:10.1016/j.cell.2015.07.035 · Cited by 172
Nuclear bodies: multifunctional companions of the genome
Dundr, M. (2012) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2012.03.010 · Cited by 172
Izeddin, I., Beheiry, M. E., Andilla, J., Ciepielewski, D., Darzacq, X., & Dahan, M. (2012) · Optics Express · doi:10.1364/oe.20.004957 · Cited by 168
APEX Fingerprinting Reveals the Subcellular Localization of Proteins of Interest
Lee, S.-Y., Kang, M., Park, J. S., Lee, G., Ting, A. Y., & Rhee, H. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.064 · Cited by 168
Soto, G. E., Young, S. J., Martone, M. E., Deerinck, T. J., Lamont, S., Carragher, B. O., Hama, K., & Ellisman, M. H. (1994) · NeuroImage · doi:10.1006/nimg.1994.1008 · Cited by 147
FISH-ing for captured contacts: towards reconciling FISH and 3C
Fudenberg, G., & Imakaev, M. (2017) · Nature Methods · doi:10.1038/nmeth.4329 · Cited by 141
Markaki, Y., Gunkel, M., Schermelleh, L., Beichmanis, S., Neumann, J., Heidemann, M., Leonhardt, H., Eick, D., Cremer, C. G., & Cremer, T. J. (2010) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2010.75.042 · Cited by 138
Closing the loop: 3C versus DNA FISH
Giorgetti, L., & Heard, E. (2016) · Genome Biology · doi:10.1186/s13059-016-1081-2 · Cited by 131
Genome-scale analysis of replication timing: from bench to bioinformatics
Ryba, T., Battaglia, D., Pope, B. D., Hiratani, I., & Gilbert, D. M. (2011) · Nature Protocols · doi:10.1038/nprot.2011.328 · Cited by 131
Gros, M. A. L., Clowney, E. J., Magklara, A., Yen, A., Markenscoff-Papadimitriou, E., Colquitt, B. M., Myllys, M., Kellis, M., Lomvardas, S., & Larabell, C. A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.10.060 · Cited by 125
Self-citationGlobal identification of yeast chromosome interactions using Genome conformation capture
Rodley, C. D. M., Bertels, F., Jones, B., & O'Sullivan, J. M. (2009) · Fungal Genetics and Biology · doi:10.1016/j.fgb.2009.07.006 · Cited by 123
Scanning angle interference microscopy reveals cell dynamics at the nanoscale
Paszek, M. J., DuFort, C. C., Rubashkin, M. G., Davidson, M. W., Thorn, K. S., Liphardt, J., & Weaver, V. M. (2012) · Nature Methods · doi:10.1038/nmeth.2077 · Cited by 121
Ma, H., Reyes‐Gutierrez, P., & Pederson, T. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319097110 · Cited by 121
Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C)
Louwers, M., Splinter, E., DRIEL, R. V., de Laat, W. L., & Stam, M. E. (2009) · Nature Protocols · doi:10.1038/nprot.2009.113 · Cited by 118
CRISPR/Cas9 for Human Genome Engineering and Disease Research
Xiong, X., Chen, M., Lim, W. A., Zhao, D., & Qi, L. S. (2016) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083115-022258 · Cited by 111
Modeling chromosomes: Beyond pretty pictures
Imakaev, M., Fudenberg, G., & Mirny, L. A. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.09.004 · Cited by 96
Self-citationRestraint‐based three‐dimensional modeling of genomes and genomic domains
Serra, F., Stefano, M. D., Spill, Y. G., Cuartero, Y., Goodstadt, M. N., Baù, D., & Martı́-Renom, M. A. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.05.012 · Cited by 86
Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH
Takei, Y., Shah, S., Harvey, S. C., Qi, L. S., & Cai, L. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2017.03.024 · Cited by 84
Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization
Martı́-Renom, M. A., & Mirny, L. A. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002125 · Cited by 84
Self-citationMulticolor Electron Microscopy for Simultaneous Visualization of Multiple Molecular Species
Adams, S., Mackey, M. R., Ramachandra, R., Palida, S. F., Steinbach, P. A., Bushong, E. A., Butko, M. T., Giepmans, B. N. G., Ellisman, M. H., & Tsien, R. Y. (2016) · Cell chemical biology · doi:10.1016/j.chembiol.2016.10.006 · Cited by 82
Quantitatively Imaging Chromosomes by Correlated Cryo-Fluorescence and Soft X-Ray Tomographies
Smith, E. A., McDermott, G., Do, M., Leung, K., Panning, B., Gros, M. A. L., & Larabell, C. A. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.09.011 · Cited by 79
Comprehensive characterization of neutrophil genome topologyPreprint
Zhu, Y., Gong, K. Q., Denholtz, M., Chandra, V. K., Kamps, M. P., Alber, F., & Murre, C. (2017) · Genes & Development · doi:10.1101/gad.293910.116 · Cited by 77
Micromechanical Studies of Mitotic Chromosomes
Poirier, M. G., & Marko, J. F. (2003) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/s0070-2153(03)01002-0 · Cited by 66
Inducible DamID systems for genomic mapping of chromatin proteins inDrosophila
Pindyurin, A. V., Pagie, L., Kozhevnikova, E. N., van Arensbergen, J., & van Steensel, B. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw176 · Cited by 49
Phan, S., Boassa, D., Nguyen, P. A. H., Wan, X., Lanman, J. K., Lawrence, A. F., & Ellisman, M. H. (2016) · Advanced Structural and Chemical Imaging · doi:10.1186/s40679-016-0021-2 · Cited by 45
The redundancy of the mammalian heterochromatic compartment
Politz, J. C. R., Scalzo, D., & Groudine, M. T. (2015) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2015.10.007 · Cited by 45
Self-citationUsing TRIP for genome-wide position effect analysis in cultured cells
Akhtar, W., Pindyurin, A. V., de Jong, J., Pagie, L., ten Hoeve, J., Berns, A. J. M., Wessels, L. F. A., van Steensel, B., & van Lohuizen, M. (2014) · Nature Protocols · doi:10.1038/nprot.2014.072 · Cited by 43
Nucleolar tethering mediates pairing between theIgHandMycloci
Strongin, D. E., Groudine, M. T., & Politz, J. C. R. (2014) · Nucleus · doi:10.4161/nucl.36233 · Cited by 17
Self-citationCTCF and Cohesin Regulate Chromatin Loop Stability with Distinct Dynamics
(2016) · doi:10.1101/093476 · Cited by 16
Physical mechanisms behind the large scale features of chromatin organization
Pombo, A., & Nicodemi, M. (2014) · Transcription · doi:10.4161/trns.28447 · Cited by 15
Direct visualization of transcriptional activation by physical enhancer–promoter proximityPreprint
Chen, H., Fujioka, M., Jaynes, J. B., & Gregor, T. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/099523 · Cited by 11
FISH-ing for captured contacts: towards reconciling FISH and 3CPreprint
Fudenberg, G., & Imakaev, M. V. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/081448 · Cited by 10
A fluorogenic nanobody array tag for prolonged single molecule imaging in live cellsPreprint
Ghosh, R. P., Draper, W. E., Franklin, J. M., Shi, Q., & Liphardt, J. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/111690 · Cited by 4
Cited by
Sorted by citations
HiGlass: web-based visual exploration and analysis of genome interaction maps
Kerpedjiev, P., Abdennur, N. A., Lekschas, F., McCallum, C., Dinkla, K., Strobelt, H., Luber, J. M., Ouellette, S., Azhir, A., Kumar, N., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1486-1 · Cited by 2,430
Self-citationThe Encyclopedia of DNA elements (ENCODE): data portal update
Davis, C. A., Hitz, B. C., Sloan, C. A., Chan, E. T., Davidson, J. M., Gabdank, I., Hilton, J. A., Jain, K., Baymuradov, U. K., Narayanan, A. K., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1081 · Cited by 1,717
The Cellosaurus, a Cell-Line Knowledge Resource
Bairoch, A. (2018) · Journal of Biomolecular Techniques JBT · doi:10.7171/jbt.18-2902-002 · Cited by 807
Atlas of Subcellular RNA Localization Revealed by APEX-Seq
Fazal, F. M., Han, S., Parker, K. R., Kaewsapsak, P., Xu, J., Boettiger, A. N., Chang, H. Y., & Ting, A. Y. (2019) · Cell · doi:10.1016/j.cell.2019.05.027 · Cited by 677
Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin
Su, J.-H., Zheng, P., Kinrot, S. S., Bintu, B., & Zhuang, X. (2020) · Cell · doi:10.1016/j.cell.2020.07.032 · Cited by 562
Metadata
- Authors
- the 4D Nucleome Network, Dekker, J., Belmont, A. S., Guttman, M., Leshyk, V. O., Lis, J. T., Lomvardas, S., Mirny, L. A., O’Shea, C. C., Park, P. J., Ren, B., Politz, J. C. R., Shendure, J., & Zhong, S.
- Affiliations
- Howard Hughes Medical Institute (US)
- California Institute of Technology (US)
- Cornell University (US)
- Mortimer B. Zuckerman Mind Brain Behavior Institute (US)
- Salk Institute for Biological Studies (US)
- Harvard University (US)
- University of California San Diego (US)
- Corresponding author
- Dekker, Job
- ORCID
- Venue
- Nature
- Published
- 2017-09-14
- Volume
- 549
- Issue
- 7671
- Pages
- 219-226
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC5617335
- OpenAlex
- W2584394140
- Cited by
- 732
- References
- 118
- Citations by year
- 2026: 63 · 2025: 74 · 2024: 81 · 2023: 74 · 2022: 96 · 2021: 110 · 2020: 82 · 2019: 73 · 2018: 65 · 2017: 13
- FWCI
- 26.04
- Type
- journal article
- Language
- en
- Update notices
- erratum (2017-11-22)
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship@UMassChan (submittedVersion, cc-by-nc-nd)
- UWA Profiles and Research Repository (UWA) (submittedVersion)
- ReIn UW (University of Warsaw) (submittedVersion, cc-by-nc-nd)
- Funders
- National Institutes of Health
- National Heart, Lung, and Blood Institute (U01HL129998, U01HL129958)
- National Institute on Drug Abuse (U01DA040582)
- NIH Office of the Director
- National Cancer Institute (U01CA200060)
- National Institute on Deafness and Other Communication Disorders (R01DC013560)
- National Institute of General Medical Sciences (P50GM085764)
- National Institute of Diabetes and Digestive and Kidney Diseases (U54DK107977, U54DK107965, U54DK107980, U54DK107979)
- National Institute of Biomedical Imaging and Bioengineering (U01EB021223)
- Common Fund (1U01DA040709)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- 3D genome organization, nuclear organization, gene expression regulation, single-cell genomics, human genome, mouse genome, chromatin dynamics
- MeSH terms
- Animals, Cell Line, Cell Nucleus, Chromatin, Chromosomes, Goals, Humans, Models, Biological, Models, Molecular, Reproducibility of Results, Genome, Genomics, Information Dissemination, Mice, Molecular Imaging, Single-Cell Analysis, Spatio-Temporal Analysis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
