The 4D nucleome project

An integrated encyclopedia of DNA elements in the human genome

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

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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 · see citing works

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 8,802 · see citing works

Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)

Rust, M. J., Bates, M., & Zhuang, X. (2006) · Nature Methods · doi:10.1038/nmeth929 · Cited by 8,109 · see citing works

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 · see citing works

Integrative analysis of 111 reference human epigenomes

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Systematic 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 · see citing works

Capturing Chromosome Conformation

Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652 · see citing works

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 3,624 · see citing works

The Transcriptional Landscape of the Mammalian Genome

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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 · see citing works

Chromosome 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 2,339 · see citing works

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 · see citing works

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 1,959 · see citing works

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 1,932 · see citing works

Dynamic 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 1,931 · see citing works

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

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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 1,728 · see citing works

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 · see citing works

Single-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 · see citing works

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 · see citing works

Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C)

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 · see citing works

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 · see citing works

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elementsPreprint

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CRISPR/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 1,165 · see citing works

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 1,163 · see citing works

Systematic 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 1,103 · see citing works

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 986 · see citing works

Single-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 · see citing works

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 · see citing works

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 · see citing works

The 3D Genome as Moderator of Chromosomal Communication

Dekker, J., & Mirny, L. (2016) · Cell · doi:10.1016/j.cell.2016.02.007 · Cited by 937 · see citing works

Topologically 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 901 · see citing works

ChromEMT: 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 872 · see citing works

Mapping 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 · see citing works

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 · see citing works

Enhancer Control of Transcriptional Bursting

Fukaya, T., Lim, B., & Levine, M. (2016) · Cell · doi:10.1016/j.cell.2016.05.025 · Cited by 721 · see citing works

In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition.

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Quantitative 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 · see citing works

Complex 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 · see citing works

Biogenesis 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 707 · see citing works

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 · see citing works

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 · see citing works

Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase

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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 · see citing works

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 · see citing works

A genetically encoded photosensitizer

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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 580 · see citing works

Sequencing 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 · see citing works

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 553 · see citing works

Global 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 548 · see citing works

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F., & Chen, L. (2011) · Nature Biotechnology · doi:10.1038/nbt.2057 · Cited by 532 · see citing works

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 532 · see citing works

RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites

Engreitz, 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 500 · see citing works

Real-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 489 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

Hughes, 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 · see citing works

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 448 · see citing works

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 · see citing works

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 · see citing works

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 425 · see citing works

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 · see citing works

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 · see citing works

Multicolor CRISPR labeling of chromosomal loci in human cells

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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 · see citing works

Initial Genomics of the Human Nucleolus

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The second decade of 3C technologies: detailed insights into nuclear organizationPreprint

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Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus

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 · see citing works

Detection of in vivo protein–DNA interactions using DamID in mammalian cells

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High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli

van Koningsbruggen, S., Gierliński, M., Schofield, P., 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 327 · see citing works

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 318 · see citing works

Single-molecule analysis of gene expression using two-color RNA labeling in live yeast

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High-density three-dimensional localization microscopy across large volumes

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Deletion of <i>DXZ4</i> on the human inactive X chromosome alters higher-order genome architecture

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CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells

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Live visualization of chromatin dynamics with fluorescent TALEs

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Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-CPreprint

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3D Trajectories Adopted by Coding and Regulatory DNA Elements: First-Passage Times for Genomic Interactions

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4C Technology: Protocols and Data Analysis

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Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation

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Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome

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