The 3D Genome as Moderator of Chromosomal Communication

A 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 · see citing works

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

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

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

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

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

Lupiáñez, D. G., Kraft, K., Heinrich, V., Krawitz, P., Brancati, F., Klopocki, E., Horn, D., Kayserili, H., Opitz, J. M., Laxova, R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.004 · Cited by 2,132 · 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

Three-dimensional folding and functional organization principles of the Drosophila genome

Sexton, T., Yaffe, E., Kenigsberg, E., Bantignies, F., Leblanc, B., Hoichman, M., Parrinello, H., Tanay, A., & Cavalli, G. (2012) · Cell · doi:10.1016/j.cell.2012.01.010 · Cited by 1,983 · see citing works

Mediator and cohesin connect gene expression and chromatin architecture

Kagey, M. H., Newman, J. J., Bilodeau, S., Zhan, Y., Orlando, D. A., van Berkum, N. L., Ebmeier, C. C., Goossens, J., Rahl, P. B., Levine, S. S., et al. (2010) · Nature · doi:10.1038/nature09380 · Cited by 1,939 · see citing works

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

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 · see citing works

The long-range interaction landscape of gene promoters

Sanyal, A., Lajoie, B. R., Jain, G., & Dekker, J. (2012) · Nature · doi:10.1038/nature11279 · Cited by 1,489 · see citing works

Cohesins: Chromosomal Proteins that Prevent Premature Separation of Sister Chromatids

Michaelis, C., Ciosk, R., & Nasmyth, K. (1997) · Cell · doi:10.1016/s0092-8674(01)80007-6 · Cited by 1,473 · 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

Structure and Mechanism of Helicases and Nucleic Acid Translocases

Singleton, M. R., Dillingham, M. S., & Wigley, D. B. (2007) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.76.052305.115300 · Cited by 1,279 · see citing works

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

Li, G., Ruan, X., Auerbach, R. K., Sandhu, K. S., Zheng, M., Wang, P., Poh, H. M., Goh, Y., Lim, J., Zhang, J., et al. (2012) · Cell · doi:10.1016/j.cell.2011.12.014 · Cited by 1,232 · 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

Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data

Dekker, J., Marti-Renom, M. A., & Mirny, L. A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3454 · Cited by 1,068 · see citing works

BioNumbers—the database of key numbers in molecular and cell biology

Milo, R., Jorgensen, P., Moran, U., Weber, G., & Springer, M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp889 · Cited by 1,055 · 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 · cited 13× · 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 972 · see citing works

Condensin-driven remodelling of X chromosome topology during dosage compensation

Crane, E. E., Bian, Q., McCord, R. P., Lajoie, B. R., Wheeler, B. S., Ralston, E. J., Uzawa, S., Dekker, J., & Meyer, B. J. (2015) · Nature · doi:10.1038/nature14450 · Cited by 972 · see citing works

Cohesin: Its Roles and Mechanisms

Nasmyth, K., & Haering, C. H. (2009) · Annual Review of Genetics · doi:10.1146/annurev-genet-102108-134233 · Cited by 967 · see citing works

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

Guo, Y., Xu, Q., Canzio, D., Shou, J., Li, J., Gorkin, D. U., Jung, I., Wu, H., Zhai, Y., Tang, Y., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.038 · Cited by 958 · see citing works

Long-Range Control of Gene Expression: Emerging Mechanisms and Disruption in Disease

Kleinjan, D. A., & van Heyningen, V. (2004) · The American Journal of Human Genetics · doi:10.1086/426833 · Cited by 868 · see citing works

A Direct Link between Sister Chromatid Cohesion and Chromosome Condensation Revealed through the Analysis of MCD1 in S. cerevisiae

Guacci, V., Koshland, D. E., & Strunnikov, A. V. (1997) · Cell · doi:10.1016/s0092-8674(01)80008-8 · Cited by 828 · see citing works

Disseminating the genome: joining, resolving, and separating sister chromatids during mitosis and meiosis

Nasmyth, K. (2001) · Annual Review of Genetics · doi:10.1146/annurev.genet.35.102401.091334 · Cited by 805 · 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

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

Zuin, J., Dixon, J. R., van der Reijden, M. I. J. A., Ye, Z., Kolovos, P., Brouwer, R. W. W., van de Corput, M. P. C., van de Werken, H. J. G., Knoch, T. A., van IJcken, W. F. J., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1317788111 · Cited by 779 · see citing works

Chromosomal silencing and localization are mediated by different domains of Xist RNA

Wutz, A., Rasmussen, T., & Jaenisch, R. (2002) · Nature Genetics · doi:10.1038/ng820 · Cited by 774 · see citing works

Genome Architecture: Domain Organization of Interphase Chromosomes

Bickmore, W. A., & van Steensel, B. (2013) · Cell · doi:10.1016/j.cell.2013.02.001 · Cited by 725 · see citing works

Single-Cell Dynamics of Genome-Nuclear Lamina Interactions

Kind, J., Pagie, L., Ortabozkoyun, H., Boyle, S., de Vries, S., Janssen, H., Amendola, M., Nolen, L. D., Bickmore, W. A., & van Steensel, B. (2013) · Cell · doi:10.1016/j.cell.2013.02.028 · Cited by 716 · see citing works

The Hierarchy of the 3D Genome

Gibcus, J. H., & Dekker, J. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.02.011 · Cited by 695 · see citing works

Intermingling of Chromosome Territories in Interphase Suggests Role in Translocations and Transcription-Dependent Associations

Branco, M. R., & Pombo, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040138 · Cited by 685 · 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

Long-range chromatin regulatory interactions in vivo

Carter, D., Chakalova, L., Osborne, C. S., Dai, Y.-F., & Fraser, P. (2002) · Nature Genetics · doi:10.1038/ng1051 · Cited by 663 · 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

Interchromosomal Interactions and Olfactory Receptor Choice

Lomvardas, S., Barnea, G., Pisapia, D. J., Mendelsohn, M. M., Kirkland, J., & Axel, R. (2006) · Cell · doi:10.1016/j.cell.2006.06.035 · Cited by 633 · see citing works

Cohesin relocation from sites of chromosomal loading to places of convergent transcription

Lengronne, A., Katou, Y., Mori, S., Yokobayashi, S., Kelly, G. P., Itoh, T., Watanabe, Y., Shirahige, K., & Uhlmann, F. (2004) · Nature · doi:10.1038/nature02742 · Cited by 588 · see citing works

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

Le, T. B. K., Imakaev, M., Mirny, L. A., & Laub, M. T. (2013) · Science · doi:10.1126/science.1242059 · Cited by 581 · see citing works

Complexity of chromatin folding is captured by the strings and binders switch model

Barbieri, M., Chotalia, M., Fraser, J., Lavitas, L.-M., Dostie, J., Pombo, A., & Nicodemi, M. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1204799109 · Cited by 570 · see citing works

At the heart of the chromosome: SMC proteins in action

Hirano, T. (2006) · Nature reviews. Molecular cell biology · doi:10.1038/nrm1909 · Cited by 569 · see citing works

Metaphase chromosome structure: evidence for a radial loop model.

Marsden, M., & Laemmli, U. K. (1979) · Cell · doi:10.1016/0092-8674(79)90325-8 · Cited by 552 · 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 545 · see citing works

Self-organization of domain structures by DNA-loop-extruding enzymes

Alipour, E., & Marko, J. F. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks925 · Cited by 540 · 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

Topology of mammalian developmental enhancers and their regulatory landscapes

de Laat, W., & Duboule, D. (2013) · Nature · doi:10.1038/nature12753 · Cited by 521 · see citing works

Structure and Dynamics of Interphase Chromosomes

Rosa, A., & Everaers, R. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000153 · Cited by 511 · see citing works

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

Hou, C., Li, L., Qin, Z. S., & Corces, V. G. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.08.031 · Cited by 503 · see citing works

Transient Anomalous Diffusion of Telomeres in the Nucleus of Mammalian Cells

Bronstein, I., Israel, Y., Kepten, E., Mai, S., Shav‐Tal, Y., Barkai, E., & Garini, Y. (2009) · Physical Review Letters · doi:10.1103/physrevlett.103.018102 · Cited by 495 · see citing works

Looping versus linking: toward a model for long-distance gene activationPreprint

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Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription

Giorgetti, L., Galupa, R., Nora, E. P., Piolot, T., Lam, F., Dekker, J., Tiana, G., & Heard, E. (2014) · Cell · doi:10.1016/j.cell.2014.03.025 · Cited by 460 · cited 1× · see citing works

Functional and topological characteristics of mammalian regulatory domains

Symmons, O., Uslu, V. V., Tsujimura, T., Ruf, S., Nassari, S., Schwarzer, W., Ettwiller, L., & Spitz, F. (2014) · Genome Research · doi:10.1101/gr.163519.113 · Cited by 455 · 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

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

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

Ulianov, S. V., Khrameeva, E. E., Gavrilov, A. A., Flyamer, I. M., Kos, P., Mikhaleva, E. A., Penin, A. A., Logacheva, M. D., Imakaev, M. V., Chertovich, A., et al. (2016) · Genome Research · doi:10.1101/gr.196006.115 · Cited by 388 · see citing works

Transient Homologous Chromosome Pairing Marks the Onset of X Inactivation

Xu, N., Tsai, C., & Lee, J. T. (2006) · Science · doi:10.1126/science.1122984 · Cited by 384 · see citing works

High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation

Simon, M. D., Pinter, S. F., Fang, R., Sarma, K., Rutenberg-Schoenberg, M., Bowman, S., Kesner, B., Maier, V., Kingston, R. E., & Lee, J. T. (2013) · Nature · doi:10.1038/nature12719 · Cited by 382 · see citing works

Live-cell imaging reveals a stable cohesin-chromatin interaction after but not before DNA replication.

Gerlich, D., Koch, B., Dupeux, F., Peters, J., & Ellenberg, J. (2006) · Current Biology · doi:10.1016/j.cub.2006.06.068 · Cited by 369 · see citing works

Condensins: universal organizers of chromosomes with diverse functionsPreprint

Hirano, T. (2012) · Genes & Development · doi:10.1101/gad.194746.112 · Cited by 366 · see citing works

Nucleosome-mediated cooperativity between transcription factors

Mirny, L. A. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0913805107 · Cited by 349 · see citing works

13S condensin actively reconfigures DNA by introducing global positive writhe: implications for chromosome condensation.

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MutS mediates heteroduplex loop formation by a translocation mechanism

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Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

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Compaction and segregation of sister chromatids via active loop extrusion

Goloborodko, A. A., Imakaev, M., Marko, J. F., & Mirny, L. A. (2016) · eLife · doi:10.7554/elife.14864 · Cited by 317 · see citing works

Structural and functional diversity of Topologically Associating Domains

Dekker, J., & Heard, É. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.08.044 · Cited by 313 · see citing works

Architecture of metaphase chromosomes and chromosome scaffolds

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Remote control of gene transcription

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From a melt of rings to chromosome territories: the role of topological constraints in genome folding

Halverson, J. D., Smrek, J., Kremer, K., & Grosberg, A. Y. (2014) · Reports on Progress in Physics · doi:10.1088/0034-4885/77/2/022601 · Cited by 292 · see citing works

Chromosome Compaction by Active Loop Extrusion

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The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions

Jhunjhunwala, S., van Zelm, M. C., Peak, M. M., Cutchin, S., Riblet, R. J., van Dongen, J. J. M., Grosveld, F. G., Knoch, T., & Murre, C. (2008) · Cell · doi:10.1016/j.cell.2008.03.024 · Cited by 287 · see citing works

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

Lucas, J., Zhang, Y., Dudko, O. K., & Murre, C. (2014) · Cell · doi:10.1016/j.cell.2014.05.036 · Cited by 239 · see citing works

Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilisPreprint

Wang, X.-D., Le, T., Lajoie, B., Dekker, J., Laub, M., & Rudner, D. (2015) · Genes & Development · doi:10.1101/gad.265876.115 · Cited by 236 · see citing works

Gene regulation through nuclear organization

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High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genomePreprint

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An Overview of Genome Organization and How We Got There: from FISH to Hi-C

Fraser, J., Williamson, I., Bickmore, W. A., & Dostie, J. (2015) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00006-15 · Cited by 218 · see citing works

Noncoding RNAs and Epigenetic Mechanisms During X-Chromosome Inactivation

Gendrel, A.-V., & Heard, É. (2014) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-101512-122415 · Cited by 217 · see citing works

Enhancer Interaction Networks as a Means for Singular Olfactory Receptor Expression

Markenscoff-Papadimitriou, E., Allen, W. E., Colquitt, B. M., Goh, T., Murphy, K. K., Monahan, K., Mosley, C. P., Ahituv, N., & Lomvardas, S. (2014) · Cell · doi:10.1016/j.cell.2014.09.033 · Cited by 214 · see citing works

Chromosome Replication and Segregation in Bacteria

Reyes‐Lamothe, R., Nicolas, É., & Sherratt, D. J. (2012) · Annual Review of Genetics · doi:10.1146/annurev-genet-110711-155421 · Cited by 207 · see citing works

Physical tethering and volume exclusion determine higher-order genome organization in budding yeastPreprint

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Monoallelic Expression of Olfactory Receptors

Monahan, K. D., & Lomvardas, S. (2015) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100814-125308 · Cited by 187 · see citing works

A CTCF Code for 3D Genome Architecture

Nichols, M. H., & Corces, V. G. (2015) · Cell · doi:10.1016/j.cell.2015.07.053 · Cited by 186 · see citing works

From a melt of rings to chromosome territories: the role of topological constraints in genome folding

Halverson, J., Smrek, J., Kremer, K., & Grosberg, A. Y. (2014) · Max Planck Digital Library · Cited by 181 · see citing works

Sensing X Chromosome Pairs Before X Inactivation via a Novel X-Pairing Region of the Xic

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ATRX Directs Binding of PRC2 to Xist RNA and Polycomb Targets

Sarma, K., Cifuentes-Rojas, C., Ergun, A., Rosario, A. M. D., Jeon, Y., White, F., Sadreyev, R. I., & Lee, J. T. (2014) · Cell · doi:10.1016/j.cell.2014.10.019 · Cited by 178 · see citing works

Identification 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 · see citing works

Co-Opting the Unfolded Protein Response to Elicit Olfactory Receptor Feedback

Dalton, R. P., Lyons, D. B., & Lomvardas, S. (2013) · Cell · doi:10.1016/j.cell.2013.09.033 · Cited by 170 · see citing works

Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders

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Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes

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Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres

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X-chromosome inactivation: new insights into cis and trans regulation

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Real-time detection of single-molecule DNA compaction by condensin I.

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