Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data
Open accessAbstract
How DNA is organized in three dimensions inside the cell nucleus and how this affects the ways in which cells access, read and interpret genetic information are among the longest standing questions in cell biology. Using newly developed molecular, genomic and computational approaches based on the chromosome conformation capture technology (such as 3C, 4C, 5C and Hi-C), the spatial organization of genomes is being explored at unprecedented resolution. Interpreting the increasingly large chromatin interaction data sets is now posing novel challenges. Here we describe several types of statistical and computational approaches that have recently been developed to analyse chromatin interaction data.
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
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?
Polymorphic cis-regulatory elements have been shown to affect CTCF binding and DNA looping.
“Polymorphic cis-REs have been shown to influence CTCF binding (71, 72) and DNA looping (73).”
From Variation in the Oxytocin Receptor Gene Predicts Brain Region–Specific Expression and Social Attachment (2016) · cites this paper as [73]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
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 · see citing works
Self-citationComprehensive 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
Self-citationTopological 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
Rubinstein, M., & Colby, R. H. (2003) · doi:10.1093/oso/9780198520597.001.0001 · Cited by 5,686 · 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
Self-citationSpatial 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
Self-citationThe accessible chromatin landscape of the human genome
Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B., et al. (2012) · Nature · doi:10.1038/nature11232 · Cited by 2,679 · see citing works
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 2,339 · 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
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
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
CTCF: Master Weaver of the Genome
Phillips‐Cremins, J. E., & Corces, V. G. (2009) · Cell · doi:10.1016/j.cell.2009.06.001 · Cited by 1,540 · 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
Self-citationIterative correction of Hi-C data reveals hallmarks of chromosome organization
Imakaev, M., Fudenberg, G., McCord, R. P., Naumova, N., Goloborodko, A., Lajoie, B. R., Dekker, J., & Mirny, L. A. (2012) · Nature Methods · doi:10.1038/nmeth.2148 · Cited by 1,423 · see citing works
Self-citationArchitecture of the human regulatory network derived from ENCODE data
Gerstein, M., Kundaje, A. B., Hariharan, M., Landt, S. G., Yan, K., Cheng, C., Mu, X. J., Khurana, E., Rozowsky, J. S., Alexander, R. P., et al. (2012) · Nature · doi:10.1038/nature11245 · Cited by 1,418 · see citing works
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
A map of the cis-regulatory sequences in the mouse genome
Shen, Y., Yue, F., McCleary, D. F., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V. V., et al. (2012) · Nature · doi:10.1038/nature11243 · Cited by 1,361 · cited 2× · see citing works
“Computational predictions based on correlations between gene activity and activity of distal elements across panels of cell lines also led to the prediction that genes are regulated by multiple distal elements 54–56 .”
BackgroundLooping 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
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 1,182 · see citing works
Self-citationFelsenfeld, G., & Groudine, M. T. (2003) · Nature · doi:10.1038/nature01411 · Cited by 1,153 · see citing works
A three-dimensional model of the yeast genome
Duan, Z., Andronescu, M., Schutz, K., McIlwain, S. J., Kim, Y. J., Lee, C., Shendure, J., Fields, S., Blau, C. A., & Noble, W. S. (2010) · Nature · doi:10.1038/nature08973 · Cited by 1,012 · see citing works
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
Gerstein, M., Lu, Z. J., Nostrand, E. L. V., Cheng, C., Arshinoff, B. I., Liu, T., Yip, K. Y.-L., Robilotto, R., Rechtsteiner, A., Ikegami, K., et al. (2010) · Science · doi:10.1126/science.1196914 · Cited by 959 · see citing works
Zhao, Z., Tavoosidana, G., Sjölinder, M., Göndör, A., Mariano, P., Wang, S., Kanduri, C., Lezcano, M., Sandhu, K. S., Singh, U., et al. (2006) · Nature Genetics · doi:10.1038/ng1891 · Cited by 957 · 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
Deng, W., Lee, J., Wang, H., Miller, J., Reik, A., Gregory, P. D., Dean, A., & Blobel, G. A. (2012) · Cell · doi:10.1016/j.cell.2012.03.051 · Cited by 734 · see citing works
Nuclear organization of the genome and the potential for gene regulation
Fraser, P., & Bickmore, W. (2007) · Nature · doi:10.1038/nature05916 · Cited by 734 · see citing works
The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains
Caron, H. N., van Schaik, B. D. C., van der Mee, M., Baas, F., Riggins, G. J., Sluis, P. V., Hermus, M.-C., van Asperen, R., Boon, K., Voûte, P. A., et al. (2001) · Science · doi:10.1126/science.1056794 · Cited by 730 · see citing works
Schoenfelder, S., Sexton, T., Chakalova, L., Cope, N. F., Horton, A., Andrews, S., Kurukuti, S., Mitchell, J. A., Umlauf, D., Dimitrova, D. S., et al. (2009) · Nature Genetics · doi:10.1038/ng.496 · Cited by 710 · see citing works
A decade of 3C technologies: insights into nuclear organizationPreprint
de Wit, E., & de Laat, W. L. (2012) · Genes & Development · doi:10.1101/gad.179804.111 · Cited by 701 · 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
Self-citationBranco, M. R., & Pombo, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040138 · Cited by 685 · see citing works
Interphase chromosomes undergo constrained diffusional motion in living cells
Marshall, W. F., Straight, A. F., Marko, J. F., Swedlow, J. R., Dernburg, A. F., Belmont, A. S., Murray, A. W., Agard, D. A., & Sedat, J. W. (1997) · Current Biology · doi:10.1016/s0960-9822(06)00412-x · Cited by 673 · see citing works
Insulators: exploiting transcriptional and epigenetic mechanisms
Gaszner, M., & Felsenfeld, G. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1925 · Cited by 649 · see citing works
CTCF-mediated functional chromatin interactome in pluripotent cells
Handoko, L., Han, X., Li, G., Ngan, C. Y., Chew, E. G. Y., Schnapp, M., Lee, C. W. H., Ye, C., Ping, J. L. H., Mulawadi, F. H., et al. (2011) · Nature Genetics · doi:10.1038/ng.857 · Cited by 614 · see citing works
Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery
Towbin, B. D., González-Aguilera, C., Sack, R., Gaidatzis, D., Kalck, V., Meister, P., Askjaer, P., & Gasser, S. M. (2012) · Cell · doi:10.1016/j.cell.2012.06.051 · Cited by 597 · see citing works
Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome
Horike, S., Cai, S., Miyano, M., Cheng, J., & Kohwi-shigematsu, T. (2004) · Nature Genetics · doi:10.1038/ng1491 · Cited by 585 · see citing works
The fractal globule as a model of chromatin architecture in the cell
Mirny, L. A. (2011) · Chromosome Research · doi:10.1007/s10577-010-9177-0 · Cited by 581 · see citing works
Self-citationChromatin Motion Is Constrained by Association with Nuclear Compartments in Human Cells
Chubb, J. R., Boyle, S., Perry, P., & Bickmore, W. A. (2002) · Current Biology · doi:10.1016/s0960-9822(02)00695-4 · Cited by 580 · 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
The β-globin nuclear compartment in development and erythroid differentiation
Palstra, R.-J., Tolhuis, B., Splinter, E., Nijmeijer, R., Grosveld, F., & de Laat, W. (2003) · Nature Genetics · doi:10.1038/ng1244 · Cited by 559 · 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
Self-citationKalhor, R., Tjong, H., Jayathilaka, N., Alber, F., & Chen, L. (2011) · Nature Biotechnology · doi:10.1038/nbt.2057 · Cited by 532 · 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
Russel, D., Lasker, K., Webb, B., Velázquez-Muriel, J. A., Tjioe, E., Schneidman‐Duhovny, D., Peterson, B. E., & Šali, A. (2012) · PLoS Biology · doi:10.1371/journal.pbio.1001244 · Cited by 509 · see citing works
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
A cis-regulatory map of the Drosophila genome
Negre, N. N., Brown, C. D., Ma, L., Bristow, C. A., Miller, S. W., Wagner, U., Kheradpour, P., Eaton, M. L., Loriaux, P. M., Sealfon, R. S. G., et al. (2011) · Nature · doi:10.1038/nature09990 · Cited by 500 · see citing works
Proximity among Distant Regulatory Elements at the β-Globin Locus Requires GATA-1 and FOG-1
Vakoc, C. R., Letting, D. L., Gheldof, N., Sawado, T., Bender, M. A., Groudine, M., Weiss, M. J., Dekker, J., & Blobel, G. A. (2005) · Molecular Cell · doi:10.1016/j.molcel.2004.12.028 · Cited by 490 · see citing works
Self-citationEvidence for large domains of similarly expressed genes in the Drosophila genome
Spellman, P. T., & Rubin, G. M. (2002) · Journal of Biology · doi:10.1186/1475-4924-1-5 · Cited by 485 · see citing works
Active RNA polymerases are localized within discrete transcription ‘factories’ in human nuclei
Iborra, F. J., Pombo, A., Jackson, D. A., & Cook, P. R. (1996) · Journal of Cell Science · doi:10.1242/jcs.109.6.1427 · Cited by 458 · see citing works
An encyclopedia of mouse DNA elements (Mouse ENCODE)
Mouse ENCODE Consortium, Stamatoyannopoulos, J. A., Snyder, M., Hardison, R., Ren, B., Gingeras, T., Gilbert, D. M., Groudine, M., Bender, M., Kaul, R., et al. (2012) · Genome Biology · doi:10.1186/gb-2012-13-8-418 · Cited by 446 · see citing works
Self-citationThe role of topological constraints in the kinetics of collapse of macromolecules
Grosberg, A. Y., Nechaev, S. K., & Shakhnovich, E. I. (1988) · Journal de physique · doi:10.1051/jphys:0198800490120209500 · Cited by 437 · see citing works
Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila
Bantignies, F., Roure, V., Comet, I., Leblanc, B., Schuettengruber, B., Bonnet, J., Tixier, V., Mas, A., & Cavalli, G. (2011) · Cell · doi:10.1016/j.cell.2010.12.026 · Cited by 429 · see citing works
Long-range intrachromosomal interactions in the T helper type 2 cytokine locus
Spilianakis, C. G., & Flavell, R. A. (2004) · Nature Immunology · doi:10.1038/ni1115 · Cited by 425 · see citing works
Initial 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 383 · see citing works
Conformational and thermodynamic properties of supercoiled DNA
Vologodskii, A. V., Levene, S. D., Klenin, K. V., Frank-Kamenetskii, M. D., & Cozzarelli, N. R. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90533-p · Cited by 381 · see citing works
Ahmadiyeh, N., Pomerantz, M. M., Grisanzio, C., Herman, P. K., Li, J., Almendro, V., He, H. H., Brown, M. A., Liu, X. S., Davis, M., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910668107 · Cited by 358 · see citing works
The active spatial organization of the β-<i>globin</i> locus requires the transcription factor EKLF
Drissen, R., Palstra, R.-J., Gillemans, N., Splinter, E., Grosveld, F., Philipsen, S., & de Laat, W. (2004) · Genes & Development · doi:10.1101/gad.317004 · Cited by 352 · see citing works
The three 'C' s of chromosome conformation capture: controls, controls, controls
Dekker, J. (2005) · Nature Methods · doi:10.1038/nmeth823 · Cited by 347 · see citing works
Self-citationCrumpled Globule Model of the Three-Dimensional Structure of DNA
Grosberg, A. Y., Rabin, Y., Havlin, S., & Neer, A. (1993) · Europhysics Letters (EPL) · doi:10.1209/0295-5075/23/5/012 · Cited by 331 · see citing works
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
A random-walk/giant-loop model for interphase chromosomes.
Sachs, R. K., van den Engh, G., Trask, B. J., Yokota, H., & Hearst, J. E. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.7.2710 · Cited by 301 · see citing works
A Polymeric Protein Anchors the Chromosomal Origin/ParB Complex at a Bacterial Cell Pole
Bowman, G. R., Comolli, L. R., Zhu, J., Eckart, M. R., Koenig, M., Downing, K. H., Moerner, W. E., Earnest, T. N., & Shapiro, L. (2008) · Cell · doi:10.1016/j.cell.2008.07.015 · Cited by 300 · see citing works
Ebersbach, G., Briegel, A., Jensen, G. J., & Jacobs, C. (2008) · Cell · doi:10.1016/j.cell.2008.07.016 · Cited by 292 · see citing works
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
Brown, J. M., Green, J., das Neves, R. P., Wallace, H. A. C., Smith, A. J. H., Hughes, J. R., Gray, N., Taylor, S., Wood, W. G., Higgs, D. R., et al. (2008) · The Journal of Cell Biology · doi:10.1083/jcb.200803174 · Cited by 279 · see citing works
Centromere clustering is a major determinant of yeast interphase nuclear organization
Jin, Q., Fuchs, J., & Loidl, J. (2000) · Journal of Cell Science · doi:10.1242/jcs.113.11.1903 · Cited by 272 · see citing works
The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules
Baù, D., Sanyal, A., Lajoie, B. R., Capriotti, E., Byron, M., Lawrence, J. B., Dekker, J., & Martı́-Renom, M. A. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1936 · Cited by 267 · see citing works
Self-citationWright, J. B., Brown, S. J., & Cole, M. D. (2010) · Molecular and Cellular Biology · doi:10.1128/mcb.01384-09 · Cited by 255 · see citing works
Spatially confined folding of chromatin in the interphase nucleus
Langerak, J. M., Bohn, M., de Leeuw, W. C., Giromus, O., Manders, E. M. M., Verschure, P. J., Indemans, M. H. G., Gierman, H. J., Heermann, D. W., DRIEL, R. V., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809501106 · Cited by 246 · see citing works
Estimating Genomic Distance from DNA Sequence Location in Cell Nuclei by a Random Walk Model
van den Engh, G., Sachs, R. K., & Trask, B. J. (1992) · Science · doi:10.1126/science.1388286 · Cited by 244 · see citing works
Vernimmen, D., Gobbi, M. D., Sloane‐Stanley, J. A., Wood, W. G., & Higgs, D. R. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601654 · Cited by 244 · see citing works
Enhancer and promoter interactions—long distance calls
Krivega, I., & Dean, A. (2012) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2011.11.001 · Cited by 225 · see citing works
Structure and Function in the Budding Yeast Nucleus
Taddei, A., & Gasser, S. M. (2012) · Genetics · doi:10.1534/genetics.112.140608 · Cited by 225 · see citing works
Tanizawa, H., Iwasaki, O., Tanaka, A., Capizzi, J. R., Wickramasinghe, P., Lee, M., Fu, Z., & Noma, K.-I. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq955 · Cited by 223 · see citing works
Genomics tools for unraveling chromosome architecture
van Steensel, B., & Dekker, J. (2010) · Nature Biotechnology · doi:10.1038/nbt.1680 · Cited by 216 · see citing works
Self-citationThe Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation
Martı́-Renom, M. A. (2012) · Lecture notes in computer science · doi:10.1007/978-3-642-29627-7_16 · Cited by 206 · see citing works
Physical tethering and volume exclusion determine higher-order genome organization in budding yeastPreprint
Tjong, H., Gong, K. Q., Chen, L., & Alber, F. (2012) · Genome Research · doi:10.1101/gr.129437.111 · Cited by 200 · see citing works
The Three-Dimensional Architecture of a Bacterial Genome
Umbarger, M., Toro, E., Wright, M. A., Porreca, G., Baù, D., Hong, S.-H., Fero, M., Zhu, L., Martí-Renom, M., McAdams, H., et al. (2011) · Molecules and Cells · doi:10.1016/j.molcel.2011.09.010 · Cited by 200 · see citing works
Self-citationBayesian Inference of Spatial Organizations of Chromosomes
Hu, M., Deng, K., Qin, Z. S., Dixon, J. R., Selvaraj, S., Fang, J., Ren, B., & Liu, J. S. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002893 · Cited by 198 · see citing works
Long-range chromosomal interactions and gene regulation
Miele, A., & Dekker, J. (2008) · Molecular BioSystems · doi:10.1039/b803580f · Cited by 198 · see citing works
Self-citationStatistics of polymer rings in the melt: a numerical simulation study
Vettorel, T., Grosberg, A. Y., & Kremer, K. (2009) · Physical Biology · doi:10.1088/1478-3975/6/2/025013 · Cited by 197 · see citing works
Making contacts on a nucleic acid polymer
Rippe, K. (2001) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(01)01978-8 · Cited by 192 · see citing works
Majumder, P., Gomez, J. A., Chadwick, B. P., & Boss, J. M. (2008) · The Journal of Experimental Medicine · doi:10.1084/jem.20071843 · Cited by 181 · see citing works
A view of nuclear Polycomb bodies
Pirrotta, V., & Li, H. (2011) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2011.11.004 · Cited by 176 · see citing works
Entropic organization of interphase chromosomes
Cook, P. R., & Marenduzzo, D. (2009) · The Journal of Cell Biology · doi:10.1083/jcb.200903083 · Cited by 175 · see citing works
Interactions among Polycomb Domains Are Guided by Chromosome Architecture
Tolhuis, B., Blom, M., Kerkhoven, R. M., Pagie, L., Teunissen, H., Nieuwland, M., Simonis, M., de Laat, W. L., van Lohuizen, M., & van Steensel, B. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001343 · Cited by 174 · see citing works
Higher-order chromatin structure: bridging physics and biology
Fudenberg, G., & Mirny, L. A. (2012) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2012.01.006 · Cited by 169 · see citing works
Self-citationDiffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization
Bohn, M., & Heermann, D. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012218 · Cited by 168 · see citing works
Polymer Models of Meiotic and Mitotic Chromosomes
Marko, J. F., & Siggia, E. D. (1997) · Molecular Biology of the Cell · doi:10.1091/mbc.8.11.2217 · Cited by 152 · see citing works
Boyle, S., Rodesch, M. J., Halvensleben, H. A., Jeddeloh, J. A., & Bickmore, W. A. (2011) · Chromosome Research · doi:10.1007/s10577-011-9245-0 · Cited by 150 · see citing works
Shopland, L. S., Lynch, C. R., Peterson, K. A., Thornton, K. R., Kepper, N., Hase, J. V., Stein, S., Vincent, S., Molloy, K. R., Kreth, G., et al. (2006) · The Journal of Cell Biology · doi:10.1083/jcb.200603083 · Cited by 149 · see citing works
Würtele, H., & Chartrand, P. (2006) · Chromosome Research · doi:10.1007/s10577-006-1075-0 · Cited by 147 · see citing works
Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elementsPreprint
Hakim, O., Sung, M., Voss, T. C., Splinter, E., John, S., Sabo, P. J., Thurman, R. E., Stamatoyannopoulos, J. A., de Laat, W. L., & Hager, G. L. (2011) · Genome Research · doi:10.1101/gr.111153.110 · Cited by 142 · see citing works
Looping Probabilities in Model Interphase Chromosomes
Rosa, A., Becker, N. B., & Everaers, R. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2010.01.054 · Cited by 124 · see citing works
Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus
Ott, C. J., Blackledge, N. P., Kerschner, J. L., Leir, S., Crawford, G. E., Cotton, C. U., & Harris, A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900946106 · Cited by 117 · see citing works
Chromatin conformation signatures of cellular differentiation
Fraser, J., Rousseau, M., Shenker, S., Ferraiuolo, M. A., Hayashizaki, Y., Blanchette, M., & Dostie, J. (2009) · Genome biology · doi:10.1186/gb-2009-10-4-r37 · Cited by 115 · see citing works
Gheldof, N., Smith, E. M., Tabuchi, T. M., Koch, C. M., Dunham, I., Stamatoyannopoulos, J. A., & Dekker, J. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq175 · Cited by 110 · see citing works
Self-citationMiele, A., Bystricky, K., & Dekker, J. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000478 · Cited by 100 · see citing works
Self-citationMy5C: web tools for chromosome conformation capture studies
Lajoie, B. R., van Berkum, N. L., Sanyal, A., & Dekker, J. (2009) · Nature Methods · doi:10.1038/nmeth1009-690 · Cited by 88 · see citing works
Self-citationBridging 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 82 · see citing works
Self-citationPolymer models for interphase chromosomes.
Hahnfeldt, P., Hearst, J. E., Brenner, D. J., Sachs, R. K., & Hlatky, L. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.16.7854 · Cited by 79 · see citing works
The physics behind the larger scale organization of DNA in eukaryotes
Emanuel, M., Radja, N. H., Henriksson, A., & Schießel, H. (2009) · Physical Biology · doi:10.1088/1478-3975/6/2/025008 · Cited by 71 · see citing works
Kinetics of chromosome condensation in the presence of topoisomerases: a phantom chain model
Sikorav, J., & Jannink, G. (1994) · Biophysical Journal · doi:10.1016/s0006-3495(94)80859-8 · Cited by 71 · see citing works
Chromatin globules: a common motif of higher order chromosome structure?
Sanyal, A., Baù, D., Martı́-Renom, M. A., & Dekker, J. (2011) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2011.03.009 · Cited by 69 · see citing works
Self-citationMüller, I. I., Boyle, S., Singer, R. H., Bickmore, W. A., & Chubb, J. R. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011560 · Cited by 67 · see citing works
SnapShot: Chromosome Conformation Capture
Hakim, O., & Misteli, T. (2012) · Cell · doi:10.1016/j.cell.2012.02.019 · Cited by 62 · see citing works
Structure determination of genomic domains by satisfaction of spatial restraints
Baù, D., & Martı́-Renom, M. A. (2010) · Chromosome Research · doi:10.1007/s10577-010-9167-2 · Cited by 46 · see citing works
Repulsive Forces Between Looping Chromosomes Induce Entropy-Driven Segregation
Bohn, M., & Heermann, D. (2011) · PLoS ONE · doi:10.1371/journal.pone.0014428 · Cited by 43 · see citing works
A view of the chromatin landscape
Rapkin, L. M., Anchel, D., Li, R., & Bazett‐Jones, D. P. (2011) · Micron · doi:10.1016/j.micron.2011.11.007 · Cited by 43 · see citing works
Discovering genome regulation with 3C and 3C-related technologies
Ethier, S. D., Miura, H., & Dostie, J. (2011) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2011.12.004 · Cited by 41 · see citing works
Unusual chromosome structure of fission yeast DNA in mouse cells
McManus, J., Perry, P., Sumner, A. T., Wright, D. M., Thomson, E. J., Allshire, R. C., Hastie, N. D., & Bickmore, W. A. (1994) · Journal of Cell Science · doi:10.1242/jcs.107.3.469 · Cited by 34 · see citing works
Dorier, J., & Stasiak, A. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq666 · Cited by 31 · see citing works
Expression-Dependent Folding of Interphase Chromatin
Jerabek, H., & Heermann, D. W. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037525 · Cited by 30 · see citing works
Belmont, A. S., Hu, Y., Sinclair, P. B., Wu, W., Bian, Q., & Kireev, I. I. (2010) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2010.75.050 · Cited by 21 · see citing works
Stower, H. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3341 · Cited by 11 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [97]Fudenberg G Mirny LA Higher-order chromatin structure: bridging physics and biology Current Opinion in Genetics & Development 22 115 124 10.1016/j.gde.2012.01.006 2012 22360992 PMC3697851 · DOI
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 2,416 · see citing works
Self-citationThree-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction
Bkhetan, Z. A., & Plewczyński, D. (2018) · Scientific Reports · doi:10.1038/s41598-018-23276-8 · Cited by 1,663 · see citing works
Ten years of next-generation sequencing technology
van Dijk, E., Auger, H., Jaszczyszyn, Y., & Thermes, C. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.07.001 · Cited by 1,628 · see citing works
Sequencing depth and coverage: key considerations in genomic analyses
Sims, D., Sudbery, I. M., Ilott, N. E., Heger, A., & Ponting, C. P. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3642 · Cited by 1,403 · see citing works
A high-resolution map of the three-dimensional chromatin interactome in human cells
Jin, F., Li, Y., Dixon, J. R., Selvaraj, S., Ye, Z., Lee, A. Y., Yen, C.-A., Schmitt, A. D., Espinoza, C. A., & Ren, B. (2013) · Nature · doi:10.1038/nature12644 · Cited by 1,208 · see citing works
Two independent modes of chromatin organization revealed by cohesin removal
Schwarzer, W., Abdennur, N., Goloborodko, A., Pekowska, A., Fudenberg, G., Loe-Mie, Y., Fonseca, N. A., Huber, W., Haering, C. H., Mirny, L., et al. (2017) · Nature · doi:10.1038/nature24281 · Cited by 1,196 · see citing works
Self-citationMapping long-range promoter contacts in human cells with high-resolution capture Hi-C
Mifsud, B., Tavares-Cadete, F., Young, A. N., Sugar, R., Schoenfelder, S., Ferreira, L., Wingett, S. W., Andrews, S., Grey, W., Ewels, P. A., et al. (2015) · Nature Genetics · doi:10.1038/ng.3286 · Cited by 990 · 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
Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data
Pliner, H. A., Packer, J. S., McFaline-Figueroa, J. L., Cusanovich, D. A., Daza, R. M., Aghamirzaie, D., Srivatsan, S., Qiu, X., Jackson, D., Minkina, A., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.06.044 · Cited by 789 · 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
Self-citationStructural variation in the 3D genome
Spielmann, M., Lupiáñez, D. G., & Mundlos, S. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0007-0 · Cited by 719 · see citing works
Enhancers as non-coding RNA transcription units: recent insights and future perspectives
Li, W., Notani, D., & Rosenfeld, M. G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.4 · Cited by 710 · see citing works
Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding
Hsieh, T.-H. S., Cattoglio, C., Slobodyanyuk, E., Hansen, A. S., Rando, O. J., Tjian, R., & Darzacq, X. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.002 · Cited by 661 · see citing works
Multi-omics single-cell data integration and regulatory inference with graph-linked embedding
Cao, Z.-J., & Gao, G. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01284-4 · Cited by 616 · see citing works
Three-dimensional genome architecture: players and mechanisms
Pombo, A., & Dillon, N. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3965 · Cited by 571 · see citing works
Wang, Y., Song, F., Zhang, B., Zhang, L., Xu, J., Kuang, D., Li, D., Choudhary, M. N. K., Li, Y., Hu, M., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1519-9 · Cited by 552 · see citing works
Rivera, C. M., & Ren, B. (2013) · Cell · doi:10.1016/j.cell.2013.09.011 · Cited by 550 · see citing works
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient
Yang, T., Zhang, F., Yardımcı, G. G., Song, F., Hardison, R. C., Noble, W. S., Yue, F., & Li, Q. (2017) · Genome Research · doi:10.1101/gr.220640.117 · Cited by 533 · see citing works
Epigenetic control of CD8+ T cell differentiation
Henning, A. N., Roychoudhuri, R., & Restifo, N. P. (2018) · Nature reviews. Immunology · doi:10.1038/nri.2017.146 · Cited by 501 · 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
Self-citationDefining the genetic, genomic, cellular, and diagnostic architectures of psychiatric disorders
Sullivan, P. F., & Geschwind, D. H. (2019) · Cell · doi:10.1016/j.cell.2019.01.015 · Cited by 452 · see citing works
Dynamics of the epigenetic landscape during the maternal-to-zygotic transition
Eckersley-Maslin, M. A., Alda-Catalinas, C., & Reik, W. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0008-z · Cited by 431 · see citing works
Akbarian, S., Liu, C., Knowles, J. A., Vaccarino, F. M., Farnham, P. J., Crawford, G. E., Jaffe, A. E., Pinto, D., Dracheva, S., Geschwind, D. H., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.4156 · Cited by 451 · see citing works
The 3D genome in transcriptional regulation and pluripotency
Gorkin, D. U., Leung, D., & Ren, B. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.05.017 · Cited by 391 · see citing works
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
Cairns, J., Freire-Pritchett, P., Wingett, S. W., Várnai, C., Dimond, A., Plagnol, V., Zerbino, D., Schoenfelder, S., Javierre, B.-M., Osborne, C., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0992-2 · Cited by 417 · see citing works
The role of enhancers in cancer
Sur, I., & Taipale, J. (2016) · Nature reviews. Cancer · doi:10.1038/nrc.2016.62 · Cited by 382 · see citing works
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
Whole genome sequencing analysis for cancer genomics and precision medicine
Nakagawa, H., & Fujita, M. (2018) · Cancer Science · doi:10.1111/cas.13505 · Cited by 376 · see citing works
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 346 · see citing works
Feng, S.-H., Cokus, S. J., Schubert, V., Zhai, J., Pellegrini, M., & Jacobsen, S. (2014) · Molecules and Cells · doi:10.1016/j.molcel.2014.07.008 · Cited by 308 · see citing works
Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq
Fang, R., Yu, M., Li, G., Chee, S., Liu, T., Schmitt, A. D., & Ren, B. (2016) · Cell Research · doi:10.1038/cr.2016.137 · Cited by 344 · see citing works
Hannon, E., Spiers, H., Viana, J., Pidsley, R., Burrage, J., Murphy, T. M., Troakes, C., Turecki, G., O'Donovan, M., Schalkwyk, L., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.4182 · Cited by 297 · see citing works
Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data
Fortin, J.-P., & Hansen, K. D. (2015) · Genome Biology · doi:10.1186/s13059-015-0741-y · Cited by 333 · see citing works
Regulation of disease-associated gene expression in the 3D genome
Krijger, P. H. L., & de Laat, W. L. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.138 · Cited by 316 · see citing works
Chromatin and nucleosome dynamics in DNA damage and repairPreprint
Hauer, M., & Gasser, S. M. (2017) · Genes & Development · doi:10.1101/gad.307702.117 · Cited by 320 · 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
Self-citationEpigenetics, plasticity, and evolution: How do we link epigenetic change to phenotype?
Duncan, E. J., Gluckman, P. D., & Dearden, P. K. (2014) · Journal of Experimental Zoology Part B Molecular and Developmental Evolution · doi:10.1002/jez.b.22571 · Cited by 312 · see citing works
Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development
Phanstiel, D. H., Van Bortle, K., Spacek, D., Hess, G. T., Shamim, M. S., Machol, I., Love, M. I., Aiden, E. L., Bassik, M. C., & Snyder, M. P. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.08.006 · Cited by 299 · see citing works
A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples
Chen, H., Li, C., Peng, X., Zhou, Z., Weinstein, J. N., Johnson, R., Demchok, J. A., Felau, I., Kasapi, M., Ferguson, M. L., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.027 · Cited by 298 · see citing works
CRISPR/Cas9-based engineering of the epigenome
Pulecio, J., Verma, N., Mejía-Ramírez, E., Huangfu, D., & Raya, A. (2017) · Cell Stem Cell · doi:10.1016/j.stem.2017.09.006 · Cited by 300 · see citing works
Dily, F. L., Baù, D., Pohl, A., Vicent, G. P., Serra, F., Soronellas, D., Castellano, G., Wright, R. H. G., Ballaré, C., Filion, G. J. P., et al. (2014) · Genes & Development · doi:10.1101/gad.241422.114 · Cited by 297 · see citing works
Loss of lamin A function increases chromatin dynamics in the nuclear interior
Bronshtein, I., Kepten, E., Kanter, I., Berezin, S., Lindner, M., Redwood, A. B., Mai, S., Gonzalo, S., Foisner, R., Shav‐Tal, Y., et al. (2015) · Nature Communications · doi:10.1038/ncomms9044 · Cited by 302 · see citing works
Genome-wide analysis of local chromatin packing in Arabidopsis thalianaPreprint
Wang, C., Liu, C., Roqueiro, D., Grimm, D., Schwab, R., Becker, C., Lanz, C., & Weigel, D. (2014) · Genome Research · doi:10.1101/gr.170332.113 · Cited by 299 · see citing works
Serra, F., Baù, D., Goodstadt, M. N., Castillo, D., Filion, G. J. P., & Martı́-Renom, M. A. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005665 · Cited by 295 · see citing works
RNA Polymerase II cluster dynamics predict mRNA output in living cells
Cho, W., Jayanth, N., English, B. P., Inoue, T., Andrews, J. O., Conway, W., Grimm, J. B., Spille, J.-H., Lavis, L. D., Lionnet, T., et al. (2016) · eLife · doi:10.7554/elife.13617 · Cited by 280 · see citing works
Veloso, A., Kirkconnell, K. S., Magnuson, B., Biewen, B., Paulsen, M. T., Wilson, T. E., & Ljungman, M. (2014) · Genome Research · doi:10.1101/gr.171405.113 · Cited by 281 · see citing works
Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping
Morgan, S. L., Mariano, N. C., Bermudez, A., Arruda, N. L., Wu, F., Luo, Y., Shankar, G., Jia, L., Chen, H., Hu, J.-F., et al. (2017) · Nature Communications · doi:10.1038/ncomms15993 · Cited by 279 · see citing works
Liu, C., Cheng, Y., Wang, J., & Weigel, D. (2017) · Nature Plants · doi:10.1038/s41477-017-0005-9 · Cited by 270 · see citing works
Lamina-associated domains: peripheral matters and internal affairs
Briand, N., & Collas, P. (2020) · Genome biology · doi:10.1186/s13059-020-02003-5 · Cited by 269 · see citing works
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 254 · see citing works
Cremer, T., Cremer, M., Hübner, B., Strickfaden, H., Smeets, D., Popken, J., Sterr, M., Markaki, Y., Rippe, K., & Cremer, C. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.05.037 · Cited by 246 · see citing works
Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolutionPreprint
Liu, C., Wang, C., Wang, G., Becker, C., Zaidem, M., & Weigel, D. (2016) · Genome Research · doi:10.1101/gr.204032.116 · Cited by 243 · see citing works
Comparison of computational methods for the identification of topologically associating domains
Zufferey, M., Tavernari, D., Oricchio, E., & Ciriello, G. (2018) · Genome biology · doi:10.1186/s13059-018-1596-9 · Cited by 226 · see citing works
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
Regulatory Enhancer–Core-Promoter Communication via Transcription Factors and Cofactors
Zabidi, M. A., & Stark, A. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.10.003 · Cited by 228 · see citing works
Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2
Kaul, A., Bhattacharyya, S., & Ay, F. (2020) · Nature Protocols · doi:10.1038/s41596-019-0273-0 · Cited by 226 · see citing works
Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genome
Lu, J. Y., Chang, L., Li, T., Wang, T., Yin, Y., Zhan, G., Han, X., Zhang, K., Tao, Y., Percharde, M., et al. (2021) · Cell Research · doi:10.1038/s41422-020-00466-6 · Cited by 205 · see citing works
Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci
Jäger, R., Migliorini, G., Henrion, M., Kandaswamy, R., Speedy, H. E., Heindl, A., Whiffin, N., Carnicer, M. J., Broome, L. R., Dryden, N. H., et al. (2015) · Nature Communications · doi:10.1038/ncomms7178 · Cited by 210 · see citing works
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 · see citing works
HiCPlotter integrates genomic data with interaction matrices
Akdemir, K. C., & Chin, L. (2015) · Genome biology · doi:10.1186/s13059-015-0767-1 · Cited by 214 · see citing works
Mechanisms and principles of homology search during recombination
Renkawitz, J., Lademann, C. A., & Jentsch, S. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3805 · Cited by 211 · see citing works
Nucleosomal arrays self‐assemble into supramolecular globular structures lacking 30‐nm fibers
Maeshima, K., Rogge, R. A., Tamura, S., Joti, Y., Hikima, T., Szerlong, H. J., Krause, C., Herman, J., Seidel, E., DeLuca, J. G., et al. (2016) · The EMBO Journal · doi:10.15252/embj.201592660 · Cited by 208 · see citing works
The maintenance of chromosome structure: positioning and functioning of SMC complexes
Jeppsson, K. E., Kanno, T., Shirahige, K., & Sjögren, C. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3857 · Cited by 206 · see citing works
Xu, J., Ma, H., Jin, J., Uttam, S., Fu, R., Huang, Y., & Liu, Y. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.06.085 · Cited by 206 · see citing works
Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps
Burton, J. N., Liachko, I., Dunham, M. J., & Shendure, J. (2014) · G3 Genes Genomes Genetics · doi:10.1534/g3.114.011825 · Cited by 203 · see citing works
Polymer physics of chromosome large-scale 3D organisation
Chiariello, A. M., Annunziatella, C., Bianco, S., Esposito, A., & Nicodemi, M. (2016) · Scientific Reports · doi:10.1038/srep29775 · Cited by 194 · see citing works
King, L. B., Walum, H., Inoue, K., Eyrich, N. W., & Young, L. J. (2016) · Biological Psychiatry · doi:10.1016/j.biopsych.2015.12.008 · Cited by 191 · see citing works
“Furthermore, biochemical analyses, including chromatin immunoprecipitation followed by sequencing, chromosome conformation capture (73), and in vitro transcription assays could be used to investigate interactions between CTCF binding, DNA looping, and Oxtr regulation.”
Reinius, B., & Sandberg, R. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3888 · Cited by 187 · see citing works
Brackley, C. A., Johnson, J., Kelly, S. L., Cook, P. R., & Marenduzzo, D. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw135 · Cited by 181 · see citing works
Haplotype-resolved genome sequencing: experimental methods and applications
Snyder, M. W., Adey, A., Kitzman, J. O., & Shendure, J. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3903 · Cited by 189 · see citing works
Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers
Yan, J., Chen, S.-A. A., Local, A., Liu, T., Qiu, Y., Lee, A. Y., Jung, I., Preißl, S., Rivera, C. M., Wang, C., et al. (2018) · Cell Research · doi:10.1038/cr.2018.1 · Cited by 198 · see citing works
Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers
Hodges, H. C., Stanton, B. Z., Čermáková, K., Chang, C.-Y., Miller, E. L., Kirkland, J. G., Ku, W. L., Veverka, V., Zhao, K., & Crabtree, G. R. (2017) · Nature Structural & Molecular Biology · doi:10.1038/s41594-017-0007-3 · Cited by 191 · see citing works
Ring Polymers in the Melt State: The Physics of Crumpling
Rosa, A., & Everaers, R. (2014) · Physical Review Letters · doi:10.1103/physrevlett.112.118302 · Cited by 188 · see citing works
The road ahead in genetics and genomics
McGuire, A. L., Gabriel, S., Tishkoff, S. A., Wonkam, A., Chakravarti, A., Furlong, E. E. M., Treutlein, B., Meissner, A., Chang, H. Y., López-Bigas, N., et al. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0272-6 · Cited by 188 · see citing works
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 186 · see citing works
Visualizing transcription factor dynamics in living cells
Liu, Z. J., & Tjian, R. (2018) · The Journal of Cell Biology · doi:10.1083/jcb.201710038 · Cited by 182 · see citing works
High-throughput genome scaffolding from in vivo DNA interaction frequency
Kaplan, N., & Dekker, J. (2013) · Nature Biotechnology · doi:10.1038/nbt.2768 · Cited by 177 · see citing works
Self-citationIn search of the determinants of enhancer–promoter interaction specificity
van Arensbergen, J., van Steensel, B., & Bussemaker, H. J. (2014) · Trends in Cell Biology · doi:10.1016/j.tcb.2014.07.004 · Cited by 172 · see citing works
Smeets, D., Markaki, Y., Schmid, V. J., Kraus, F., Tattermusch, A., Cerase, A., Sterr, M., Fiedler, S., Demmerle, J., Popken, J., et al. (2014) · Epigenetics & Chromatin · doi:10.1186/1756-8935-7-8 · Cited by 177 · see citing works
Ito, J., Sugimoto, R., Nakaoka, H., YAMADA, S., Kimura, T., Hayano, T., & Inoue, I. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006883 · Cited by 179 · see citing works
Machine learning meets omics: applications and perspectives
Li, R., Li, L., Xu, Y., & Yang, J. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab460 · Cited by 180 · see citing works
CTCF-mediated topological boundaries during development foster appropriate gene regulationPreprint
Narendra, V. K., Bulajić, M., Dekker, J., Mazzoni, E. O., & Reinberg, D. (2016) · Genes & Development · doi:10.1101/gad.288324.116 · Cited by 172 · see citing works
Self-citationReprogramming of Meiotic Chromatin Architecture during Spermatogenesis
Wang, Y., Wang, H., Zhang, Y., Du, Z., Si, W., Fan, S., Qin, D., Wang, M., Duan, Y., Li, L., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2018.11.019 · Cited by 164 · see citing works
Analysis methods for studying the 3D architecture of the genome
Ay, F., & Noble, W. S. (2015) · Genome biology · doi:10.1186/s13059-015-0745-7 · Cited by 165 · see citing works
Comparison of Hi-C results using in-solution versus in-nucleus ligation
Nagano, T., Várnai, C., Schoenfelder, S., Javierre, B.-M., Wingett, S. W., & Fraser, P. (2015) · Genome Biology · doi:10.1186/s13059-015-0753-7 · Cited by 166 · see citing works
The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain
Jiang, Y. P., Loh, Y. E., Rajarajan, P., Hirayama, T., Liao, W., Kassim, B. S., Javidfar, B., Hartley, B. J., Kleofas, L., Park, R., et al. (2017) · Nature Genetics · doi:10.1038/ng.3906 · Cited by 162 · see citing works
Vara, C., Paytuví-Gallart, A., Cuartero, Y., Dily, F. L., Garcia, F., Salvà-Castro, J., Gómez-H, L., Julià, E., Moutinho, C., Cigliano, R. A., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.06.037 · Cited by 165 · see citing works
Reorganization of chromosome architecture in replicative cellular senescence
Criscione, S. W., De Cecco, M., Siranosian, B., Zhang, Y., Kreiling, J. A., Sedivy, J. M., & Neretti, N. (2016) · Science Advances · doi:10.1126/sciadv.1500882 · Cited by 164 · see citing works
Cattoni, D. I., Gizzi, A. M. C., Georgieva, M., Stefano, M. D., Valeri, A., Chamousset, D., Houbron, C., Déjardin, S., Fiche, J.-B., González, I., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01962-x · Cited by 165 · see citing works
Nagano, T., Lubling, Y., Yaffe, E., Wingett, S., Dean, W., Tanay, A., & Fraser, P. (2015) · Nature Protocols · doi:10.1038/nprot.2015.127 · Cited by 159 · see citing works
Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells
Freire-Pritchett, P., Schoenfelder, S., Várnai, C., Wingett, S. W., Cairns, J., Collier, A. J., García-Vílchez, R., Furlan-Magaril, M., Osborne, C. S., Fraser, P., et al. (2017) · eLife · doi:10.7554/elife.21926 · Cited by 161 · see citing works
“Over the last decade, chromosome conformation capture (3C) and derived methods have enabled the biochemical mapping of looping interactions to offer new insights into their architecture across different cell types (Dekker et al., 2013; de Laat and Duboule, 2013; Schmitt et al., 2016).”
BackgroundRamos-Rodríguez, M., Raurell‐Vila, H., Colli, M. L., Alvelos, M. I., Subirana-Granés, M., Juan‐Mateu, J., Norris, R., Turatsinze, J., Nakayasu, E. S., Webb‐Robertson, B., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0524-6 · Cited by 155 · see citing works
Microchromosomes are building blocks of bird, reptile, and mammal chromosomes
Waters, P. D., Patel, H. R., Ruiz-Herrera, A., Álvarez-González, L., Lister, N. C., Simakov, O., Ezaz, T., Kaur, P., Frere, C., Grützner, F., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2112494118 · Cited by 153 · see citing works
Potential energy landscapes identify the information-theoretic nature of the epigenome
Jenkinson, G., Pujadas, E., Goutsias, J. I., & Feinberg, A. P. (2017) · Nature Genetics · doi:10.1038/ng.3811 · Cited by 152 · see citing works
Deletions of chromosomal regulatory boundaries are associated with congenital disease
Ibn-Salem, J., Köhler, S., Love, M. I., Chung, H.-R., Huang, N., Hurles, M. E., Haendel, M., Washington, N. L., Smedley, D., Mungall, C. J., et al. (2014) · Genome Biology · doi:10.1186/s13059-014-0423-1 · Cited by 143 · see citing works
Looking beyond the genes: the role of non-coding variants in human disease
Spielmann, M., & Mundlos, S. (2016) · Human Molecular Genetics · doi:10.1093/hmg/ddw205 · Cited by 143 · see citing works
Promoter bivalency favors an open chromatin architecture in embryonic stem cells
Martín, G. M., Blanco, E., Ballaré, C., Sansó, M., Spill, Y. G., Hu, D., Aoi, Y., Dily, F. L., Shilatifard, A., Martı́-Renom, M. A., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0218-5 · Cited by 148 · see citing works
Constructing 3D interaction maps from 1D epigenomes
Zhu, Y., Chen, Z., Zhang, K., Wang, M., Medovoy, D., Whitaker, J. W., Ding, B., Li, N., Zheng, L., & Wang, W. (2016) · Nature Communications · doi:10.1038/ncomms10812 · Cited by 139 · see citing works
Capturing pairwise and multi-way chromosomal conformations using chromosomal walks
Olivares‐Chauvet, P., Mukamel, Z., Lifshitz, A., Schwartzman, O., Elkayam, N. O., Lubling, Y., Deikus, G. Y., Sebra, R., & Tanay, A. (2016) · Nature · doi:10.1038/nature20158 · Cited by 141 · see citing works
Detecting hierarchical genome folding with network modularity
Norton, H. K., Emerson, D. J., Huang, H., Kim, J., Titus, K. R., Gu, S., Bassett, D. S., & Phillips-Cremins, J. E. (2018) · Nature Methods · doi:10.1038/nmeth.4560 · Cited by 146 · see citing works
- Authors
- Dekker, J., Marti-Renom, M. A., & Mirny, L. A.
- Affiliations
- University of Massachusetts Chan Medical School (US)
- Massachusetts Institute of Technology (US)
- Corresponding author
- Dekker, Job
- Venue
- Nature Reviews Genetics
- Published
- 2013-05-09
- Volume
- 14
- Issue
- 6
- Pages
- 390-403
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- PMC
- PMC3874835
- OpenAlex
- W1574083126
- Cited by
- 1,068
- References
- 113
- Citations by year
- 2026: 24 · 2025: 38 · 2024: 65 · 2023: 50 · 2022: 73 · 2021: 79 · 2020: 75 · 2019: 81 · 2018: 107 · 2017: 122 · 2016: 122 · 2015: 121 · 2014: 80 · 2013: 30
- FWCI
- 11.08
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Nature Reviews Genetics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- The Journal of the American Medical Association (JAMA) Network (American Medical Association) (submittedVersion)
- PMC
- Funders
- W. M. Keck Foundation
- European Commission (282510)
- Ministerio de Ciencia e Innovación (BFU2010-19310)
- National Institutes of Health (HG003143)
- National Human Genome Research Institute (HG003143, HG003143-06S1, R01HG003143)
- National Cancer Institute (U54CA143874)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- 3D genome organization, chromatin interactions, chromosome conformation capture, Hi-C, 4Cs, 5C, nuclear organization, gene expression regulation, chromatin accessibility
- MeSH terms
- Animals, Chromatin, Chromosome Mapping, Chromosomes, Human, Epistasis, Genetic, Humans, Models, Genetic, Nucleic Acid Conformation, Genome, Human
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