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Functional implications of genome topology
Open accessAbstract
Although genomes are defined by their sequence, the linear arrangement of nucleotides is only their most basic feature. A fundamental property of genomes is their topological organization in three-dimensional space in the intact cell nucleus. The application of imaging methods and genome-wide biochemical approaches, combined with functional data, is revealing the precise nature of genome topology and its regulatory functions in gene expression and genome maintenance. The emerging picture is one of extensive self-enforcing feedback between activity and spatial organization of the genome, suggestive of a self-organizing and self-perpetuating system that uses epigenetic dynamics to regulate genome function in response to regulatory cues and to propagate cell-fate memory.
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“The proper topological structure of chromatin is essential in gene expression and genome maintenance (55).”
From Epigenetic Modifications in Stress Response Genes Associated With Childhood Trauma (2019) · cites this paper as [55]
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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
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
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129
The Role of Chromatin during Transcription
Li, B., Carey, M., & Workman, J. L. (2007) · Cell · doi:10.1016/j.cell.2007.01.015 · Cited by 3,503
Mapping and analysis of chromatin state dynamics in nine human cell types
Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature · doi:10.1038/nature09906 · Cited by 2,898
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
The 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
Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions
Guelen, L., Pagie, L., Brasset, É., Meuleman, W. R. A., Faza, M. B., Talhout, W., Eussen, B. H. J., de Klein, A., Wessels, L. F. A., de Laat, W. L., et al. (2008) · Nature · doi:10.1038/nature06947 · Cited by 2,042
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
Wang, K., Yang, Y. W., Liu, B., Sanyal, A., Corces, M. R., Chen, Y., Lajoie, B. R., Protacio, A., Flynn, R. A., Gupta, R. A., et al. (2011) · Nature · doi:10.1038/nature09819 · Cited by 2,005
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
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Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes
Dowen, J. M., Fan, Z. P., Hnisz, D., Ren, G., Abraham, B. J., Zhang, L. N., Weintraub, A. S., Schuijers, J., Lee, T. I., Zhao, K., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.030 · Cited by 884
Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus
Quinodoz, S. A., Ollikainen, N., Tabak, B., Palla, A., Schmidt, J. M., Detmar, E., Lai, M. M., Shishkin, A. A., Bhat, P., Takei, Y., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.024 · Cited by 892
Epigenetic regulation of ageing: linking environmental inputs to genomic stability
Benayoun, B. A., Pollina, E. A., & Brunet, A. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm4048 · Cited by 610
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
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
Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control
Hnisz, D., Day, D. S., & Young, R. A. (2016) · Cell · doi:10.1016/j.cell.2016.10.024 · Cited by 420
The Role of Chromosome Domains in Shaping the Functional Genome
Sexton, T., & Cavalli, G. (2015) · Cell · doi:10.1016/j.cell.2015.02.040 · Cited by 427
Self-citationAriel, F., Jégu, T., Latrasse, D., Romero-Barrios, N., Christ, A., Benhamed, M., & Crespi, M. D. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.06.011 · Cited by 404
Stadhouders, R., Vidal, E., Serra, F., Stefano, B. D., Dily, F. L., Quilez, J., Gómez, A., Collombet, S., Berenguer, C., Cuartero, Y., et al. (2018) · Nature Genetics · doi:10.1038/s41588-017-0030-7 · Cited by 362
Nuclear architecture dictates HIV-1 integration site selection
Marini, B., Kertész‐Farkas, A., Ali, H., Lucic, B., Lisek, K., Manganaro, L., Pongor, S., Luzzati, R., Recchia, A., Mavilio, F., et al. (2015) · Nature · doi:10.1038/nature14226 · Cited by 360
Long noncoding RNAs: an emerging link between gene regulation and nuclear organization
Quinodoz, S. A., & Guttman, M. (2014) · Trends in Cell Biology · doi:10.1016/j.tcb.2014.08.009 · Cited by 327
Comparison of computational methods for Hi-C data analysis
Forcato, M., Nicoletti, C., Pal, K., Livi, C. M., Ferrari, F., & Bicciato, S. (2017) · Nature Methods · doi:10.1038/nmeth.4325 · Cited by 314
Erdel, F., Rademacher, A., Vlijm, R., Tünnermann, J., Frank, L., Weinmann, R., Schweigert, E., Yserentant, K., Hummert, J., Bauer, C., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.02.005 · Cited by 292
Epigenetic Modifications in Stress Response Genes Associated With Childhood Trauma
Jiang, S., Postovit, L., Cattaneo, A., Binder, E. B., & Aitchison, K. J. (2019) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2019.00808 · Cited by 288
“The proper topological structure of chromatin is essential in gene expression and genome maintenance (55).”
BackgroundLong Non-Coding RNAs and their Biological Roles in Plants
Liu, X., Hao, L., Li, D., Zhu, L., & Hu, S. (2015) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2015.02.003 · Cited by 268
Long-Range Chromatin Interactions
Dekker, J., & Misteli, T. (2015) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a019356 · Cited by 255
Self-citationThe role of transcription in shaping the spatial organization of the genome
van Steensel, B., & Furlong, E. E. M. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0114-6 · Cited by 247
Battles and hijacks: noncoding transcription in plants
Ariel, F., Romero-Barrios, N., Jégu, T., Benhamed, M., & Crespi, M. D. (2015) · Trends in Plant Science · doi:10.1016/j.tplants.2015.03.003 · Cited by 238
Gene Insertion Into Genomic Safe Harbors for Human Gene Therapy
Papapetrou, E. P., & Schambach, A. (2016) · Molecular Therapy · doi:10.1038/mt.2016.38 · Cited by 238
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 232
Identification of alternative topological domains in chromatin
Filippova, D., Patro, R., Duggal, G., & Kingsford, C. (2014) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-9-14 · Cited by 224
Replication timing and transcriptional control: beyond cause and effect — part III
Rivera‐Mulia, J. C., & Gilbert, D. M. (2016) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2016.03.022 · Cited by 214
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 222
How retrotransposons shape genome regulation
Mita, P., & Boeke, J. D. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.01.001 · Cited by 217
McArthur, E., & Capra, J. A. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.01.001 · Cited by 207
Chromatin topology is coupled to Polycomb group protein subnuclear organization
Wani, A. H., Boettiger, A. N., Schorderet, P., Ergün, A., Munger, C., Sadreyev, R. I., Zhuang, X., Kingston, R. E., & Francis, N. J. (2016) · Nature Communications · doi:10.1038/ncomms10291 · Cited by 191
Cytoskeletal Control of Nuclear Morphology and Chromatin Organization
Ramdas, N. M., & Shivashankar, G. V. (2014) · Journal of Molecular Biology · doi:10.1016/j.jmb.2014.09.008 · Cited by 200
Brackley, C. A., Johnson, J., Kelly, S. L., Cook, P. R., & Marenduzzo, D. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw135 · Cited by 185
Mechanobiology of Tumor Growth
Chaudhuri, P. K., Low, B. C., & Lim, C. T. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00042 · Cited by 200
Chromosome conformation capture technologies and their impact in understanding genome function
Sati, S., & Cavalli, G. (2016) · Chromosoma · doi:10.1007/s00412-016-0593-6 · Cited by 195
Self-citationClustering of Tissue-Specific Sub-TADs Accompanies the Regulation of HoxA Genes in Developing Limbs
Berlivet, S., Paquette, D., Dumouchel, A., Langlais, D., Dostie, J., & Kmita, M. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1004018 · Cited by 170
Espinola, S. M., Götz, M., Bellec, M., Messina, O., Fiche, J.-B., Houbron, C., Dejean, M., Reim, I., Cardozo Gizzi, A. M., Lagha, M., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00816-z · Cited by 174
Wang, K., & Chang, H. Y. (2018) · Circulation Research · doi:10.1161/circresaha.118.310998 · Cited by 180
Nucleoporin-mediated regulation of cell identity genesPreprint
Ibarra, A., Benner, C. W., Tyagi, S., Cool, J., & Hetzer, M. W. (2016) · Genes & Development · doi:10.1101/gad.287417.116 · Cited by 163
Epigenetic regulation: A new frontier for biomedical engineers
Chen, Z., Li, S., Subramaniam, S., Shyy, J. Y.-J., & Chien, S. (2017) · Annual Review of Biomedical Engineering · doi:10.1146/annurev-bioeng-071516-044720 · Cited by 163
Identification of hierarchical chromatin domains
Weinreb, C., & Raphael, B. J. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv485 · Cited by 159
Cajal bodies are linked to genome conformation
Wang, Q., Sawyer, I. A., Sung, M.-H., Sturgill, D., Shevtsov, S. P., Pegoraro, G., Hakim, O., Baek, S., Hager, G. L., & Dundr, M. (2016) · Nature Communications · doi:10.1038/ncomms10966 · Cited by 164
Nuclear landscape of HIV-1 infection and integration
Lušić, M., & Siliciano, R. F. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.162 · Cited by 168
Fu, Y., Rocha, P. P., Luo, V. M., Raviram, R., Deng, Y., Mazzoni, E. O., & Skok, J. A. (2016) · Nature Communications · doi:10.1038/ncomms11707 · Cited by 148
Bunting, K. L., Soong, T. D., Singh, R., Jiang, Y., Béguelin, W., Poloway, D. W., Swed, B. L., Hatzi, K., Reisacher, W., Teater, M., et al. (2016) · Immunity · doi:10.1016/j.immuni.2016.08.012 · Cited by 141
Amaral, P., Leonardi, T., Han, N., Viré, E. A., Gascoigne, D. K., Arias‐Carrasco, R., Büscher, M., Pandolfini, L., Zhang, A., Pluchino, S., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1405-5 · Cited by 136
Pascual‐García, P., Debo, B. M., Aleman, J. R., Talamas, J. A., Lan, Y., Nguyen, N., Won, K., & Capelson, M. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.02.020 · Cited by 130
Cycles in spatial and temporal chromosomal organization driven by the circadian clock
Aguilar‐Arnal, L., Hakim, O., Patel, V. R., Baldi, P., Hager, G. L., & Sassone‐Corsi, P. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2667 · Cited by 128
Gros, M. A. L., Clowney, E. J., Magklara, A., Yen, A., Markenscoff-Papadimitriou, E., Colquitt, B. M., Myllys, M., Kellis, M., Lomvardas, S., & Larabell, C. A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.10.060 · Cited by 125
Quantifying Genome-Editing Outcomes at Endogenous Loci with SMRT Sequencing
Hendel, A., Kildebeck, E., Fine, E. J., Clark, J. T., Punjya, N., Sebastiano, V., Bao, G., & Porteus, M. H. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.02.040 · Cited by 124
Protein Modeling: What Happened to the “Protein Structure Gap”?
Schwede, T. F. (2013) · Structure · doi:10.1016/j.str.2013.08.007 · Cited by 128
Li, W.-C., Huang, C., Chen, C., Chuang, Y.-C., Tung, S., & Wang, T. (2017) · Biotechnology for Biofuels · doi:10.1186/s13068-017-0825-x · Cited by 117
Nongenetic functions of the genome
Bustin, M., & Misteli, T. (2016) · Science · doi:10.1126/science.aad6933 · Cited by 119
Self-citationIn the loop: promoter–enhancer interactions and bioinformatics
Mora, A., Sandve, G. K., Gabrielsen, O. S., & Eskeland, R. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv097 · Cited by 126
Jégu, T., Latrasse, D., Delarue, M., Hirt, H., Domenichini, S., Ariel, F., Crespi, M. D., Bergounioux, C., Raynaud, C., & Benhamed, M. (2014) · The Plant Cell · doi:10.1105/tpc.113.114454 · Cited by 119
Orientation and repositioning of chromosomes correlate with cell geometry–dependent gene expression
Wang, Y., Nagarajan, M., Uhler, C., & Shivashankar, G. V. (2017) · Molecular Biology of the Cell · doi:10.1091/mbc.e16-12-0825 · Cited by 117
Kidiyoor, G. R., Li, Q., Bastianello, G., Bruhn, C., Giovannetti, I., Adhil, M., Beznoussenko, G. V., Mironov, A., Raab, M., Piel, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18580-9 · Cited by 111
Polycomb silencing: from linear chromatin domains to 3D chromosome folding
Cheutin, T., & Cavalli, G. (2014) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2013.11.016 · Cited by 102
Self-citationFunctional organization of the human 4D Nucleome
Chen, H., Chen, J., Muir, L. A., Ronquist, S., Meixner, W., Ljungman, M. E., Ried, T., Smale, S. T., & Rajapakse, I. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1505822112 · Cited by 105
Regulation of Cohesin-Mediated Chromosome Folding by Eco1 and Other Partners
Dauban, L., Montagne, R., Thierry, A., Lazar‐Stefanita, L., Bastié, N., Gadal, O., Cournac, A., Koszul, R., & Beckouët, F. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.01.019 · Cited by 116
Jost, D., & Vaillant, C. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky009 · Cited by 84
Fractal dimension of chromatin: potential molecular diagnostic applications for cancer prognosis
Metze, K. (2013) · Expert Review of Molecular Diagnostics · doi:10.1586/14737159.2013.828889 · Cited by 97
Hi-C analysis: from data generation to integration
Pal, K., Forcato, M., & Ferrari, F. (2018) · Biophysical Reviews · doi:10.1007/s12551-018-0489-1 · Cited by 102
Chromosome territories and the global regulation of the genome
Fritz, A. J., Sehgal, N., Pliss, A., Xu, J., & Berezney, R. (2019) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22732 · Cited by 102
Integrating ChIP-seq with other functional genomics data
Jiang, S., & Mortazavi, A. (2018) · Briefings in Functional Genomics · doi:10.1093/bfgp/ely002 · Cited by 96
Cajal body function in genome organization and transcriptome diversity
Sawyer, I. A., Sturgill, D. M., Sung, M., Hager, G. L., & Dundr, M. (2016) · BioEssays · doi:10.1002/bies.201600144 · Cited by 87
Imaging Specific Genomic DNA in Living Cells
Chen, B., Guan, J., & Huang, B. (2016) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-062215-010830 · Cited by 77
Joyce, E. F., Apostolopoulos, N., Beliveau, B. J., & Wu, C.-T. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1004013 · Cited by 78
Understanding the 3D genome: Emerging impacts on human disease
Krumm, A., & Duan, Z. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.07.004 · Cited by 76
Cau, P., Navarro, C. L., Harhouri, K., Roll, P., Sigaudy, S., Kaspi, É., Perrin, S., Sandre‐Giovannoli, A. D., & Lévy, N. (2014) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2014.03.021 · Cited by 80
Computational Models of Large-Scale Genome Architecture
Rosa, A., & Zimmer, C. (2014) · International review of cytology · doi:10.1016/b978-0-12-800046-5.00009-6 · Cited by 78
Three-Dimensional Genome Organization and Function in Drosophila
Schwartz, Y. B., & Cavalli, G. (2017) · Genetics · doi:10.1534/genetics.115.185132 · Cited by 77
Self-citationArbona, J., Herbert, S., Fabre, E., & Zimmer, C. (2017) · Genome biology · doi:10.1186/s13059-017-1199-x · Cited by 78
Put your 3D glasses on: plant chromatin is on show
Rodriguez‐Granados, N. Y., Ramirez-Prado, J. S., Veluchamy, A., Latrasse, D., Raynaud, C., Crespi, M. D., Ariel, F., & Benhamed, M. (2016) · Journal of Experimental Botany · doi:10.1093/jxb/erw168 · Cited by 73
Shaping epigenetic memory via genomic bookmarking
Michieletto, D., Chiang, M., Colì, D., Papantonis, A., Orlandini, E., Cook, P. R., & Marenduzzo, D. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1200 · Cited by 72
Hormone-control regions mediate steroid receptor–dependent genome organizationPreprint
Dily, F. L., Vidal, E., Cuartero, Y., Quilez, J., Nacht, A. S., Vicent, G. P., Carbonell‐Caballero, J., Sharma, P., Villanueva‐Cañas, J. L., Ferrari, R., et al. (2018) · Genome Research · doi:10.1101/gr.243824.118 · Cited by 70
Wang, X. Q. D., & Dostie, J. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw966 · Cited by 68
Signaling by Steroid Hormones in the 3D Nuclear Space
Dily, F. L., & Beato, M. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19020306 · Cited by 76
Causes and consequences of nuclear gene positioning
Shachar, S., & Misteli, T. (2017) · Journal of Cell Science · doi:10.1242/jcs.199786 · Cited by 66
Self-citationGene Regulation in and out of Equilibrium
Wong, F. J., & Gunawardena, J. (2020) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-121219-081542 · Cited by 68
The interdependence of gene-regulatory elements and the 3D genome
Vermunt, M. W., Zhang, D., & Blobel, G. A. (2018) · The Journal of Cell Biology · doi:10.1083/jcb.201809040 · Cited by 72
The lncRNA MARS modulates the epigenetic reprogramming of the marneral cluster in response to ABA
Roulé, T., Christ, A., Hussain, N., Huang, Y., Hartmann, C., Benhamed, M., Gutierrez‐Marcos, J., Ariel, F., Crespi, M. D., & Blein, T. (2022) · Molecular Plant · doi:10.1016/j.molp.2022.02.007 · Cited by 65
Tark‐Dame, M., Jerabek, H., Manders, E. M. M., Heermann, D. W., & DRIEL, R. V. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003877 · Cited by 60
Determining chromatin architecture with Micro Capture-C
Hamley, J. C., Li, H., Denny, N., Downes, D. J., & Davies, J. O. J. (2023) · Nature Protocols · doi:10.1038/s41596-023-00817-8 · Cited by 62
The 10-nm chromatin fiber and its relationship to interphase chromosome organization
Hansen, J. C., Connolly, M., McDonald, C. J., Pan, A., Pryamkova, A., Ray, K. P., Seidel, E., Tamura, S., Rogge, R. A., & Maeshima, K. (2017) · Biochemical Society Transactions · doi:10.1042/bst20170101 · Cited by 66
Metze, K., Adam, R. L., & Florindo, J. B. (2019) · Expert Review of Molecular Diagnostics · doi:10.1080/14737159.2019.1597707 · Cited by 62
Spectral identification of topological domains
Chen, J., Hero, A. O., & Rajapakse, I. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw221 · Cited by 59
A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions
Paulsen, J., Rødland, E. A., Holden, L., Holden, M., & Hovig, E. J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku738 · Cited by 61
Huang, W.-C., Ferris, E., Cheng, T., Hörndli, C. S., Gleason, K., Tamminga, C. A., Wagner, J. D., Boucher, K. M., Christian, J. L., & Gregg, C. J. (2017) · Neuron · doi:10.1016/j.neuron.2017.01.033 · Cited by 59
Shaping epigenetic memory via genomic bookmarking
Michieletto, D., Chiang, M., Colì, D., Papantonis, A., Orlandini, E., Cook, P. R., & Marenduzzo, D. (2018) · Kölner Universitäts PublikationsServer (Universität zu Köln) · Cited by 59
Novo, C. L., Tang, C., Ahmed, K., Djuric, U., Fussner, E., Mullin, N. P., Morgan, N. P., Hayre, J. K., Sienerth, A. R., Elderkin, S., et al. (2016) · Genes & Development · doi:10.1101/gad.275685.115 · Cited by 64
Macromolecular Topology Engineering
Qu, Z., Cheng, S. Z. D., & Zhang, W. (2021) · Trends in Chemistry · doi:10.1016/j.trechm.2021.02.002 · Cited by 60
Nuclear pores as versatile platforms for gene regulation
Pascual‐García, P., & Capelson, M. (2014) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2013.12.009 · Cited by 55
Laporte, D., Courtout, F., Tollis, S., & Sagot, I. (2016) · Molecular Biology of the Cell · doi:10.1091/mbc.e16-01-0069 · Cited by 55
Chromatin structure in double strand break repair
Gospodinov, A. G., & Herceg, Z. (2013) · DNA repair · doi:10.1016/j.dnarep.2013.07.006 · Cited by 56
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Woringer, M., Darzacq, X., & Izeddin, I. (2014) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2014.05.009 · Cited by 53
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Metadata
- Authors
- Cavalli, G., & Misteli, T.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- National Institutes of Health (US)
- Corresponding author
- Cavalli, Giacomo
- Misteli, Tom
- Venue
- Nature Structural & Molecular Biology
- Published
- 2013-03
- Volume
- 20
- Issue
- 3
- Pages
- 290-299
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- PMC
- PMC6320674
- OpenAlex
- W2036663020
- Cited by
- 415
- References
- 136
- Citations by year
- 2026: 13 · 2025: 10 · 2024: 18 · 2023: 11 · 2022: 22 · 2021: 30 · 2020: 26 · 2019: 32 · 2018: 37 · 2017: 37 · 2016: 58 · 2015: 53 · 2014: 47 · 2013: 21
- FWCI
- 5.61
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion)
- Funders
- National Institutes of Health
- National Cancer Institute (ZIABC010309)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- genome topology, 3D genome organization, nuclear organization, gene expression regulation, genome maintenance, epigenetic dynamics, self-organization, chromatin organization
- MeSH terms
- Cell Nucleus, Chromatin, DNA Repair, DNA Replication, Gene Expression Regulation, Models, Molecular, Transcription, Genetic, Genome, Epigenesis, Genetic
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