Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus
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Abstract
Eukaryotic genomes are packaged into a 3-dimensional structure in the nucleus. Current methods for studying genome-wide structure are based on proximity ligation. However, this approach can fail to detect known structures, such as interactions with nuclear bodies, because these DNA regions can be too far apart to directly ligate. Accordingly, our overall understanding of genome organization remains incomplete. Here, we develop split-pool recognition of interactions by tag extension (SPRITE), a method that enables genome-wide detection of higher-order interactions within the nucleus. Using SPRITE, we recapitulate known structures identified by proximity ligation and identify additional interactions occurring across larger distances, including two hubs of inter-chromosomal interactions that are arranged around the nucleolus and nuclear speckles. We show that a substantial fraction of the genome exhibits preferential organization relative to these nuclear bodies. Our results generate a global model whereby nuclear bodies act as inter-chromosomal hubs that shape the overall packaging of DNA in the nucleus.
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Both GAM and SPRITE could successfully reveal multi-way contacts across TADs and chromosomes, but their resolution currently limits robust detection of individual CRUs.
“While both methods could successfully reveal multi-way contacts across TADs and chromosomes, their resolution currently limits robust detection of individual CRUs.”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [403]
The Results section reports that SPRITE measures simultaneous contacts among multiple DNA molecules and that larger clusters show interactions between distinct TADs; the Key Resources Table also identifies TAD triplets detected by GAM. But our copy does not say that the resolution of either method limits robust detection of individual CRUs. No page numbers are available in the indexed passages. (LLM, conf=0.85)
Experimental — accuracy not yet measuredProximity ligation methods have played an important role in identifying key interactions, such as promoter and enhancer associations.
“In the last decade, proximity ligation methods have played an important role in identifying these key interactions, such as promoter and enhancer associations (Kempfer and Pombo, 2020; Oudelaar et al., 2018; Quinodoz et al., 2018).”
From Unraveling Hematopoiesis through the Lens of Genomics (2020) · cites this paper as Quinodoz et al., 2018
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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
Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.035 · Cited by 4,143 · 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
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
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
Chromatin architecture reorganization during stem cell differentiation
Dixon, J. R., Jung, I., Selvaraj, S., Shen, Y., Antosiewicz-Bourget, J. E., Lee, A. Y., Ye, Z., Kim, A., Rajagopal, N., Xie, W., et al. (2015) · Nature · doi:10.1038/nature14222 · Cited by 1,646 · see citing works
Boisvert, F., van Koningsbruggen, S., Navascués, J., & Lamond, A. (2007) · Nature reviews. Molecular cell biology · doi:10.1038/nrm2184 · Cited by 1,581 · see citing works
Architectural protein subclasses shape 3D organization of genomes during lineage commitment
Phillips-Cremins, J. E., Sauria, M. E. G., Sanyal, A., Gerasimova, T. I., Lajoie, B. R., Bell, J. S. K., Ong, C.-T., Hookway, T. A., Guo, C., Sun, Y., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.053 · Cited by 1,187 · see citing works
The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3
McHugh, C. A., Chen, C., Chow, A. Y., Surka, C., Tran, C., McDonel, P. E., Pandya‐Jones, A., Blanco, M. R., Burghard, C. P., Moradian, A., et al. (2015) · Nature · doi:10.1038/nature14443 · Cited by 1,163 · see citing works
Lichter, P., Cremer, T., Borden, J., Manuelidis, L., & Ward, D. C. (1988) · Human Genetics · doi:10.1007/bf01790090 · Cited by 1,160 · see citing works
Charting histone modifications and the functional organization of mammalian genomes
Zhou, V. W., Goren, A., & Bernstein, B. E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2905 · Cited by 1,147 · see citing works
HiChIP: efficient and sensitive analysis of protein-directed genome architecture
Mumbach, M. R., Rubin, A. J., Flynn, R. A., Dai, C., Khavari, P. A., Greenleaf, W. J., & Chang, H. Y. (2016) · Nature Methods · doi:10.1038/nmeth.3999 · Cited by 1,139 · see citing works
Chromosome TerritoriesPreprint
Cremer, T. J., & Cremer, M. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a003889 · Cited by 1,115 · see citing works
Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation
Peric-Hupkes, D., Meuleman, W., Pagie, L., Bruggeman, S. W. M., Solovei, I., Brugman, W., Gräf, S., Flicek, P., Kerkhoven, R. M., van Lohuizen, M., et al. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.03.016 · Cited by 1,050 · see citing works
Hutchinson, J. N., Ensminger, A. W., Clemson, C., Lynch, C. R., Lawrence, J. B., & Chess, A. J. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-39 · Cited by 997 · 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
Super-resolution imaging reveals distinct chromatin folding for different epigenetic states
Boettiger, A. N., Bintu, B., Moffitt, J. R., Wang, S. S., Beliveau, B. J., Fudenberg, G., Imakaev, M., Mirny, L. A., Wu, C.-T., & Zhuang, X. (2016) · Nature · doi:10.1038/nature16496 · Cited by 877 · see citing works
Nuclear SpecklesPreprint
Spector, D. L., & Lamond, A. I. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000646 · Cited by 842 · see citing works
P-Bodies and Stress Granules: Possible Roles in the Control of Translation and mRNA DegradationPreprint
Decker, C. J., & Parker, R. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a012286 · Cited by 806 · see citing works
A long nuclear‐retained non‐coding RNA regulates synaptogenesis by modulating gene expression
Bernard, D., Prasanth, K. V., Tripathi, V., Colasse, S., Nakamura, T., Xuan, Z., Zhang, M. Q., Sedel, F., Jourdren, L., Coulpier, F., et al. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.199 · Cited by 738 · 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
Interchromosomal associations between alternatively expressed loci
Spilianakis, C. G., Lalioti, M. D., Town, T., Lee, G. R., & Flavell, R. A. (2005) · Nature · doi:10.1038/nature03574 · Cited by 726 · see citing works
Complex multi-enhancer contacts captured by genome architecture mapping
Beagrie, R. A., Scialdone, A., Schueler, M., Kraemer, D. C. A., Chotalia, M., Xie, S. Q., Barbieri, M., de Santiago, I., Lavitas, L.-M., Branco, M. R., et al. (2017) · Nature · doi:10.1038/nature21411 · Cited by 715 · see citing works
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
Branco, M. R., & Pombo, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040138 · Cited by 685 · see citing works
RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)
Siegfried, N. A., Busan, S., Rice, G. M., Nelson, J. A. E., & Weeks, K. M. (2014) · Nature Methods · doi:10.1038/nmeth.3029 · Cited by 662 · 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
Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre
Hacisuleyman, E., Goff, L. A., Trapnell, C., Williams, A., Henao‐Mejia, J., Sun, L., McClanahan, P. D., Hendrickson, D. G., Sauvageau, M., Kelley, D. R., et al. (2014) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2764 · Cited by 624 · see citing works
Spatial organization of chromatin domains and compartments in single chromosomes
Wang, S., Su, J.-H., Beliveau, B. J., Bintu, B., Moffitt, J. R., Wu, C.-T., & Zhuang, X. (2016) · Science · doi:10.1126/science.aaf8084 · Cited by 600 · see citing works
Jonkers, I., Kwak, H., & Lis, J. T. (2014) · eLife · doi:10.7554/elife.02407 · Cited by 581 · 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
PML Nuclear BodiesPreprint
Lallemand-Breitenbach, V., & de Thé, H. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000661 · Cited by 561 · see citing works
Massively multiplex single-cell Hi-C
Ramani, V., Deng, X., Qiu, R., Gunderson, K. L., Steemers, F. J., Distèche, C. M., Noble, W. S., Duan, Z., & Shendure, J. (2017) · Nature Methods · doi:10.1038/nmeth.4155 · Cited by 532 · see citing works
Engreitz, J., Sirokman, K., McDonel, P. E., Shishkin, A. A., Surka, C., Russell, P. H., Grossman, S. R., Chow, A. Y., Guttman, M., & Lander, E. S. (2014) · Cell · doi:10.1016/j.cell.2014.08.018 · Cited by 500 · see citing works
Meuleman, W., Peric-Hupkes, D., Kind, J., Beaudry, J.-B., Pagie, L., Kellis, M., Reinders, M., Wessels, L., & van Steensel, B. (2013) · Genome Research · doi:10.1101/gr.141028.112 · Cited by 462 · see citing works
The Human and Mouse Replication-Dependent Histone Genes
Marzluff, W. F., Gongidi, P., Woods, K., Jin, J., & Maltais, L. J. (2002) · Genomics · doi:10.1006/geno.2002.6850 · Cited by 461 · see citing works
Pederson, T. (2011) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000638 · Cited by 455 · see citing works
CTCF Mediates Interchromosomal Colocalization Between Igf2/H19 and Wsb1/Nf1
Ling, J. Q., Li, T., Hu, J., Vu, T. H., Chen, H. L., Qiu, X. W., Cherry, A. M., & Hoffman, A. R. (2006) · Science · doi:10.1126/science.1123191 · Cited by 434 · see citing works
Functional implications of genome topology
Cavalli, G., & Misteli, T. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2474 · Cited by 415 · see citing works
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 400 · 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
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
Meaburn, K. J., & Misteli, T. (2007) · Nature · doi:10.1038/445379a · Cited by 367 · see citing works
Golgi Bypass: Skirting Around the Heart of Classical SecretionPreprint
Grieve, A. G., & Rabouille, C. (2011) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a005298 · Cited by 359 · see citing works
Highly multiplexed simultaneous detection of RNAs and proteins in single cells
Frei, A. P., Bava, F.-A., Zunder, E. R., Hsieh, E. W. Y., Chen, S.-Y., Nolan, G. P., & Gherardini, P. F. (2016) · Nature Methods · doi:10.1038/nmeth.3742 · Cited by 330 · see citing works
RNA Polymerase II Targets Pre-mRNA Splicing Factors to Transcription Sites In Vivo
Misteli, T., & Spector, D. L. (1999) · Molecular Cell · doi:10.1016/s1097-2765(01)80002-2 · Cited by 326 · see citing works
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 316 · see citing works
IP3 Receptors: Toward Understanding Their ActivationPreprint
Taylor, C. W., & Tovey, S. C. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a004010 · Cited by 301 · see citing works
Mahy, N. L., Perry, P. E., & Bickmore, W. A. (2002) · The Journal of Cell Biology · doi:10.1083/jcb.200207115 · Cited by 295 · see citing works
Blecher-Gonen, R., Barnett-Itzhaki, Z., Jaitin, D., Amann-Zalcenstein, D., Lara-Astiaso, D., & Amit, I. (2013) · Nature Protocols · doi:10.1038/nprot.2013.023 · Cited by 289 · see citing works
Simultaneous generation of many RNA-seq libraries in a single reaction
Shishkin, A. A., Giannoukos, G., Küçükural, A., Ciulla, D., Busby, M., Surka, C., Chen, J., Bhattacharyya, R. P., Rudy, R. F., Patel, M. M., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3313 · Cited by 282 · see citing works
The DNA sequence and analysis of human chromosome 6
Mungall, A. J. J., Palmer, S., Sims, S. K., Edwards, C. A., Ashurst, J. L., Wilming, L. G., Jones, M. C., Horton, R., Hunt, S. E., Scott, C., et al. (2003) · Nature · doi:10.1038/nature02055 · Cited by 281 · 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
The Cajal Body and Histone Locus BodyPreprint
Nizami, Z. F., Deryusheva, S., & Gall, J. G. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000653 · Cited by 276 · see citing works
Deletion of <i>DXZ4</i> on the human inactive X chromosome alters higher-order genome architecture
Darrow, E. M., Huntley, M. H., Dudchenko, O., Stamenova, E. K., Durand, N. C., Sun, Z., Huang, S.-C., Sanborn, A. L., Machol, I., Shamim, M., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1609643113 · Cited by 276 · see citing works
Biogenesis of Nuclear BodiesPreprint
Dundr, M., & Misteli, T. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000711 · Cited by 274 · see citing works
Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing
Chen, C., Blanco, M. R., Jackson, C., Aznauryan, E. I., Ollikainen, N., Surka, C., Chow, A. Y., Cerase, A., McDonel, P. E., & Guttman, M. (2016) · Science · doi:10.1126/science.aae0047 · Cited by 262 · see citing works
Nucleolar organizer regions: genomic ‘dark matter’ requiring illuminationPreprint
McStay, B. (2016) · Genes & Development · doi:10.1101/gad.283838.116 · Cited by 256 · see citing works
Miyagawa, R., Tano, K., Mizuno, R., Nakamura, Y., Ijiri, K., Rakwal, R., Shibato, J., Masuo, Y., Mayeda, A., Hirose, T., et al. (2012) · RNA · doi:10.1261/rna.028639.111 · Cited by 237 · see citing works
Williamson, I., Berlivet, S., Eskeland, R., Boyle, S., Illingworth, R. S., Paquette, D., Dostie, J., & Bickmore, W. A. (2014) · Genes & Development · doi:10.1101/gad.251694.114 · Cited by 229 · 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
Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains
Shopland, L. S., Johnson, C. V., Byron, M., McNeil, J. A., & Lawrence, J. B. (2003) · The Journal of Cell Biology · doi:10.1083/jcb.200303131 · Cited by 209 · see citing works
Genome organization in and around the nucleolus
Németh, A., & Längst, G. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.01.002 · Cited by 208 · see citing works
Concerted copy number variation balances ribosomal DNA dosage in human and mouse genomes
Gibbons, J. G., Branco, A. T., Godinho, S. A., Yu, S., & Lemos, B. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1416878112 · Cited by 198 · see citing works
Erratum: Organization and function of the 3D genome
Bonev, B., & Cavalli, G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.147 · Cited by 184 · see citing works
Cajal bodies and coilin—moving towards function
Ogg, S. C., & Lamond, A. I. (2002) · The Journal of Cell Biology · doi:10.1083/jcb.200206111 · Cited by 182 · see citing works
Nucleolus and nuclear periphery: Velcro for heterochromatin
Padeken, J., & Heun, P. (2014) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2014.03.001 · Cited by 179 · see citing works
Population-based 3D genome structure analysis reveals driving forces in spatial genome organization
Tjong, H., Li, W., Kalhor, R., Dai, C., Hao, S., Gong, K. Q., Zhou, Y., Li, H., Zhou, X. J., Gros, M. A. L., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1512577113 · Cited by 177 · see citing works
Kruhlak, M. J., Lever, M. A., Fischle, W., Verdin, E. M., Bazett‐Jones, D. P., & Hendzel, M. J. (2000) · The Journal of Cell Biology · doi:10.1083/jcb.150.1.41 · Cited by 174 · see citing works
HSP70 Transgene Directed Motion to Nuclear Speckles Facilitates Heat Shock Activation
Khanna, N., Hu, Y., & Belmont, A. S. (2014) · Current Biology · doi:10.1016/j.cub.2014.03.053 · Cited by 170 · see citing works
Chromosome crosstalk in three dimensions
Göndör, A., & OHLSSON, R. I. (2009) · Nature · doi:10.1038/nature08453 · Cited by 151 · see citing works
U1 and U2 small nuclear RNAs are present in nuclear speckles.
Huang, S., & Spector, D. L. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.1.305 · Cited by 149 · see citing works
“Cat’s Cradling” the 3D Genome by the Act of LncRNA Transcription
Melé, M., & Rinn, J. L. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.011 · Cited by 143 · 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
FISH-ing for captured contacts: towards reconciling FISH and 3C
Fudenberg, G., & Imakaev, M. (2017) · Nature Methods · doi:10.1038/nmeth.4329 · Cited by 141 · see citing works
Immuno-PCR: An ultrasensitive immunoassay for biomolecular detection
Chang, L., Li, J., & Wang, L. (2016) · Analytica Chimica Acta · doi:10.1016/j.aca.2015.12.039 · Cited by 139 · see citing works
Closing the loop: 3C versus DNA FISH
Giorgetti, L., & Heard, E. (2016) · Genome Biology · doi:10.1186/s13059-016-1081-2 · Cited by 131 · see citing works
RNA and dynamic nuclear organization
Rinn, J. L., & Guttman, M. (2014) · Science · doi:10.1126/science.1252966 · Cited by 129 · see citing works
Molenaar, C., Abdulle, A., Gena, A., Tanke, H. J., & Dirks, R. W. (2004) · The Journal of Cell Biology · doi:10.1083/jcb.200310139 · Cited by 125 · see citing works
Rajapakse, I., & Groudine, M. T. (2011) · The Journal of Cell Biology · doi:10.1083/jcb.201010129 · Cited by 122 · see citing works
NUCLEOLUS ORGANIZERS IN MUS MUSCULUS SUBSPECIES AND IN THE RAG MOUSE CELL LINE
Dev, V. G., Tantravahi, R. V., Miller, D. A., & Miller, O. J. (1977) · Genetics · doi:10.1093/genetics/86.2.389 · 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
Newport, J. W., & Dunphy, W. G. (1992) · The Journal of Cell Biology · doi:10.1083/jcb.116.2.295 · Cited by 109 · see citing works
The Coilin Interactome Identifies Hundreds of Small Noncoding RNAs that Traffic through Cajal Bodies
Machyna, M., Kehr, S., Straube, K., Kappei, D., Buchholz, F., Butter, F., Ule, J., Jana Hertel, A., Stadler, P. F., & Neugebauer, K. M. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.10.004 · Cited by 103 · see citing works
The Nucleoplasmin Homolog NLP Mediates Centromere Clustering and Anchoring to the Nucleolus
Padeken, J., Mendiburo, M. J., Chlamydas, S., Schwarz, H.-J., Kremmer, E., & Heun, P. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.03.002 · Cited by 103 · see citing works
ChIA-PET analysis of transcriptional chromatin interactions
Zhang, J., Poh, H. M., Peh, S. Q., Sia, Y. Y., Li, G., Mulawadi, F. H., Goh, Y., Fullwood, M. J., Sung, W.-K. K., Ruan, X., et al. (2012) · Methods · doi:10.1016/j.ymeth.2012.08.009 · Cited by 93 · see citing works
Formation of nuclear heterochromatin
Guetg, C., & Santoro, R. (2012) · Epigenetics · doi:10.4161/epi.21072 · Cited by 91 · see citing works
The Human and Mouse Replication-Dependent Histone Genes
Marzluff, W. F., Gongidi, P., Woods, K., et al. (2002) · Genomics · doi:10.1016/s0888-7543(02)96850-3 · Cited by 91 · see citing works
3C-based technologies to study the shape of the genome
de Laat, W., & Dekker, J. (2012) · Methods · doi:10.1016/j.ymeth.2012.11.005 · Cited by 84 · see citing works
Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH
Takei, Y., Shah, S., Harvey, S. C., Qi, L. S., & Cai, L. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2017.03.024 · Cited by 84 · see citing works
Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data
Li, W., Gong, K. Q., Li, Q., Alber, F., & Zhou, X. J. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu747 · Cited by 71 · see citing works
Structure and Epigenetics of Nucleoli in Comparison With Non-nucleolar Compartments
Bártová, E., Horáková, A. H., Uhlířová, R., Raška, I., Galiová, G., Orlova, D. Y., & Kozubek, S. (2009) · Journal of Histochemistry & Cytochemistry · doi:10.1369/jhc.2009.955435 · Cited by 68 · see citing works
Chromosome intermingling—the physical basis of chromosome organization in differentiated cells
Maharana, S., Iyer, K. V., Jain, N., Nagarajan, M., Wang, Y., & Shivashankar, G. V. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw131 · Cited by 68 · see citing works
The Perinucleolar CompartmentPreprint
Pollock, C. B., & Huang, S. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000679 · Cited by 67 · see citing works
Britton-Davidian, J., Cazaux, B., & Catalan, J. (2012) · Heredity · doi:10.1038/hdy.2011.105 · Cited by 65 · see citing works
Suzuki, H., Kurihara, Y., Kanehisa, T., & Moriwaki, K. (1990) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040598 · Cited by 64 · see citing works
Mapping the 3D genome: Aiming for consilience
Dekker, J. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.151 · Cited by 58 · see citing works
Hsp70 gene association with nuclear speckles is Hsp70 promoter specific
Hu, Y., Plutz, M., & Belmont, A. S. (2010) · The Journal of Cell Biology · doi:10.1083/jcb.201004041 · Cited by 57 · see citing works
The statistical-mechanics of chromosome conformation capture
O'Sullivan, J. M., Hendy, M. D., Pichugina, T., Wake, G. C., & Langowski, J. (2013) · Nucleus · doi:10.4161/nucl.26513 · Cited by 55 · see citing works
Chromosomal locations of Ag-NORs and clusters of ribosomal DNA in laboratory strains of mice
Kurihara, Y., Suh, D., Suzuki, H., & Moriwaki, K. (1994) · Mammalian Genome · doi:10.1007/bf00360550 · Cited by 43 · see citing works
Gene associations: true romance or chance meeting in a nuclear neighborhood?
Lawrence, J. B., & Clemson, C. (2008) · The Journal of Cell Biology · doi:10.1083/jcb.200808121 · Cited by 37 · see citing works
Pollock, C. B., & Huang, S. (2009) · Journal of Cellular Biochemistry · doi:10.1002/jcb.22107 · Cited by 31 · see citing works
Nucleolar tethering mediates pairing between theIgHandMycloci
Strongin, D. E., Groudine, M. T., & Politz, J. C. R. (2014) · Nucleus · doi:10.4161/nucl.36233 · Cited by 16 · see citing works
Heterogeneity and Intrinsic Variation in Spatial Genome OrganizationPreprint
Finn, E. H., Pegoraro, G., Brandão, H. B., Valton, A.-L., Oomen, M. E., Dekker, J., Mirny, L. A., & Misteli, T. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/171801 · Cited by 12 · see citing works
Centromeres in nuclear architecture
Padeken, J., & Heun, P. (2013) · Cell Cycle · doi:10.4161/cc.26697 · Cited by 7 · see citing works
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Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells
Bintu, B., Mateo, L. J., Su, J.-H., Sinnott-Armstrong, N. A., Parker, M., Kinrot, S., Yamaya, K., Boettiger, A. N., & Zhuang, X. (2018) · Science · doi:10.1126/science.aau1783 · Cited by 976 · see citing works
The role of 3D genome organization in development and cell differentiation
Zheng, H., & Xie, W. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0132-4 · Cited by 711 · see citing works
The Self-Organizing Genome: Principles of Genome Architecture and Function
Misteli, T. (2020) · Cell · doi:10.1016/j.cell.2020.09.014 · Cited by 706 · see citing works
Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome
Shin, Y., Chang, Y.-C., Lee, D. S. W., Berry, J., Sanders, D. W., Ronceray, P., Wingreen, N. S., Haataja, M., & Brangwynne, C. P. (2018) · Cell · doi:10.1016/j.cell.2018.10.057 · Cited by 676 · see citing works
Pol II phosphorylation regulates a switch between transcriptional and splicing condensates
Guo, Y. E., Manteiga, J. C., Henninger, J. E., Sabari, B. R., Dall’Agnese, A., Hannett, N. M., Spille, J.-H., Afeyan, L. K., Zamudio, A. V., Shrinivas, K., et al. (2019) · Nature · doi:10.1038/s41586-019-1464-0 · Cited by 676 · see citing works
Ultrastructural Details of Mammalian Chromosome Architecture
Krietenstein, N., Abraham, S., Venev, S. V., Abdennur, N., Gibcus, J., Hsieh, T.-H. S., Parsi, K. M., Yang, L., Maehr, R., Mirny, L. A., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.003 · Cited by 622 · see citing works
Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin
Su, J.-H., Zheng, P., Kinrot, S. S., Bintu, B., & Zhuang, X. (2020) · Cell · doi:10.1016/j.cell.2020.07.032 · Cited by 562 · see citing works
Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data
Robinson, J., Turner, D., Durand, N. C., Thorvaldsdóttir, H., Mesirov, J. P., & Aiden, E. L. (2018) · Cell Systems · doi:10.1016/j.cels.2018.01.001 · Cited by 566 · 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
Transcription factors and 3D genome conformation in cell-fate decisions
Stadhouders, R., Filion, G. J. P., & Graf, T. (2019) · Nature · doi:10.1038/s41586-019-1182-7 · Cited by 519 · see citing works
A guide to membraneless organelles and their various roles in gene regulation
Hirose, T., Ninomiya, K., Nakagawa, S., & Yamazaki, T. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00558-8 · Cited by 496 · see citing works
Methods for mapping 3D chromosome architecture
Kempfer, R., & Pombo, A. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0195-2 · Cited by 502 · see citing works
Three-dimensional genome structures of single diploid human cells
Tan, L., Xing, D., Chang, C.-H., Li, H., & Xie, X. S. (2018) · Science · doi:10.1126/science.aat5641 · Cited by 479 · see citing works
Revealing lncRNA Structures and Interactions by Sequencing-Based Approaches
Qian, X., Zhao, J., Yeung, P. Y., Zhang, Q. C., & Kwok, C. K. (2018) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2018.09.012 · Cited by 436 · see citing works
Integrated spatial genomics reveals global architecture of single nuclei
Takei, Y., Yun, J., Zheng, S., Ollikainen, N., Pierson, N. G., White, J. A., Shah, S., Thomassie, J., Suo, S., Eng, C.-H. L., et al. (2021) · Nature · doi:10.1038/s41586-020-03126-2 · Cited by 399 · see citing works
Understanding 3D genome organization by multidisciplinary methods
Jerković, I., & Cavalli, G. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00362-w · Cited by 389 · see citing works
RNA promotes the formation of spatial compartments in the nucleus
Quinodoz, S. A., Jachowicz, J. W., Bhat, P., Ollikainen, N., Banerjee, A. K., Goronzy, I. N., Blanco, M. R., Chovanec, P., Chow, A. Y., Markaki, Y., et al. (2021) · Cell · doi:10.1016/j.cell.2021.10.014 · Cited by 384 · see citing works
Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly
Nair, S. J., Lu, Y., Meluzzi, D., Oh, S., Yang, F., Friedman, M. J., Wang, S. S., Suter, T., Alshareedah, I., Gamliel, A., et al. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0190-5 · Cited by 366 · see citing works
Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity
Alexander, J. M., Guan, J., Li, B., Maliskova, L., Song, M., Shen, Y., Huang, B., Lomvardas, S., & Weiner, O. D. (2019) · eLife · doi:10.7554/elife.41769 · Cited by 346 · see citing works
The SARS-CoV-2 RNA–protein interactome in infected human cells
Schmidt, N., Lareau, C. A., Keshishian, H., Ganskih, S., Schneider, C., Hennig, T., Melanson, R., Werner, S., Wei, Y., Zimmer, M. M., et al. (2020) · Nature Microbiology · doi:10.1038/s41564-020-00846-z · Cited by 320 · see citing works
Probing and engineering liquid-phase organelles
Bracha, D., Walls, M. T., & Brangwynne, C. P. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0341-6 · Cited by 322 · see citing works
The relationship between genome structure and function
Oudelaar, A. M., & Higgs, D. R. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00303-x · Cited by 304 · see citing works
Deciphering the multi-scale, quantitative cis-regulatory code
Kim, S., & Wysocka, J. (2023) · Molecular Cell · doi:10.1016/j.molcel.2022.12.032 · Cited by 282 · see citing works
Mechanisms and Functions of Chromosome Compartmentalization
Hildebrand, E. M., & Dekker, J. (2020) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2020.01.002 · Cited by 268 · 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
Liquid–liquid phase separation in tumor biology
Tong, X., Tang, R., Xu, J., Wang, W., Zhao, Y., Yu, X., & Shi, S. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01076-x · Cited by 256 · see citing works
The 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 · see citing works
Nuclear compartmentalization as a mechanism of quantitative control of gene expression
Bhat, P., Honson, D. D., & Guttman, M. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00387-1 · Cited by 230 · see citing works
Chromatin-associated RNAs as facilitators of functional genomic interactions
Li, X., & Fu, X. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0135-1 · Cited by 229 · see citing works
Two major mechanisms of chromosome organization
Mirny, L. A., Imakaev, M., & Abdennur, N. A. (2019) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2019.05.001 · Cited by 222 · 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
The liquid nucleome – phase transitions in the nucleus at a glance
Strom, A. R., & Brangwynne, C. P. (2019) · Journal of Cell Science · doi:10.1242/jcs.235093 · Cited by 223 · 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
“Third, chromatin compartmentalization may be further reinforced and stabilized through the attachment of repeat DNA sequences to subnuclear structures such as the nucleolus and nuclear speckles.(109) Evidence to support this notion includes our observation that L1 repeats are preferentially localized at the nuclear an…”
BackgroundNeuron-specific signatures in the chromosomal connectome associated with schizophrenia risk
Rajarajan, P., Borrman, T., Liao, W., Schrode, N., Flaherty, E., Casiño, C., Powell, S., Yashaswini, C., LaMarca, E. A., Kassim, B., et al. (2018) · Science · doi:10.1126/science.aat4311 · Cited by 219 · see citing works
Cell-type specialization is encoded by specific chromatin topologies
Winick‐Ng, W., Kukalev, A., Harabula, I., Zea-Redondo, L., Szabó, D., Meijer, M., Serebreni, L., Zhang, Y., Bianco, S., Chiariello, A. M., et al. (2021) · Nature · doi:10.1038/s41586-021-04081-2 · Cited by 205 · see citing works
McCord, R. P., Kaplan, N., & Giorgetti, L. (2020) · Molecular Cell · doi:10.1016/j.molcel.2019.12.021 · Cited by 204 · see citing works
Mechanisms of Interplay between Transcription Factors and the 3D Genome
Kim, S., & Shendure, J. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.08.010 · Cited by 204 · see citing works
In situ genome sequencing resolves DNA sequence and structure in intact biological samples
Payne, A. C., Chiang, Z., Reginato, P., Mangiameli, S. M., Murray, E. M., Yao, C., Markoulaki, S., Earl, A., Labade, A. S., Jaenisch, R., et al. (2021) · Science · doi:10.1126/science.aay3446 · Cited by 198 · see citing works
Regulatory Landscaping: How Enhancer-Promoter Communication Is Sculpted in 3D
Robson, M. I., Ringel, A. R., & Mundlos, S. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.05.032 · Cited by 188 · see citing works
Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains
Oudelaar, A. M., Davies, J. O. J., Hanssen, L. L. P., Telenius, J. M., Schwessinger, R., Liu, Y., Brown, J. M., Downes, D. J., Chiariello, A. M., Bianco, S., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0253-2 · Cited by 196 · see citing works
Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale
Zhou, J. (2022) · Nature Genetics · doi:10.1038/s41588-022-01065-4 · Cited by 177 · see citing works
Akhoundova, D., & Rubin, M. A. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.08.011 · Cited by 188 · see citing works
Genome organization around nuclear speckles drives mRNA splicing efficiency
Bhat, P., Chow, A. Y., Emert, B. L., Ettlin, O., Quinodoz, S. A., Strehle, M. M., Takei, Y., Burr, A., Goronzy, I. N., Chen, A. W., et al. (2024) · Nature · doi:10.1038/s41586-024-07429-6 · Cited by 182 · see citing works
Nucleolus: A Central Hub for Nuclear Functions
Iarovaia, O. V., Minina, E. P., Sheval, E. V., Onichtchouk, D., Dokudovskaya, S., Razin, S. V., & Vassetzky, Y. S. (2019) · Trends in Cell Biology · doi:10.1016/j.tcb.2019.04.003 · Cited by 181 · see citing works
Detection of RNA–DNA binding sites in long noncoding RNAs
Kuo, C., Hänzelmann, S., Cetin, N. S., Frank, S., Zajzon, B., Derks, J.-P., Akhade, V. S., Ahuja, G., Kanduri, C., Grummt, I., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz037 · Cited by 180 · see citing works
How the epigenome integrates information and reshapes the synapse
Campbell, R. R., & Wood, M. A. (2019) · Nature reviews. Neuroscience · doi:10.1038/s41583-019-0121-9 · Cited by 175 · see citing works
The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data
Reiff, S. B., Schroeder, A. J., Kırlı, K., Cosolo, A., Bakker, C., Mercado, L., Lee, S., Veit, A. D., Balashov, A. K., Vitzthum, C. M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29697-4 · Cited by 173 · see citing works
A supervised learning framework for chromatin loop detection in genome-wide contact maps
Salameh, T. J., Wang, X., Song, F., Zhang, B., Wright, S. M., Khunsriraksakul, C., Ruan, Y., & Yue, F. (2020) · Nature Communications · doi:10.1038/s41467-020-17239-9 · Cited by 165 · see citing works
Bonetti, A., Agostini, F., Suzuki, A. M., Hashimoto, K., Pascarella, G., Gimenez, J., Roos, L., Nash, A. J., Ghilotti, M., Cameron, C. J. F., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14337-6 · Cited by 163 · see citing works
Unraveling Hematopoiesis through the Lens of Genomics
Liggett, L. A., & Sankaran, V. G. (2020) · Cell · doi:10.1016/j.cell.2020.08.030 · Cited by 163 · see citing works
How subtle changes in 3D structure can create large changes in transcription
Xiao, J. Y., Hafner, A., & Boettiger, A. N. (2021) · eLife · doi:10.7554/elife.64320 · Cited by 162 · see citing works
Francis, A. C., Marin, M., Singh, P. K., Achuthan, V., Prellberg, M. J., Palermino-Rowland, K., Lan, S., Tedbury, P. R., Sarafianos, S. G., Engelman, A. N., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17256-8 · Cited by 159 · see citing works
Genomic Repeats Categorize Genes with Distinct Functions for Orchestrated Regulation
Lu, J., Shao, W., Chang, L., Yin, Y., Li, T., Zhang, H., Hong, Y., Percharde, M., Guo, L., Wu, Z., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.02.048 · Cited by 151 · see citing works
Deshpande, A. S., Ulahannan, N., Pendleton, M., Dai, X., Ly, L., Behr, J. M., Schwenk, S., Liao, W., Augello, M. A., Tyer, C., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01289-z · Cited by 155 · see citing works
The spatial organization of transcriptional control
Hafner, A., & Boettiger, A. N. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00526-0 · Cited by 150 · see citing works
Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions
Xiong, K., & Ma, J. (2019) · Nature Communications · doi:10.1038/s41467-019-12954-4 · Cited by 143 · see citing works
Genome organization around nuclear speckles
Chen, Y., & Belmont, A. S. (2019) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2019.06.008 · Cited by 150 · see citing works
Paulsen, J., Ali, T. M. L., Nekrasov, M., Delbarre, E., Baudement, M.-O., Kurscheid, S., Tremethick, D. J., & Collas, P. (2019) · Nature Genetics · doi:10.1038/s41588-019-0392-0 · Cited by 140 · see citing works
Evidence for and against Liquid-Liquid Phase Separation in the Nucleus
Peng, A., & Weber, S. C. (2019) · Non-Coding RNA · doi:10.3390/ncrna5040050 · Cited by 144 · see citing works
Transcription organizes euchromatin via microphase separation
Hilbert, L., Sato, Y., Kuznetsova, K., Bianucci, T., Kimurâ, H., Jülicher, F., Honigmann, A., Zaburdaev, V., & Vastenhouw, N. L. (2021) · Nature Communications · doi:10.1038/s41467-021-21589-3 · Cited by 144 · see citing works
Uyehara, C. M., & Apostolou, E. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112068 · Cited by 143 · see citing works
Genome Organization in and around the Nucleolus
Bersaglieri, C., & Santoro, R. (2019) · Cells · doi:10.3390/cells8060579 · Cited by 141 · see citing works
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics
Belaghzal, H., Borrman, T. M., Stephens, A. D., Lafontaine, D. L. J., Venev, S. V., Weng, Z., Marko, J. F., & Dekker, J. (2021) · Nature Genetics · doi:10.1038/s41588-021-00784-4 · Cited by 132 · see citing works
Zhang, L., Zhang, Y., Chen, Y., Gholamalamdari, O., Wang, Y., Ma, J., & Belmont, A. S. (2020) · Genome Research · doi:10.1101/gr.266239.120 · Cited by 137 · see citing works
Conte, M., Fiorillo, L., Bianco, S., Chiariello, A. M., Esposito, A., & Nicodemi, M. (2020) · Nature Communications · doi:10.1038/s41467-020-17141-4 · Cited by 123 · see citing works
Ulianov, S. V., Velichko, A. K., Magnitov, M. D., Luzhin, A. V., Golov, A. K., Ovsyannikova, N., Kireev, I. I., Gavrikov, A. S., Mishin, A. S., Garaev, A. K., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab249 · Cited by 137 · see citing works
Fixation can change the appearance of phase separation in living cells
Irgen-Gioro, S., Yoshida, S. R., Walling, V., & Chong, S. (2022) · eLife · doi:10.7554/elife.79903 · Cited by 134 · see citing works
Computer vision for pattern detection in chromosome contact maps
Matthey-Doret, C., Baudry, L., Breuer, A., Montagne, R., Guiglielmoni, N., Scolari, V. F., Jean, É., Campeas, A., Chanut, P. H., Oriol, E., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19562-7 · Cited by 120 · see citing works
N6-methyladenosine modification of MALAT1 promotes metastasis via reshaping nuclear speckles
Wang, X., Liu, C., Zhang, S., Yan, H., Zhang, L., Jiang, A., Liu, Y., Feng, Y., Li, D., Guo, Y., et al. (2021) · Developmental Cell · doi:10.1016/j.devcel.2021.01.015 · Cited by 131 · see citing works
RNA-driven phase transitions in biomolecular condensates
Wadsworth, G. M., Srinivasan, S., Lai, L. B., Datta, M., Gopalan, V., & Banerjee, P. R. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.09.005 · Cited by 131 · see citing works
Interchromosomal interactions: A genomic love story of kissing chromosomes
Maass, P. G., Barutcu, A. R., & Rinn, J. L. (2018) · The Journal of Cell Biology · doi:10.1083/jcb.201806052 · Cited by 124 · see citing works
Single-cell measurement of higher-order 3D genome organization with scSPRITE
Arrastia, M. V., Jachowicz, J. W., Ollikainen, N., Curtis, M. S., Lai, C., Quinodoz, S. A., Selck, D. A., Ismagilov, R. F., & Guttman, M. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00998-1 · Cited by 126 · see citing works
Advances in Chromatin Imaging at Kilobase-Scale Resolution
Boettiger, A. N., & Murphy, S. E. (2020) · Trends in Genetics · doi:10.1016/j.tig.2019.12.010 · Cited by 119 · see citing works
MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
Juric, I., Yu, M., Abnousi, A., Raviram, R., Fang, R., Zhao, Y., Zhang, Y., Qiu, Y., Yang, Y., Li, Y., et al. (2019) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006982 · Cited by 121 · see citing works
Gene expression amplification by nuclear speckle association
Kim, J., Venkata, N. C., Gonzalez, G. A. H., Khanna, N., & Belmont, A. S. (2019) · The Journal of Cell Biology · doi:10.1083/jcb.201904046 · Cited by 121 · see citing works
Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatinPreprint
Vertii, A., Ou, J., Yu, J., Yan, A., Pagès, H., Liu, H., Zhu, L. J., & Kaufman, P. D. (2019) · Genome Research · doi:10.1101/gr.247072.118 · Cited by 120 · see citing works
Single-cell nuclear architecture across cell types in the mouse brain
Takei, Y., Zheng, S., Yun, J., Shah, S., Pierson, N. G., White, J. A., Schindler, S., Tischbirek, C. H., Yuan, G., & Cai, L. (2021) · Science · doi:10.1126/science.abj1966 · Cited by 111 · see citing works
SPIN reveals genome-wide landscape of nuclear compartmentalization
Wang, Y., Zhang, Y., Zhang, R., van Schaik, T., Zhang, L., Sasaki, T., Peric‐Hupkes, D., Chen, Y., Gilbert, D. M., van Steensel, B., et al. (2021) · Genome biology · doi:10.1186/s13059-020-02253-3 · Cited by 114 · see citing works
Fan, Z., Wu, C., Chen, M., Jiang, Y., Wu, Y., Mao, R., & Fan, Y. (2021) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2021.09.010 · Cited by 117 · see citing works
Nuclear speckles – a driving force in gene expression
Faber, G. P., Nadav-Eliyahu, S., & Shav‐Tal, Y. (2022) · Journal of Cell Science · doi:10.1242/jcs.259594 · Cited by 114 · see citing works
Jachowicz, J. W., Strehle, M. M., Banerjee, A. K., Blanco, M. R., Thai, J., & Guttman, M. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00739-1 · Cited by 113 · see citing works
p53 mediates target gene association with nuclear speckles for amplified RNA expression
Alexander, K. A., Coté, A., Nguyen, S. C., Zhang, L., Gholamalamdari, O., Agudelo-Garcia, P. A., Lin-Shiao, E., Tanim, K. M. A. A., Lim, J., Biddle, N., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.03.006 · Cited by 112 · see citing works
The chromosome folding problem and how cells solve it
Dekker, J., & Mirny, L. A. (2024) · Cell · doi:10.1016/j.cell.2024.10.026 · Cited by 112 · see citing works
Belmont, A. S. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a041268 · Cited by 111 · see citing works
Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open QuestionsPreprint
Mirny, L. A., & Dekker, J. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a040147 · Cited by 102 · see citing works
A lncRNA-SWI/SNF complex crosstalk controls transcriptional activation at specific promoter regions
Grossi, E., Raimondi, I., Goñi, E., González, J., Marchese, F. P., Chapaprieta, V., Martín-Subero, J. I., Guo, S., & Huarte, M. (2020) · Nature Communications · doi:10.1038/s41467-020-14623-3 · Cited by 109 · see citing works
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Bizhanova, A., & Kaufman, P. D. (2020) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2020.194666 · Cited by 107 · see citing works
CTCF as a boundary factor for cohesin-mediated loop extrusion: evidence for a multi-step mechanism
Hansen, A. S. (2020) · Nucleus · doi:10.1080/19491034.2020.1782024 · Cited by 101 · see citing works
To loop or not to loop: what is the role of TADs in enhancer function and gene regulation?
Cavalheiro, G. R., Pollex, T., & Furlong, E. E. M. (2021) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.12.015 · Cited by 101 · see citing works
Epigenetic Reprogramming in Early Animal DevelopmentPreprint
Du, Z., Zhang, K., & Xie, W. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a039677 · Cited by 103 · see citing works
HiChIRP reveals RNA-associated chromosome conformation
Mumbach, M. R., Granja, J. M., Flynn, R. A., Roake, C. M., Satpathy, A. T., Rubin, A. J., Qi, Y., Jiang, Z., Shams, S., Louie, B. H., et al. (2019) · Nature Methods · doi:10.1038/s41592-019-0407-x · Cited by 104 · see citing works
Cremer, T., Cremer, M., Hübner, B., Silahtaroglu, A., Hendzel, M. J., Lanctôt, C., Strickfaden, H., & Cremer, C. G. (2020) · BioEssays · doi:10.1002/bies.201900132 · Cited by 101 · see citing works
Unraveling the 3D Genome Architecture in Plants: Present and Future
Ouyang, W., Xiong, D., Li, G., & Li, X. (2020) · Molecular Plant · doi:10.1016/j.molp.2020.10.002 · Cited by 95 · see citing works
Quantitative nucleotide resolution profiling of RNA cytidine acetylation by ac4C-seq
Gamage, S. T., Sas‐Chen, A., Schwartz, S., & Meier, J. L. (2021) · Nature Protocols · doi:10.1038/s41596-021-00501-9 · Cited by 97 · see citing works
RNA granules: functional compartments or incidental condensates?Preprint
Putnam, A., Thomas, L. L., & Seydoux, G. (2023) · Genes & Development · doi:10.1101/gad.350518.123 · Cited by 77 · see citing works
Cancer aneuploidies are shaped primarily by effects on tumour fitness
Shih, J., Sarmashghi, S., Zhakula-Kostadinova, N., Zhang, S., Georgis, Y., Hoyt, S. H., Cuoco, M. S., Gao, G. F., Spurr, L. F., Berger, A. C., et al. (2023) · Nature · doi:10.1038/s41586-023-06266-3 · Cited by 101 · see citing works
Trac-looping measures genome structure and chromatin accessibility
Lai, B., Tang, Q., Jin, W., Hu, G., Wangsa, D., Cui, K., Stanton, B. Z., Ren, G., Ding, Y., Zhao, M., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0107-y · Cited by 85 · see citing works
Popay, T. M., & Dixon, J. R. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102117 · Cited by 94 · see citing works
Time-dependent effect of 1,6-hexanediol on biomolecular condensates and 3D chromatin organization
Liu, X., Jiang, S., Ma, L., Qu, J., Zhao, L., Zhu, X. Q., & Ding, J. (2021) · Genome biology · doi:10.1186/s13059-021-02455-3 · Cited by 95 · see citing works
Conte, M., Irani, E., Chiariello, A. M., Abraham, A., Bianco, S., Esposito, A., & Nicodemi, M. (2022) · Nature Communications · doi:10.1038/s41467-022-31856-6 · Cited by 90 · see citing works
- Authors
- Quinodoz, S. A., Ollikainen, N., Tabak, B., Palla, A., Schmidt, J. M., Detmar, E., Lai, M. M., Shishkin, A. A., Bhat, P., Takei, Y., Trinh, V., Aznauryan, E., Russell, P., Cheng, C., Jovanovic, M., Chow, A., Cai, L., McDonel, P., Garber, M., & Guttman, M.
- Affiliations
- California Institute of Technology (US)
- University of Massachusetts Chan Medical School (US)
- Colorado School of Public Health (US)
- Boston University (US)
- Corresponding author
- Guttman, Mitchell
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2018-07
- Volume
- 174
- Issue
- 3
- Pages
- 744-757.e24
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC6548320
- OpenAlex
- W2806123558
- Cited by
- 892
- References
- 108
- Citations by year
- 2026: 78 · 2025: 101 · 2024: 107 · 2023: 115 · 2022: 118 · 2021: 131 · 2020: 112 · 2019: 100 · 2018: 28
- FWCI
- 33.35
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- The Journal of the American Medical Association (JAMA) Network (American Medical Association) (submittedVersion)
- Funders
- HHMI Gilliam Fellowship
- NSF GRFP Fellowship
- NIGMS (T32 GM008042)
- UCLA-Caltech MSTP (NIGMS T32 GM008042)
- NIH 4DN Program (U01 DA040612, U01 HL130007)
- NHGRI GGR Program (U01 HG007910)
- New York Stem Cell Foundation (NYSCF-R-I13)
- Sontag Foundation
- Caltech
- 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 › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- 3D genome organization, interchromosomal interactions, nuclear bodies, nucleolus, nuclear speckles, sprites, long-range chromatin interactions, DNA packaging
- MeSH terms
- Cell Nucleolus, Cell Nucleus, Chromosome Mapping, Chromosomes, DNA, Humans, Structure-Activity Relationship, Genome, Eukaryota
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.
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