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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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“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]
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“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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Cites
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
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
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
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
Capturing Chromosome Conformation
Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652
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
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
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
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
Boisvert, F., van Koningsbruggen, S., de Navascués, J., & Lamond, A. I. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2184 · Cited by 1,671
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Joo, J., Cho, S., Hong, S., Min, S., Kim, K., Kumar, R., Choi, J., Shin, Y., & Jung, I. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad211 · Cited by 13
Visualising three-dimensional genome organisation in two dimensions
Ing‐Simmons, E., & Vaquerizas, J. M. (2019) · Development · doi:10.1242/dev.177162 · Cited by 13
Pratt, B. M., & Won, H. (2021) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2021.08.013 · Cited by 13
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Conte, M., Fiorillo, L., Annunziatella, C., Esposito, A., Musella, F., Abraham, A., Bianco, S., & Chiariello, A. M. (2021) · Physical review. E · doi:10.1103/physreve.104.054402 · Cited by 14
Baudement, M.-O., Cournac, A., Court, F., Seveno, M., Parrinello, H., Reynès, C., Sabatier, R., Bouschet, T., Yi, Z., Sallis, S., et al. (2018) · Genome Research · doi:10.1101/gr.237073.118 · Cited by 13
Zhang, L., Zhang, Y., Chen, Y., Gholamalamdari, O., Wang, Y., Ma, J., & Belmont, A. S. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/824433 · Cited by 13
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Dai, S., Liu, S., Zhou, C., Yu, F., Zhu, G., Zhang, W., Deng, H., Burlingame, A. L., Yu, W., Wang, T., et al. (2023) · Molecular Plant · doi:10.1016/j.molp.2023.03.013 · Cited by 11
Lei, X., Tian, X., Wang, H., Xu, X., Li, G., Liu, W., Wang, D., Xiao, Z., Zhang, M., Li, M. J., et al. (2023) · EMBO Reports · doi:10.15252/embr.202256212 · Cited by 10
Gizzi, A. M. C. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.780822 · Cited by 13
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Winick‐Ng, W., Kukalev, A., Harabula, I., Redondo, L. Z., Szabó, D., Meijer, M., Serebreni, L., Zhang, Y., Bianco, S., Chiariello, A. M., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.02.020990 · Cited by 11
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Hao, Y., Wang, D., Wu, S., Li, X., Shao, C., Zhang, P., Chen, J., Lim, D., Fu, X., Chen, R., et al. (2020) · Genome Research · doi:10.1101/gr.256131.119 · Cited by 10
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Zhan, Y., Yıldırım, A., Boninsegna, L., & Alber, F. (2025) · Genome biology · doi:10.1186/s13059-024-03472-8 · Cited by 8
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Metadata
- 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 › Biochemistry, Genetics and Molecular Biology › Genetics › 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
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