The DOI matches its Crossref record; 37 of the 37 references it cites were found in a registry or an index.
Capturing Chromosome Conformation
Abstract
We describe an approach to detect the frequency of interaction between any two genomic loci. Generation of a matrix of interaction frequencies between sites on the same or different chromosomes reveals their relative spatial disposition and provides information about the physical properties of the chromatin fiber. This methodology can be applied to the spatial organization of entire genomes in organisms from bacteria to human. Using the yeast Saccharomyces cerevisiae , we could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis. We also analyzed yeast chromosome III at the G 1 stage of the cell cycle. We found that chromatin is highly flexible throughout. Furthermore, functionally distinct AT- and GC-rich domains were found to exhibit different conformations, and a population-average 3D model of chromosome III could be determined. Chromosome III emerges as a contorted ring.
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“As applied to enhancers in vertebrate animals, this model received strong confirmation after the development of methods for studying the spatial organization of the genome using the proximity ligation technique [29].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [29]
Citations
Cites
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Self-citationChromatin Structure and Function
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THE LEPTOTENE-ZYGOTENE TRANSITION OF MEIOSIS
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- Supplementary details of experimental procedures are available on Science Online at www.sciencemag.org/cgi/content/full/295/5558/1306/DC1.
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Nakaoka, H., Gurumurthy, A., Hayano, T., Ahmadloo, S., Omer, W. H., Yoshihara, K., Yamamoto, A., Kurose, K., Enomoto, T., Akira, S., et al. (2016) · PLOS Genetics · doi:10.1371/journal.pgen.1005893 · Cited by 46
3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes
Babaei, S., Akhtar, W., de Jong, J., Reinders, M., & de Ridder, J. (2015) · Nature Communications · doi:10.1038/ncomms7381 · Cited by 37
Gilbert, B. R., Thornburg, Z. R., Lam, V., Rashid, F.-Z. M., Glass, J. I., Villa, E., Dame, R. T., & Luthey-Schulten, Z. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.644133 · Cited by 30
Ye, B.-Y., Shen, W.-L., Wang, D., Li, P., Zhang, Z., Shi, M.-L., Zhang, Y., Zhang, F.-X., & Zhao, Z.-H. (2016) · Molecular Biology · doi:10.1134/s0026893316030031 · Cited by 26
Actual Ligation Frequencies in the Chromosome Conformation Capture Procedure
Gavrilov, A. A., Golov, A. K., & Razin, S. V. (2013) · PLoS ONE · doi:10.1371/journal.pone.0060403 · Cited by 25
Hovenga, V., Oluwadare, O., & Kalita, J. (2021) · doi:10.1101/2021.11.29.470405 · Cited by 21
Dynamics of chromosome organization in a minimal bacterial cell
Gilbert, B. R., Thornburg, Z. R., Brier, T. A., Stevens, J. A., Grünewald, F., Stone, J. E., Marrink, S. J., & Luthey-Schulten, Z. (2023) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2023.1214962 · Cited by 19
“…of next-generation sequencing (Goodwin et al., 2016) catalyzed the proliferation of sequence-based techniques that assess genome-wide interactions such as DNA-protein binding using CHIP-seq (Park, 2009) and DNA-DNA proximity using chromosome conformation capture (3C) (Dekker et al., 2002).”
Between form and function: the complexity of genome folding
Oudelaar, A. M., Hanssen, L. L. P., Hardison, R. C., Kassouf, M. T., Hughes, J. R., & Higgs, D. R. (2017) · Human Molecular Genetics · doi:10.1093/hmg/ddx306 · Cited by 16
Enhancer Function in the 3D Genome
Razin, S. V., Ulianov, S. V., & Iarovaia, O. V. (2023) · Genes · doi:10.3390/genes14061277 · Cited by 15
Federico, C., Pappalardo, A. M., Ferrito, V., Tosi, S., & Saccone, S. (2017) · Chromosome Research · doi:10.1007/s10577-017-9560-1 · Cited by 15
Brancato, D., Bruno, F., Coniglio, E., Sturiale, V., Saccone, S., & Federico, C. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25126602 · Cited by 9
Interpreting noncoding genetic variation in complex traits and human disease
Ward, L. D., & Kellis, M. (2012) · Nature Biotechnology · doi:10.1038/nbt.2422 · Cited by 6
Topological Approaches in Animal Comparative Genomics
Schultz, D. T., & Simakov, O. (2026) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-030424-084541 · Cited by 1
Metadata
- Authors
- Dekker, J., Rippe, K., Dekker, M., & Kleckner, N.
- Affiliations
- Harvard University (US)
- German Cancer Research Center (DE)
- 2e Oosterparklaan 272, 3544 AX Utrecht, Netherlands.
- Corresponding author
- Dekker, Job
- Venue
- Science
- Published
- 2002-02-15
- Volume
- 295
- Issue
- 5558
- Pages
- 1306-1311
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2073026107
- Cited by
- 3,652
- References
- 37
- Citations by year
- 2026: 94 · 2025: 123 · 2024: 161 · 2023: 174 · 2022: 190 · 2021: 228 · 2020: 280 · 2019: 263 · 2018: 260 · 2017: 208 · 2016: 249 · 2015: 221 · 2014: 165 · 2013: 166 · 2012: 190
- FWCI
- 9.99
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- The Journal of the American Medical Association (JAMA) Network (American Medical Association) (submittedVersion)
- Funders
- National Institute of General Medical Sciences (GM-44794, GM 25326, R01GM044794)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Keywords
- chromosome conformation, 3D genome organization, chromatin fiber, Saccharomyces cerevisiae, meiosis
- MeSH terms
- Cell Fractionation, Cell Nucleus, Centromere, Chromatin, Cross-Linking Reagents, Formaldehyde, Mathematics, Meiosis, Mitosis, Protein Conformation, Saccharomyces cerevisiae, Deoxyribonuclease EcoRI, Chromosomes, Fungal, Polymerase Chain Reaction, G1 Phase, Telomere, Genome, Fungal, AT Rich Sequence, GC Rich Sequence
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