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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The looping model for enhancer-promoter communication received strong confirmation after the development of methods for studying spatial organization of the genome using proximity ligation.
“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]
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Wen, Z., Huang, Z.-T., Zhang, R., & Peng, C. (2018) · Cell Biology and Toxicology · doi:10.1007/s10565-018-9443-z · Cited by 41 · see citing works
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3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes
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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 · see citing works
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Dynamics of chromosome organization in a minimal bacterial cell
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“…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).”
Enhancer Function in the 3D Genome
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- 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
- 0
- 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 › Agricultural and Biological Sciences › Plant Science › 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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