Cited by 3,652Genomics and Chromatin DynamicsChromosomal and Genetic VariationsNuclear Structure and Function

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Capturing Chromosome Conformation

Dekker, Job, Rippe, Karsten, Dekker, Martijn, Kleckner, Nancy·2002·Science

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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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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
ORCID: Dekker, Job
Rippe, Karsten
Kleckner, Nancy
Venue: Science
Publisher: American Association for the Advancement of Science (AAAS)
Published: 2002-02-15
Volume: 295
Issue: 5558
Pages: 1306-1311
ISSN: 0036-8075 (ISSN-L)
1095-9203
DOI: 10.1126/science.1067799
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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