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Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
Open accessAbstract
How DNA is organized in three dimensions inside the cell nucleus and how this affects the ways in which cells access, read and interpret genetic information are among the longest standing questions in cell biology. Using newly developed molecular, genomic and computational approaches based on the chromosome conformation capture technology (such as 3C, 4C, 5C and Hi-C), the spatial organization of genomes is being explored at unprecedented resolution. Interpreting the increasingly large chromatin interaction data sets is now posing novel challenges. Here we describe several types of statistical and computational approaches that have recently been developed to analyse chromatin interaction data.
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“Polymorphic cis-REs have been shown to influence CTCF binding (71, 72) and DNA looping (73).”
From Variation in the Oxytocin Receptor Gene Predicts Brain Region–Specific Expression and Social Attachment (2016) · cites this paper as [73]
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Metadata
- Authors
- Dekker, J., Marti-Renom, M. A., & Mirny, L. A.
- Affiliations
- University of Massachusetts Chan Medical School (US)
- Massachusetts Institute of Technology (US)
- Corresponding author
- Dekker, Job
- Venue
- Nature Reviews Genetics
- Published
- 2013-05-09
- Volume
- 14
- Issue
- 6
- Pages
- 390-403
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- PMC
- PMC3874835
- OpenAlex
- W1574083126
- Cited by
- 1,068
- References
- 113
- Citations by year
- 2026: 24 · 2025: 38 · 2024: 65 · 2023: 50 · 2022: 73 · 2021: 79 · 2020: 75 · 2019: 81 · 2018: 107 · 2017: 122 · 2016: 122 · 2015: 121 · 2014: 80 · 2013: 30
- FWCI
- 11.08
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Nature Reviews Genetics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- The Journal of the American Medical Association (JAMA) Network (American Medical Association) (submittedVersion)
- PMC
- Funders
- W. M. Keck Foundation
- European Commission (282510)
- Ministerio de Ciencia e Innovación (BFU2010-19310)
- National Institutes of Health (HG003143)
- National Human Genome Research Institute (HG003143, HG003143-06S1, R01HG003143)
- National Cancer Institute (U54CA143874)
- 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 › Chromatin Remodeling and Cancer
- Keywords
- 3D genome organization, chromatin interactions, chromosome conformation capture, Hi-C, 4Cs, 5C, nuclear organization, gene expression regulation, chromatin accessibility
- MeSH terms
- Animals, Chromatin, Chromosome Mapping, Chromosomes, Human, Epistasis, Genetic, Humans, Models, Genetic, Nucleic Acid Conformation, Genome, Human
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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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