Three-dimensional folding and functional organization principles of the Drosophila genome
Open accessAbstract
Chromosomes are the physical realization of genetic information and thus form the basis for its readout and propagation. Here we present a high-resolution chromosomal contact map derived from a modified genome-wide chromosome conformation capture approach applied to Drosophila embryonic nuclei. The data show that the entire genome is linearly partitioned into well-demarcated physical domains that overlap extensively with active and repressive epigenetic marks. Chromosomal contacts are hierarchically organized between domains. Global modeling of contact density and clustering of domains show that inactive domains are condensed and confined to their chromosomal territories, whereas active domains reach out of the territory to form remote intra- and interchromosomal contacts. Moreover, we systematically identify specific long-range intrachromosomal contacts between Polycomb-repressed domains. Together, these observations allow for quantitative prediction of the Drosophila chromosomal contact map, laying the foundation for detailed studies of chromosome structure and function in a genetically tractable system.
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Eukaryotic chromosomes are partitioned into topologically associated domains (TADs).
“Second, it was demonstrated that eukaryotic chromosomes are partitioned into so-called topologically associated domains (TADs) [35,36,37], which appear to restrict the areas of enhancer action [38,39,40,41].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [37]
The Introduction describes domains with sharp boundaries in fly embryonic chromosomes, and “Domain-Based Hierarchical Chromosomal Architecture” reports that those chromosomes partition into physical domains. This supports the claim for Drosophila, but the paper’s findings alone do not establish the stated generalization to eukaryotic chromosomes broadly. The later enhancer-action clause has separate citations and is not attributed to this source here. (LLM, conf=0.83)
Experimental — accuracy not yet measuredTopologically associating domains (TADs) exist at intermediate scales (100 kb to 1 Mb).
“At intermediate scales (100 kb to 1 Mb), a major discovery is the existence of topologically associating domains (TADs) (Dixon et al., 2012, Nora et al., 2012, Sexton et al., 2012).”
From Multiscale 3D Genome Rewiring during Mouse Neural Development (2017) · cites this paper as Sexton et al., 2012
Genome-wide, high-resolution understanding of chromosome cell-cycle dynamics is still limited by current technologies.
“genome-wide, high-resolution understanding of chromosome cell-cycle dynamics11 is still limited by current technologies”
From Cell-cycle dynamics of chromosomal organization at single-cell resolution (2017) · cites this paper as [3]
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- Authors
- Sexton, T., Yaffe, E., Kenigsberg, E., Bantignies, F., Leblanc, B., Hoichman, M., Parrinello, H., Tanay, A., & Cavalli, G.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Weizmann Institute of Science (IL)
- Montpellier GenomiX (FR)
- Corresponding author
- Tanay, Amos
- Cavalli, Giacomo
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2012-02
- Volume
- 148
- Issue
- 3
- Pages
- 458-472
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2056482755
- Cited by
- 1,983
- References
- 50
- Citations by year
- 2026: 72 · 2025: 88 · 2024: 106 · 2023: 117 · 2022: 130 · 2021: 180 · 2020: 168 · 2019: 182 · 2018: 176 · 2017: 169 · 2016: 159 · 2015: 139 · 2014: 107 · 2013: 124 · 2012: 62
- FWCI
- 55.50
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 532 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Funders
- Association pour la Recherche sur le Cancer
- Agence Nationale de la Recherche (ANR-10-INBS-0009)
- Israel Science Foundation
- Centre National de la Recherche Scientifique
- 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 › Chromatin Remodeling and Cancer
- Keywords
- chromosome conformation, 3D genome organization, chromatin domains, epigenetic modifications, chromosome structure
- MeSH terms
- Animals, Cell Nucleus, Drosophila melanogaster, Models, Statistical, Drosophila Proteins, Genome, Insect, Chromosomes, Insect, Polycomb Repressive Complex 1
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