Complexity of chromatin folding is captured by the strings and binders switch model
Open accessAbstract
Chromatin has a complex spatial organization in the cell nucleus that serves vital functional purposes. A variety of chromatin folding conformations has been detected by single-cell imaging and chromosome conformation capture-based approaches. However, a unified quantitative framework describing spatial chromatin organization is still lacking. Here, we explore the “strings and binders switch” model to explain the origin and variety of chromatin behaviors that coexist and dynamically change within living cells. This simple polymer model recapitulates the scaling properties of chromatin folding reported experimentally in different cellular systems, the fractal state of chromatin, the processes of domain formation, and looping out. Additionally, the strings and binders switch model reproduces the recently proposed “fractal–globule” model, but only as one of many possible transient conformations.
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Chromosomal contacts follow the law of constrained Brownian motion, with contact probabilities showing a strong power-law dependence on linear genomic distance.
“Chromosomal contacts follow the law of constrained Brownian motion (reviewed in [465]), with the contact probabilities showing a strong power–law dependence on the “linear” genomic distance [272, 466].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [466]
Cites
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829 · see citing works
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895 · see citing works
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Formation of chromosomal domains by loop extrusion
Fudenberg, G., Imakaev, M., Lu, C., Goloborodko, A., Abdennur, N., & Mirny, L. A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.085 · Cited by 2,003 · see citing works
Cohesin Loss Eliminates All Loop Domains
Rao, S. S. P., Huang, S.-C., Glenn St Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.026 · Cited by 1,883 · see citing works
Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data
Dekker, J., Marti-Renom, M. A., & Mirny, L. A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3454 · Cited by 1,068 · see citing works
The 3D Genome as Moderator of Chromosomal Communication
Dekker, J., & Mirny, L. (2016) · Cell · doi:10.1016/j.cell.2016.02.007 · Cited by 937 · see citing works
Genome Architecture: Domain Organization of Interphase Chromosomes
Bickmore, W. A., & van Steensel, B. (2013) · Cell · doi:10.1016/j.cell.2013.02.001 · Cited by 725 · see citing works
Cohesin and CTCF control the dynamics of chromosome folding
Mach, P., Kos, P. I., Zhan, Y., Cramard, J., Gaudin, S., Tünnermann, J., Marchi, E., Eglinger, J., Zuin, J., Kryzhanovska, M., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01232-7 · Cited by 269 · see citing works
Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains
Oudelaar, A. M., Davies, J. O. J., Hanssen, L. L. P., Telenius, J. M., Schwessinger, R., Liu, Y., Brown, J. M., Downes, D. J., Chiariello, A. M., Bianco, S., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0253-2 · Cited by 196 · see citing works
Huang, H., Zhu, Q., Jussila, A., Han, Y., Bintu, B., Kern, C., Conte, M., Zhang, Y., Bianco, S., Chiariello, A. M., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00863-6 · Cited by 187 · see citing works
Self-citationFISH-ing for captured contacts: towards reconciling FISH and 3C
Fudenberg, G., & Imakaev, M. (2017) · Nature Methods · doi:10.1038/nmeth.4329 · Cited by 141 · see citing works
Benedetti, F., Dorier, J., Burnier, Y., & Stasiak, A. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1353 · Cited by 113 · see citing works
Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome
Brückner, D. B., Chen, H., Barinov, L., Zoller, B., & Gregor, T. (2023) · Science · doi:10.1126/science.adf5568 · Cited by 112 · see citing works
Transcriptional enhancers and their communication with gene promoters
Ray-Jones, H., & Spivakov, M. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03903-w · Cited by 81 · see citing works
Hovenga, V., Oluwadare, O., & Kalita, J. (2021) · doi:10.1101/2021.11.29.470405 · Cited by 21
- Authors
- Barbieri, M., Chotalia, M., Fraser, J., Lavitas, L.-M., Dostie, J., Pombo, A., & Nicodemi, M.
- Affiliations
- Istituto Nazionale di Fisica Nucleare, Sezione di Napoli (IT)
- Hammersmith Hospital (GB)
- McGill University (CA)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2012-09-17
- Volume
- 109
- Issue
- 40
- Pages
- 16173-16178
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3479593
- OpenAlex
- W2098497185
- Cited by
- 570
- References
- 2
- Citations by year
- 2026: 16 · 2025: 44 · 2024: 44 · 2023: 44 · 2022: 46 · 2021: 52 · 2020: 56 · 2019: 39 · 2018: 48 · 2017: 46 · 2016: 51 · 2015: 39 · 2014: 22 · 2013: 21 · 2012: 2
- FWCI
- 10.81
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (submittedVersion)
- Funders
- Canadian Institutes of Health Research (86716_1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Keywords
- chromatin folding, nuclear organization, polymer models, chromatin looping, scaling behavior
- MeSH terms
- Chromatin, Computer Simulation, Gene Expression Regulation, Models, Chemical, Monte Carlo Method, Genome, In Situ Hybridization, Fluorescence, Chromatin Assembly and Disassembly
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