The DOI matches its Crossref record; 47 of the 48 references it cites were found in a registry or an index.
Self-organization of domain structures by DNA-loop-extruding enzymes
Open accessAbstract
The long chromosomal DNAs of cells are organized into loop domains much larger in size than individual DNA-binding enzymes, presenting the question of how formation of such structures is controlled. We present a model for generation of defined chromosomal loops, based on molecular machines consisting of two coupled and oppositely directed motile elements which extrude loops from the double helix along which they translocate, while excluding one another sterically. If these machines do not dissociate from DNA (infinite processivity), a disordered, exponential steady-state distribution of small loops is obtained. However, if dissociation and rebinding of the machines occurs at a finite rate (finite processivity), the steady state qualitatively changes to a highly ordered 'stacked' configuration with suppressed fluctuations, organizing a single large, stable loop domain anchored by several machines. The size of the resulting domain can be simply regulated by boundary elements, which halt the progress of the extrusion machines. Possible realizations of these types of molecular machines are discussed, with a major focus on structural maintenance of chromosome complexes and also with discussion of type I restriction enzymes. This mechanism could explain the geometrically uniform folding of eukaryote mitotic chromosomes, through extrusion of pre-programmed loops and concomitant chromosome compaction.
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“this favors a linear tracking mechanism,47 known as the “loop extrusion model”.8,9,48”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [48]
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Pinto, A., Pradhan, B., Tetiker, D., Schmitt, M. P., Kim, E., & Virnau, P. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.05.709531
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Identification and characterization of Polycomb repressed gene-enhancer loops
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“An increasing amount of evidence supports the notion that the common molecular mechanism that underlies the action of SMC complexes is their ability to create and progressively enlarge loops of DNA (Alipour and Marko, 2012; Goloborodko et al., 2016; Nasmyth, 2001).”
BackgroundTools to analyze single-particle tracking data in mammalian cells
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Gene coregulation in cis within the 3D genome – A single-molecule imaging study
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DNA methylation changes CTCF binding and reorganizes 3D genome structure in breast cancer cells
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van der Hoek, P. H. W., Rosa, A., Ghobadpour, E., & Everaers, R. (2026) · The Journal of Chemical Physics · doi:10.1063/5.0344224
“1(a)) as they form plectonemes due to supercoiling [1–4], undergo loop extrusion [5–9], or maximize the entropy of the crumpled [10] territorial [11] arrangement of inter-phase chromosomes arising from the decondensation of topologically untangled metaphase chromosomes [12–14].”
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Understanding the role of chromatin accessibility and compaction on loop extrusion dynamicsPreprint
Pellet, N., Pastrana, C. L., Delamarre, A., D’Asaro, D., Bernard, P., & Jost, D. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.10.12.758711
“In this process, loop extruding factors (LEF), such as cohesin or condensin, load onto the chromatin fiber and translocate along the DNA, progressively enlarging a loop until they encounter barriers (eg, CTCF-binding sites for cohesin) or until they dissociate [16, 18, 19].”
Condensins-mediated mitotic folding persists as a structural echo in interphase chromatin
Yunusova, A., Tsoi, E., Smirnov, A. V., Шнайдер, Т. А., Pristyazhnuk, I., Gridina, M. M., Евгений, Ф. К., Kireev, I. I., Myakinkov, I., Nuriddinov, M., et al. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag1014 · Cited by 1
“Throughout interphase, cohesin extrudes genomic DNA into loops until it encounters barrier proteins such as CTCF or is removed from chromatin by WAPL [ 13 , 15–18 ].”
Metadata
- Authors
- Alipour, E., & Marko, J. F.
- Affiliations
- UConn Health (US)
- Northwestern University (US)
- Corresponding author
- Alipour, E.
- Marko, J. F.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-10-15
- Volume
- 40
- Issue
- 22
- Pages
- 11202-11212
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3526278
- OpenAlex
- W2100148696
- Cited by
- 540
- References
- 48
- Citations by year
- 2026: 26 · 2025: 45 · 2024: 44 · 2023: 46 · 2022: 38 · 2021: 55 · 2020: 71 · 2019: 61 · 2018: 54 · 2017: 52 · 2016: 27 · 2015: 10 · 2014: 7 · 2013: 3
- FWCI
- 2.56
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Science Foundation (1206868, 1022117, 0715099)
- National Institutes of Health (MCB-1022117, DMR-1206868)
- National Cancer Institute (U54CA143869)
- Division of Materials Research (DMR-1206868)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Keywords
- DNA loop extrusion, self-organization, molecular machines, DNA translocation, processivity, loop size distribution, chromosome compaction, type I restriction enzymes, boundary elements
- MeSH terms
- Chromosomes, Computer Simulation, DNA, Enzymes, Models, Genetic, Nucleic Acid Conformation
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