Cited by 540Genomics and Chromatin DynamicsDiffusion and Search DynamicsDNA Repair Mechanisms

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Self-organization of domain structures by DNA-loop-extruding enzymes

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Alipour, E., Marko, J. F.·2012·Nucleic Acids Research

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Abstract

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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(1980) · Elsevier eBooks · doi:10.1016/c2013-0-10754-4 · Cited by 19,385
Exact stochastic simulation of coupled chemical reactions
Gillespie, D. T. (1977) · The Journal of Physical Chemistry · doi:10.1021/j100540a008 · Cited by 10,215
Scaling Concepts in Polymer Physics
de Gennes, P. G., & Witten, T. A. (1980) · Physics Today · doi:10.1063/1.2914118 · Cited by 9,348
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898 · cited 1×
“Furthermore, analyses of DNA juxtapositions inside eukaryote nuclei reveal that loci up to tens of megabases apart along chromosomes are positioned near one another in the nucleus (9,10), with statistical properties inconsistent with randompolymer organization (10).”
Background
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Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652
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Kagey, M. H., Newman, J. J., Bilodeau, S., Zhan, Y., Orlando, D. A., van Berkum, N. L., Ebmeier, C. C., Goossens, J., Rahl, P. B., Levine, S. S., et al. (2010) · Nature · doi:10.1038/nature09380 · Cited by 1,939
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Wendt, K. S., Yoshida, K., Itoh, T., Bando, M., Koch, B., Schirghuber, E., Tsutsumi, S., Nagae, G., Ishihara, K., Mishiro, T., et al. (2008) · Nature · doi:10.1038/nature06634 · Cited by 1,193 · cited 1×
“It is thought that ‘chromatin-bridging’ proteins (12) somehow stabilize these loop structures, but the processes by which sequence-defined chromatin loops are established and maintained are unknown.”
Background
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Cremer, T., Cremer, M., Dietzel, S., Müller, S., Solovei, I. V., & Fakan, S. (2006) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2006.04.007 · Cited by 601 · cited 1×
“In eukaryote cells, interphase chromosomes in differentiated cells occupy distinct territories (8).”
Background
Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells.
Ono, T., Losada, A., Hirano, M., Myers, M., Neuwald, A. F., & Hirano, T. (2003) · Cell · doi:10.1016/s0092-8674(03)00724-4 · Cited by 588
A heterodimeric coiled-coil protein required for mitotic chromosome condensation in vitro.
Hirano, T., & Mitchison, T. (1994) · Cell · doi:10.1016/0092-8674(94)90254-2 · Cited by 559 · cited 1×
“Immuno-inactivation of condensin complexes in Xenopus egg extracts (an in vitro system capable of assembling mitotic chromosomes) (22), or siRNA depletion of even one subunit of condensin complexes (23,24) in tissue culture cells, causes defective mitotic chromosome condensation.”
Background

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Method
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“model of random bridge formation (5, 6) (Supplementary Fig.”
Background
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“[2].”
Background
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“[6] E.”
Background
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Method
An Investigation of Segmental Duplications across Topologically Associating Domains
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Background
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Background
Organization and Role of Bacterial SMC, MukBEF, MksBEF, Wadjet, and RecN Complexes
Morozova, N. E., Potysyeva, A. S., & Vedyaykin, A. D. (2024) · Cell and Tissue Biology · doi:10.1134/s1990519x23700074
“The process of loop extrusion was first postulated in 2001 (Nasmyth, 2001) and theoretically formalized in 2012 (Alipour and Marko, 2012).”
Using Free Energy-Based Modeling to Predict Chromatin Loops in the Human Genome
Dawson, W., Łaźniewski, M., & Plewczyński, D. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-95502-7.00043-9
Replicating Chromosomes in Whole-Cell Models of Bacteria
Gilbert, B. R., & Luthey-Schulten, Z. A. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-3930-6_29
Cohesin-dependent loop extrusion: molecular mechanics and role in cell physiology
Golov, A. K., & Gavrilov, A. A. (2024) · Biochemistry (Moscow) · doi:10.31857/s0320972524040024
Understanding and Simulating the Dynamics of a Polymer-Like Chromatin
Câmara, A. S., & Mascher, M. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-4228-3_16
Different relative scalings between transient forces and thermal fluctuations tune regimes of dynamic clustering
Coletti, A., Newhall, K. A., Walker, B. L., & Bloom, K. (2025) · Physical review. E · doi:10.1103/physreve.111.044407
Coarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci
Mader, A., Rodriguez, A. I., Yuan, T., Surovtsev, I. V., King, M. C., & Mochrie, S. G. J. (2025) · Biophysical Journal · doi:10.1016/j.bpj.2025.05.008
SMC complex unidirectionally translocates DNA by coupling segment capture with an asymmetric kleisin path
Yamauchi, M., Brandani, G. B., Terakawa, T., & Takada, S. (2026) · eLife · doi:10.7554/elife.106752
Calyculin A Induces Premature Chromosome Condensation and Chromatin Compaction in G 1 -Phase HeLa Cells without Histone H1 PhosphorylationPreprint
Kochanova, N. Y., Vermeren, M., Prevo, B., Ustun, I., Webb, S., Xie, L., Earnshaw, W. C., & Paulson, J. R. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.16.665228
Criticality-driven enhancer-promoter dynamics in Drosophila chromosomesPreprint
Ganesh, G., Fiche, J.-B., Nöllmann, M., & Mozziconacci, J. (2025) · eLife · doi:10.7554/elife.108117.1
Criticality-driven enhancer-promoter dynamics in Drosophila chromosomesPreprint
Ganesh, G., Fiche, J.-B., Nöllmann, M., & Mozziconacci, J. (2025) · eLife · doi:10.7554/elife.108117 · Cited by 1
Yeast condensin acts as a transient intermolecular crosslinker in entangled DNA
Conforto, F., Valdés, A., Vanderlinden, W., & Michieletto, D. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag044 · Cited by 2
“However, this hypothesis would be at odds with a large fraction of the current loop extrusion models which posit that SMCs mostly perform intra-chain loop extrusion and no bridging, leading to mostly unentangled, bottle-brush-like chromosome structures [2, 4, 16, 47].”
Contact networks encode the ATP-induced dynamic structural asymmetry of condensin head domains
Xu, C., & Chu, X. (2025) · The Journal of Chemical Physics · doi:10.1063/5.0295393
Involvement of the inner surface residues of bacterial SMC protein MukB in the ssDNA binding in vitro
Akiyama, K., Yano, K., & Niki, H. (2025) · Communications Biology · doi:10.1038/s42003-025-09345-5
Cohesin constrains histone modification-driven chromatin dynamicsPreprint
Fujino, T., Ochi, Y., Goyama, S., Shimosato, Y., Shikata, S., Kon, A., Mori, T., Sakata, T., Honda, H., Koseki, H., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.13.694149 · Cited by 1
Additional file 1 of Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription
Shaban, H. A., Barth, R., & Bystricky, K. (2020) · Figshare · doi:10.6084/m9.figshare.13250993
Additional file 4 of RAD21 is the core subunit of the cohesin complex involved in directing genome organization
Sun, Y., Xu, X., Zhao, W., Zhang, Y., Chen, K., Li, Y., Wang, X., Zhang, M., Xue, B., Yu, W., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26600449
Additional file 1 of Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection
Jia, Z., Li, J., Ge, X., Wu, Y., Guo, Y., & Wu, Q. (2020) · Figshare · doi:10.6084/m9.figshare.12211295
Additional file 2 of Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection
Jia, Z., Li, J., Ge, X., Wu, Y., Guo, Y., & Wu, Q. (2020) · Figshare · doi:10.6084/m9.figshare.12211298
Additional file 2 of RAD21 is the core subunit of the cohesin complex involved in directing genome organization
Sun, Y., Xu, X., Zhao, W., Zhang, Y., Chen, K., Li, Y., Wang, X., Zhang, M., Xue, B., Yu, W., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26600443
Additional file 2 of HiCognition: a visual exploration and hypothesis testing tool for 3D genomics
Langer, C. C. H., Mitter, M., Stocsits, R. R., & Gerlich, D. W. (2023) · Figshare · doi:10.6084/m9.figshare.23632650
Additional file 1 of HiCognition: a visual exploration and hypothesis testing tool for 3D genomics
Langer, C. C. H., Mitter, M., Stocsits, R. R., & Gerlich, D. W. (2023) · Figshare · doi:10.6084/m9.figshare.23632647

Authors: Alipour, E., & Marko, J. F.
Affiliations: UConn Health (US)
Northwestern University (US)
Corresponding author: Alipour, E.
Marko, J. F.
ORCID: 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
DOI: 10.1093/nar/gks925
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: cc-by-nc
creativecommons.org/licenses/by-nc/3.0 (vor, 1450 d)
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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Self-organization of domain structures by DNA-loop-extruding enzymes

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