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Chromosome organization by one-sided and two-sided loop extrusion
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Abstract
SMC complexes, such as condensin or cohesin, organize chromatin throughout the cell cycle by a process known as loop extrusion. SMC complexes reel in DNA, extruding and progressively growing DNA loops. Modeling assuming two-sided loop extrusion reproduces key features of chromatin organization across different organisms. In vitro single-molecule experiments confirmed that yeast condensins extrude loops, however, they remain anchored to their loading sites and extrude loops in a ‘one-sided’ manner. We therefore simulate one-sided loop extrusion to investigate whether ‘one-sided’ complexes can compact mitotic chromosomes, organize interphase domains, and juxtapose bacterial chromosomal arms, as can be done by ‘two-sided’ loop extruders. While one-sided loop extrusion cannot reproduce these phenomena, variants can recapitulate in vivo observations. We predict that SMC complexes in vivo constitute effectively two-sided motors or exhibit biased loading and propose relevant experiments. Our work suggests that loop extrusion is a viable general mechanism of chromatin organization.
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“and simulations incorporating two-sided extrusion, rather than one-sided, better reproduce the juxtaposition of bacterial chromosomal arms.78”
From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [78]
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Cites
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Items 101–130 of 130
Chromatin as a Coevolutionary Graph: Modeling the Interplay of Replication with Chromatin DynamicsPreprint
Korsak, S., Banecki, K. H., Buka, K., Agarwal, A., Borkowska, J., Chai, H.-X., Górski, P. J., Ruan, Y.-J., & Plewczynski, D. (2025) · bioRxiv · doi:10.1101/2025.03.31.646315 · Cited by 1
Tsukamoto, S., & Mofrad, M. R. K. (2025) · Journal of Chemical Physics · doi:10.1063/5.0232328 · Cited by 1
Multicontact statistics distinguish models of chromosome organization
Harju, J., Messelink, J. J. B., & Broedersz, C. P. (2025) · Physical review. E · doi:10.1103/physreve.111.014403 · Cited by 1
“This prediction scheme can also be adapted to describe other contact conformations by considering which loops have the shortest combined genomic length, and by presuming that these loops form independently [21].”
BackgroundVinayak, V., Basir, R., Golloshi, R., Toth, J. M., Sant'Anna, L. E., Lakadamyali, M., McCord, R. P., & Shenoy, V. B. (2024) · bioRxiv · doi:10.1101/2024.10.08.617296 · Cited by 1
“Among the various contributing factors to out-of-equilibrium chromatin dynamics, cohesin-and condensin-dependent looping mechanisms are very well understood[49].”
BackgroundPhysical models for chromosome organization to predict multi-contact statisticsPreprint
Harju, J., Messelink, J. J. B., & Broedersz, C. P. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.17.492279 · Cited by 1
Mitra, D., Pande, S., & Chatterji, A. (2021) · doi:10.48550/arxiv.2112.11707 · Cited by 1
Komoto, T., Fujii, M., & Awazu, A. (2021) · bioRxiv · doi:10.2142/biophysico.bppb-v19.0018 · Cited by 1
Bastié, N., Chapard, C., Dauban, L., Gadal, O., Beckouёt, F., & Koszul, R. (2021) · bioRxiv · doi:10.1101/2021.04.21.440823 · Cited by 1
“Smc3 acetylation is maintained throughout the G2 and M stages and only removed at the onset of anaphase by the deacetylase Hos1, following the cleavage of Scc1 by Separase (Beckouet et al., 2010; Nasmyth and Haering, 2009).”
BackgroundInfluentialZhang, C., Xie, Y.-M., Tan, C., Chen, Z.-C., Cao, H.-M., Guo, M., Zhao, L.-Y., Weng, Z., & Tang, C. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag995
“Yet, some scientists might suggest that TAD forms from both sides [ 29 ].”
SMCHD1 loss rewires MYOD1 enhancer nexuses and chromatin accessibility landscapes in muscle cells
Huang, Z., Cui, W., Klaiss, A., & Pfeifer, G. P. (2026) · Science Advances · doi:10.1126/sciadv.aeh7499
“Like CTCF, cohesin and SMC protein complexes primarily shape the 3D chromatin structure, including topologically associating domains, and loop boundaries ( 70 – 76 ).”
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
“Nevertheless, this latter case can be viewed as a straightforward extension of our formalism, in which there is an alternation of stochastic moves in opposite directions according to the same rules [19].”
Mechanisms of transcription control by distal enhancers from single-gene nanoscopy
Cheng, L., De, C., Li, J., Korff, R., & Pertsinidis, A. (2026) · Cell · doi:10.1016/j.cell.2026.09.028 · Cited by 33
Roles of meiotic and mitotic cohesin in stem cell gene regulation and genome stability
Cho, S. M., Kim, Y. E., & Choi, E.-H. (2026) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2026.103100
“18,81 Given this background, the incorporation of meiotic REC8/STAG3 complexes provides a complementary, longer-lived pool of cohesin that helps preserve key regulatory contacts across the rapid cell cycle, partially decoupling gene-regulatory architecture from the cohesin-stripping events of each…”
Chromatin accessibility classification of TAD boundaries discloses new architectural proteins
Jácome-López, K., Ledesma-Dominguez, L., Esquivel-López, A., Pérez-Molina, R., Pénagos-Puig, A., Aguilar-Lomas, A., Gómora-García, J., & Furlan-Magaril, M. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag796
“Many reports have demonstrated that genetic boundary alterations can have a functional impact on gene expression regulation by either forming or re-stricting chromatin contacts between regulatory elements such as enhancers and promoters [ 3 , 55 ].”
Chervinskaya, A., Gelfand, M. S., Metzler, R., & Polovnikov, K. (2026) · bioRxiv · doi:10.64898/2026.08.20.745948
Al-Kurdi, B., Hernandez, J. A., Lewis, A. H., Snyder, L. M., Markus, S. M., & Swygert, S. G. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.10.737861
“26,91,92 In this case, stripes begin and end at the same sites, consistent with loading sites also being extrusion barriers.”
InfluentialRepliSage: a stochastic graph-based framework for 3D chromatin modeling across the cell cycle
Korsak, S., Banecki, K. H., Agarwal, A., Borkowska, J., Górski, P. J., Chai, H., Ruan, Y., Jodkowska, K., & Plewczyński, D. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag618 · Cited by 2
Pobegalov, G., Sha, R.-Z., Dobrokhotov, O., Higashi, T., Brackley, C., Uhlmann, F., & Molodtsov, M. (2026) · bioRxiv · doi:10.64898/2026.06.08.730904
“Because one-sided loop extrusion is often not sufficient by itself to explain the full range of chromosome-organization features [15], alternative scenarios were proposed and received experimental support.”
Cohesin activity accelerates the homology searchPreprint
Matsuo, T. H., Marín-González, A., & Ha, T. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.08.730890
“Similarly to (12, 14), we partitioned the 150 Mb polymer into 50 identical 3 Mb regions with a DSB centered in each, then averaged over each region and over each of 5 independent replicates of the simulation to achieve a total n=250 searches.”
Learning the dynamic organization of a replicating bacterial chromosome from time-course Hi-C dataPreprint
Harju, J., Messelink, J. J. B., Tröger, L., Gradziuk, G., Rathnayaka, I., Billini, M., Thanbichler, M. R., van Teeseling, M. C. F., & Broedersz, C. P. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.03.647011 · Cited by 1
“Molecular dynamics simulations to model chromosome segregation were conducted as in [11, 12], based on earlier simulations using the polychrom wrapper for OpenMM [41, 42] and the looplib package for loop extrusion simulations [70] (see SI Appendix for details).”
Chromosome segregation in a minimal bacterial cell driven by SMC protein complexes
Maytin, A. K., Gilbert, B. R., & Luthey-Schulten, Z. (2026) · Protein Science · doi:10.1002/pro.70604
“Simulations from the Mirny group have shed light on chromosome partitioning dynamics and enabled inference of SMC binding/unbinding and blocking/bypassing parameters from Bacillus subtilis Hi-C data (Banigan et al., 2020; Brand ˜ ao et al., 2021; Goloborodko et al., 2016; Liao et al., 2025).”
Chen, L.-Y., Zhang, Z.-Q., Wang, Z.-H., Yu, X.-C., & Zhang, J.-J. (2026) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2026.112472
Structural Basis of Condensin Recruitment for X Chromosome Repression
Gutierrez, A. V., Amudhan, G., Bernasconi, D., Erkan, S., Hassler, M., Suter, I., Wilde, B., Bender, J., Warscheid, B., Meister, P., et al. (2026) · bioRxiv · doi:10.64898/2026.03.13.711519
HiCInterpolate: 4D Spatiotemporal Interpolation of Hi-C Data for Genome Architecture AnalysisPreprint
Chowdhury, H. M. A. M., & Oluwadare, O. (2026) · bioRxiv · doi:10.64898/2026.02.06.704438
“Chromatin loops arise from intra-chromatin interactions constrained by CTCF extrusion barriers and play a key role in gene regulation [4, 26].”
Effects of Extruder Dynamics and Noise on Simulated Chromatin Contact Probability Curves
Konstantinov, V., Shadskiy, A., & Lagunov, T. (2026) · bioRxiv · doi:10.1101/2025.06.09.658566
Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
Feng, F., Moran, S., Hansen, A., Zhang, X.-T., & Liu, J. (2025) · Genome Research · doi:10.1101/gr.280132.124
“The stripes reflect interactions be-tween a single locus (stripe anchor) and a continuum of genomic regions (Banigan et al. 2020).”
Statistical approach for predicting genome architecture and the major challenges
Menon, S., Lui, V. C. H., & Tam, P. K. H. (2022) · World Journal of Advanced Research and Reviews · doi:10.30574/wjarr.2022.13.1.0022
“This outcome in expanded collaboration recurrence between loci limited by cohesin, shown on Hi-C guides as circles (two-point cooperations) or stripes (one-to-many-focus associations) [10].”
BackgroundZhang, X., Gogoshin, G., & Branciamore, S. (2021) · bioRxiv · doi:10.1101/2021.06.28.450073
“Fourth, the movement of DNA predicted 30 by the DNA extrusion model has been confirmed by the in vitro system[17][18].”
MethodGenomic contacts reveal the control of sister chromosome decatenation in E. coliPreprint
Conin, B., Billault-Chaumartin, I., Sayyed, H. E., Cockram, C. A., Koszul, R., & Espéli, O. (2021) · bioRxiv · doi:10.1101/2021.05.17.444411
Developmental Regulation of Mitotic Chromosome Formation Revealed by Condensin Reporter MicePreprint
Taylor, G., Macdonald, L., Bui, M., Scott, L., Christodoulou, I., Bukowski-Wills, J.-C., Papadopoulos, D., & Wood, A. (2020) · bioRxiv · doi:10.1101/2020.11.04.367847
Metadata
- Authors
- Banigan, E. J., van den Berg, A. A., Brandão, H. B., Marko, J. F., & Mirny, L. A.
- Affiliations
- Massachusetts Institute of Technology (US)
- Harvard University (US)
- Northwestern University (US)
- Corresponding author
- Mirny, Leonid A
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2020-04-06
- Volume
- 9
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC7295573
- OpenAlex
- W3014551288
- Cited by
- 146
- References
- 182
- Citations by year
- 2026: 21 · 2025: 26 · 2024: 16 · 2023: 15 · 2022: 28 · 2021: 26 · 2020: 13
- FWCI
- 6.65
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Funders
- National Institutes of Health (U54DK107980, U54CA193419, GM114190)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Keywords
- loop extrusion, SMC complex, condensin, cohesin, chromatin organization
- MeSH terms
- Bacterial Proteins, Chromatin, Chromosomes, Chromosomes, Bacterial, Interphase, Models, Molecular, Molecular Conformation, Cell Cycle Proteins, Molecular Dynamics Simulation
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