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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Table of Integrals, Series, and Products
(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).”
BackgroundCapturing Chromosome Conformation
Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652
Mediator and cohesin connect gene expression and chromatin architecture
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
Cohesin mediates transcriptional insulation by CCCTC-binding factor
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.”
BackgroundChromosome territories – a functional nuclear landscape
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).”
BackgroundOno, 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
Flagged first, then by citations
1 of the 48 references couldn’t be matched to a known paper.
Research works printed but not linked: 2
- 2009, PHYS A, 389, 2997
- 1999, Cell, 98, 239:248
Cited by
Sorted by citations
Items 201–300 of 540
Gene functioning and storage within a folded genome
Razin, S. V., & Ulianov, S. V. (2017) · Cellular & Molecular Biology Letters · doi:10.1186/s11658-017-0050-4 · Cited by 37
“The capability of looping DNA was demonstrated for cohesins and condensins experimentally [117].”
BackgroundLoop extrusion rules: the next generation.
Corsi, F., Rusch, E., & Goloborodko, A. (2023) · Current Opinion in Genetics and Development · doi:10.1016/j.gde.2023.102061 · Cited by 27
Paul, M. R., Markowitz, T. E., Hochwagen, A., & Ercan, S. (2018) · Genetics · doi:10.1534/genetics.118.301217 · Cited by 31
DNA Supercoiling, Topoisomerases, and Cohesin: Partners in Regulating Chromatin Architecture?
Björkegren, C., & Baranello, L. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19030884 · Cited by 31
Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development
Owens, D. D. G., Anselmi, G., Oudelaar, A. M., Downes, D. J., Cavallo, A., Harman, J. R., Schweßinger, R., Bucakci, A., Greder, L. V., Ornellas, S. D., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28376-8 · Cited by 33
“The mechanism behind its establishment is likely CTCF/cohesin-mediated loop extrusion (Alipour and Marko 2012, Fudenberg et al. 2016, Nasmyth 2001, Sanborn et al. 2015) as a predominant convergence of CTCF motifs was observed at the main Runx1 TAD boundaries, similar to what was found at other TADs…”
ResultSMC complexes sweeping through the chromosome: going with the flow and against the tide
Gruber, S. (2018) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.10.004 · Cited by 33
Epigenetic characteristics of the mitotic chromosome in 1D and 3D
Oomen, M. E., & Dekker, J. (2017) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2017.1287160 · Cited by 32
The ubiquitin–proteasome system regulates meiotic chromosome organization
Xiao, Y., Song, M., Wang, Y., Tan, T., Tian, Z., Zhai, B., Yang, X., Tan, Y., Cao, Y., Dai, S., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2106902119 · Cited by 30
CTCF and Its Partners: Shaper of 3D Genome during Development
Sun, X., Zhang, J., & Cao, C. (2022) · Genes · doi:10.3390/genes13081383 · Cited by 34
Dynamics of microcompartment formation at the mitosis-to-G1 transition
Goel, V. Y., Aboreden, N. G., Jusuf, J. M., Zhang, H., Mori, L., Mirny, L. A., Blobel, G. A., Banigan, E. J., & Hansen, A. S. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01687-2 · Cited by 35
ESA1 regulates meiotic chromosome axis and crossover frequency via acetylating histone H4
Wang, Y., Zhai, B., Tan, T., Xiao, Y., Zhang, J., Song, M., Tan, Y., Yang, X., Chu, T., Zhang, S., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab722 · Cited by 30
A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH
Jia, B. B., Jussila, A., Kern, C., Zhu, Q., & Ren, B. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01568-9 · Cited by 30
Loop formation by SMC complexes: turning heads, bending elbows, and fixed anchors
Sedeño Cacciatore, Á., & Rowland, B. D. (2019) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2019.04.010 · Cited by 24
Many facades of CTCF unified by its coding for three-dimensional genome architecture
Wu, Q., Liu, P., & Wang, L. (2020) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2020.06.008 · Cited by 26
Contessoto, V. G., Dudchenko, O., Aiden, E. L., Wolynes, P. G., Onuchic, J. N., & Pierro, M. D. (2023) · Nature Communications · doi:10.1038/s41467-023-35909-2 · Cited by 27
Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription
Shaban, H. A., Barth, R., & Bystricky, K. (2020) · Genome biology · doi:10.1186/s13059-020-02185-y · Cited by 28
Devenish, L. P., Mhlanga, M. M., & Negishi, Y. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.662565 · Cited by 27
Abdulla, A. Z., Vaillant, C., & Jost, D. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac702 · Cited by 26
“P (Mi) = (k/k0)(ρs(i) + ε ∑ j ̸=i ρs(j) ∗ Pc(i, j)(1 + rδj,M )) (k/k0)(ρs(i) + ε ∑ j ̸=i ρs(j) ∗ Pc(i, j)(1 + rδj,M )) + 1 (5)”
Modeling the functions of condensin in chromosome shaping and segregation
Sakai, Y., Mochizuki, A., Kinoshita, K., Hirano, T., & Tachikawa, M. (2018) · PLoS Comput. Biol. · doi:10.1371/journal.pcbi.1006152 · Cited by 24
Emerging views of genome organization in Archaea
Takemata, N., & Bell, S. D. (2020) · Journal of Cell Science · doi:10.1242/jcs.243782 · Cited by 26
Three-dimensional genome organization via triplex-forming RNAs
Farabella, I., Stefano, M. D., Soler-Vila, P., Marti-Marimon, M., & Martı́-Renom, M. A. (2021) · Nature Structural & Molecular Biology · doi:10.1038/s41594-021-00678-3 · Cited by 26
Deciphering the structure of the condensin protein complex
Krepel, D., Cheng, R. R., Pierro, M. D., & Onuchic, J. N. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1812770115 · Cited by 26
Chromosome structure in Drosophila is determined by boundary pairing not loop extrusion
Bing, X., Ke, W., Fujioka, M., Kurbidaeva, A., Levitt, S. J., Levine, M., Schedl, P. D., & Jaynes, J. B. (2024) · eLife · doi:10.7554/elife.94070 · Cited by 35
“The endpoints of the loops were initially thought to be determined by the location of the first two roadblocks encountered by the cohesin complex ( Alipour and Marko, 2012 ).”
BackgroundŁaźniewski, M., Dawson, W., Rusek, A. M., & Plewczyński, D. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.08.003 · Cited by 24
“In the LE model, originally proposed by Marko and coworkers [98] and further developed by several other groups [99, 100], the chromatin is represented as a polymer consisting of beads separated by some specific distance; e.”
MethodSMC condensin: promoting cohesion of replicon arms
Burmann, F., & Gruber, S. (2015) · Nature Structural &Molecular Biology · doi:10.1038/nsmb.3082 · Cited by 26
Three-dimensional nuclear organization in Arabidopsis thaliana
Pontvianne, F., & Grob, S. (2020) · Journal of Plant Research · doi:10.1007/s10265-020-01185-0 · Cited by 23
RotoStep: A Chromosome Dynamics Simulator Reveals Mechanisms of Loop ExtrusionPreprint
Lawrimore, J., Friedman, B., Doshi, A., & Bloom, K. (2017) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2017.82.033696 · Cited by 26
DNA-Topology Simplification by Topoisomerases
Hanke, A., Ziraldo, R., & Levene, S. D. (2021) · Molecules · doi:10.3390/molecules26113375 · Cited by 23
Three-dimensional loop extrusion
Bonato, A., & Michieletto, D. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.11.015 · Cited by 23
Chromatin Compaction Leads to a Preference for Peripheral Heterochromatin
MacPherson, Q., Beltran, B. G., & Spakowitz, A. J. (2020) · Biophysical Journal · doi:10.1016/j.bpj.2020.01.034 · Cited by 26
“pairs of beads are held together by LEFs, we follow (37) by running a Gil-”
MethodThe interplay between asymmetric and symmetric DNA loop extrusion
Banigan, E., & Mirny, L. (2020) · bioRxiv · doi:10.7554/elife.63528 · Cited by 19
“In the loop extrusion model, a loop-extruding factor (LEF), such as a condensin motor, binds the chromosome and progressively grows a DNA/chromatin loop by translocating along and processively collecting the nearby chromatin fiber (Riggs, 1990; Alipour and Marko, 2012; Goloborodko et al., 2016a).”
BackgroundInfluentialTiana, G., & Giorgetti, L. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.10.016 · Cited by 19
Mechanism and regulation of class switch recombination by IgH transcriptional control elements
Oudinet, C., Braikia, F.-Z., Dauba, A., & Khamlichi, A. A. (2020) · Advances in immunology · doi:10.1016/bs.ai.2020.06.003 · Cited by 24
Valletta, M., Russo, R., Baglivo, I., Russo, V., Ragucci, S., Sandomenico, A., Iaccarino, E., Ruvo, M., Feis, I. D., Angelini, C., et al. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21238950 · Cited by 23
Uncovering the Principles of Genome Folding by 3D Chromatin ModelingPreprint
Yıldırım, A., Boninsegna, L., Zhan, Y., & Alber, F. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a039693 · Cited by 25
Higher order assembly: folding the chromosome
Sewitz, S. A., Fahmi, Z., & Lipkow, K. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.02.004 · Cited by 22
Large-scale chromatin organisation in interphase, mitosis and meiosis
MacGregor, I. A., Adams, I. R., & Gilbert, N. (2019) · Biochemical Journal · doi:10.1042/bcj20180512 · Cited by 23
Cohesin prevents cross-domain gene coactivation
Dong, P., Zhang, S., Gandin, V., Xie, L., Wang, L., Lemire, A. L., Li, W., Otsuna, H., Kawase, T., Lander, A. D., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01852-1 · Cited by 26
Miron, E., Oldenkamp, R., Brown, J. M., Pinto, D. M. S., Xu, C. S., Faria, A. R., Shaban, H. A., Rhodes, J. D. P., Innocent, C., de Ornellas, S., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/566638 · Cited by 21
Matityahu, A., & Onn, I. (2021) · Journal of Cell Science · doi:10.1242/jcs.247577 · Cited by 22
Chromatin Alterations in Neurological Disorders and Strategies of (Epi)Genome Rescue
Janowski, M., Milewska, M., Zare, P., & Pękowska, A. (2021) · Pharmaceuticals · doi:10.3390/ph14080765 · Cited by 21
Bacterial chromosome organization by collective dynamics of SMC condensins
Miermans, C. A., & Broedersz, C. (2018) · Journal of the Royal Society Interface · doi:10.1098/rsif.2018.0495 · Cited by 21
“In this picture, condensin would actively extrude DNAloops, possibly by feeding DNA duplexes through its ring-like structure [36, 37, 38, 39].”
BackgroundGenome organization via loop extrusion, insights from polymer physics models
Ghosh, S. K., & Jost, D. (2019) · Briefings in Functional Genomics · doi:10.1093/bfgp/elz023 · Cited by 24
“Another fundamental difference is the treatment of colliding LEFs and of LEF unbinding: in [32], LEFs follow a simple exclusion rule and may unbind stochastically chromatin at any time as in [39]; in [31], one of the two interfering LEFs dissociates randomly unless one LEF is already stalled at a BE and thus remains b…”
BackgroundMethodResultInfluentialComplementary chromosome folding by transcription factors and cohesinPreprint
Pereira, M. C. F., Brackley, C. A., Michieletto, D., Annunziatella, C., Bianco, S., Chiariello, A. M., Nicodemi, M., & Marenduzzo, D. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/305359 · Cited by 19
Probing transient protein-mediated DNA linkages using nanoconfinement
Roushan, M., Kaur, P., Karpusenko, A., Countryman, P. J., Ortiz, C., Lim, S. F., Wang, H., & Riehn, R. E. (2014) · Biomicrofluidics · doi:10.1063/1.4882775 · Cited by 19
The mechanics of mitotic chromosomes
Man, T., Witt, H., Peterman, E. J. G., & Wuite, G. J. L. (2021) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583521000081 · Cited by 19
“These nested loops are formed through loop extrusion by the condensin complexes, which exhibit motor activity and are believed to pull the DNA through the ring-shaped complex to form loops (Kawamura et al., 2010; Alipour and Marko, 2012; Goloborodko et al., 2016b; Terakawa et al., 2017; Ganji et al., 2018).”
BackgroundDynamics of chromosome organization in a minimal bacterial cell
Gilbert, B. R., Thornburg, Z. R., Brier, T. A., Stevens, J. A., Grünewald, F., Stone, J. E., Marrink, S. J., & Luthey-Schulten, Z. (2023) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2023.1214962 · Cited by 19
Towards a predictive model of chromatin 3D organization
Xu, C., & Corces, V. G. (2015) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2015.11.013 · Cited by 18
“This model is applicable to any DNA-loop-extruding enzyme, such as condensin or cohesin, which would form loops whose length can be regulated by the presence of architectural proteins [60].”
Xing, H., Wu, Y.-R., Zhang, M. Q., & Chen, Y. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04113-8 · Cited by 18
Integrative studies of 3D genome organization and chromatin structure
Stefano, M. D., & Cavalli, G. (2022) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2022.102493 · Cited by 23
Loops and the activity of loop extrusion factors constrain chromatin dynamics
Bailey, M. L. P., Surovtsev, I. V., Williams, J. F., Yan, H., Yuan, T., Li, K., Duseau, K., Mochrie, S. G. J., & King, M. C. (2023) · Molecular Biology of the Cell · doi:10.1091/mbc.e23-04-0119 · Cited by 22
3D Genome Organization Influences the Chromosome Translocation Pattern
McCord, R. P., & Balajee, A. S. (2018) · Advances in experimental medicine and biology · doi:10.1007/978-981-13-0593-1_8 · Cited by 18
DNA's secret weapon against knots and tangles
Dolgin, E. (2017) · Nature · doi:10.1038/544284a · Cited by 18
preciseTAD: a transfer learning framework for 3D domain boundary prediction at base-pair resolution
Stilianoudakis, S. C., Marshall, M. A., & Dozmorov, M. G. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab743 · Cited by 19
“…and cohesin) track along the DNA sequence ‘extruding’ the intervening DNA in an ATP-dependent manner and pausing at the convergent CTCF motifs (Alipour and Marko, 2012; Davidson et al. , 2019; Fudenberg et al. , 2016; Goloborodko et al. , 2016; Hansen et al. , 2018; Mirny et al. , 2019;…”
BackgroundMethodInfluentialHi-TrAC detects active sub-TADs and reveals internal organizations of super-enhancers
Cao, Y., Liu, S., Cui, K., Tang, Q., & Zhao, K. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad378 · Cited by 18
The dynamic role of cohesin in maintaining human genome architecture
Agarwal, A., Korsak, S., Choudhury, A., & Plewczyński, D. (2023) · BioEssays · doi:10.1002/bies.202200240 · Cited by 14
“[21,57] Polarity or orientation of CTCF proteins can be determined by their binding motifs from which N and C terminus of CTCF proteins can be determined.”
BackgroundFernandez, L. R., Gilgenast, T. G., & Phillips‐Cremins, J. E. (2020) · Genome biology · doi:10.1186/s13059-020-02061-9 · Cited by 17
Epigenetics and Heart Development
George, R. M., & Firulli, A. B. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.637996 · Cited by 16
“The generally accepted model for TAD formation is loop extrusion, where cohesin protein complexes are loaded and extrude chromatin into progressively larger loops until they either dissociate from chromatin, bump into each other, or run into insulator molecules such as the zinc finger CCCTC binding factor (CTCF) (Alip…”
BackgroundTopologically-associating domains: gene warehouses adapted to serve transcriptional regulation
Razin, S. V., Gavrilov, A. A., Vassetzky, Y. S., & Ulianov, S. V. (2016) · Transcription · doi:10.1080/21541264.2016.1181489 · Cited by 18
Scaling Laws for Mitotic Chromosomes
Kramer, E., Tayjasanant, P. A., & Cordone, B. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.684278 · Cited by 15
“Perhaps the most important are condensins (Nasmyth, 2001; Alipour and Marko, 2012).”
BackgroundCummings, C. T., & Rowley, M. J. (2022) · Genes · doi:10.3390/genes13040583 · Cited by 15
The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data
Raffo, A., & Paulsen, J. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad302 · Cited by 15
“Most chromatin loops are located within the boundaries of tissue-invariant TADs [22], and are formed by a process called loop extrusion [23, 24, 25].”
BackgroundFluidification of entangled polymers by loop extrusion
Conforto, F., Fosado, Y. A. G., & Michieletto, D. (2024) · Physical Review Research · doi:10.1103/physrevresearch.6.033160 · Cited by 16
Cell-type-specific loops linked to RNA polymerase II elongation in human neural differentiation
Titus, K. R., Simándi, Z., Chandrashekar, H., Paquet, D., & Phillips‐Cremins, J. E. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100606 · Cited by 17
Genome maintenance in the context of 4D chromatin condensation
Yu, S., Yang, F., & Shen, W. H. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2221-2 · Cited by 17
“Condensins facilitate the initial mitotic chromatin condensation event that forms 80- to 120-kb linear chromatin loops [7, 144].”
3D genomics imposes evolution of the domain model of eukaryotic genome organization
Razin, S. V., & Vassetzky, Y. S. (2016) · Chromosoma · doi:10.1007/s00412-016-0604-7 · Cited by 16
“Specifically, the extrusion of DNA loops constrained by CTCF/cohesion complexes is likely to shape the TAD profiles (Alipour and Marko 2012; Fudenberg et al. 2015; Sanborn et al. 2015).”
Are SMC Complexes Loop Extruding Factors? Linking Theory With Fact
Baxter, J., Oliver, A. W., & Schalbetter, S. A. (2018) · BioEssays · doi:10.1002/bies.201800182 · Cited by 18
A combination of transcription factors mediates inducible interchromosomal contacts
Kim, S., Dunham, M. J., & Shendure, J. (2019) · eLife · doi:10.7554/elife.42499 · Cited by 15
Three-dimensional chromosome organization in flowering plants
Grob, S. (2019) · Briefings in Functional Genomics · doi:10.1093/bfgp/elz024 · Cited by 16
Mitotic chromosome organization: General rules meet species-specific variability
Beseda, T., Cápal, P., Kubalová, I., Schubert, V., Doležel, J., & Šimková, H. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.01.006 · Cited by 16
“Condensins constrain the movement of chromatin fiber by forming a ring structure that holds two distant parts of the fiber together, creating a chromatin loop by loop extrusion [48,49].”
BackgroundCâmara, A. S., Schubert, V., Mascher, M., & Houben, A. (2021) · bioRxiv · doi:10.1093/nar/gkab648 · Cited by 12
“The LE worked as postulated in the loop extrusion model of (31).”
MethodInfluentialShaping chromosomes by DNA capture and release: gating the SMC rings
Gruber, S. (2017) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2017.04.002 · Cited by 16
Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains
Kumari, K., Prakash, J. R., & Padinhateeri, R. (2022) · Biophysical Journal · doi:10.1016/j.bpj.2022.06.008 · Cited by 17
Organization of replicated chromosomes by DNA loops and sister chromatid cohesion
Ochs, F., & Gerlich, D. W. (2026) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-025-00933-1 · Cited by 16
Hirano, T. (2025) · The Journal of Cell Biology · doi:10.1083/jcb.202504075 · Cited by 12
A Cohesin Traffic Pattern Genetically Linked to Gene Regulation
Valton, A.-L., Dekker, J., Venev, S. V., Mair, B., Khokhar, E. S., Pai, A. A., & Moffat, J. (2021) · HAL · Cited by 18
MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions
Rossini, R., Kumar, V., Mathelier, A., Rognes, T., & Paulsen, J. (2022) · bioRxiv · doi:10.1186/s13059-022-02815-7 · Cited by 14
“These proteins are often referred to as loop extrusion factors (LEFs) [15].”
BackgroundMethodPrinciples of Meiotic Chromosome AssemblyPreprint
Schalbetter, S., Fudenberg, G., Baxter, J., Pollard, K., & Neale, M. (2018) · bioRxiv · doi:10.1101/442038 · Cited by 16
A cohesin traffic pattern genetically linked to gene regulationPreprint
Valton, A.-L., Venev, S. V., Mair, B., Khokhar, E. S., Tong, A. H. Y., Ušaj, M., Chan, K. S. K., Pai, A. A., Moffat, J., & Dekker, J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.29.454218 · Cited by 15
“These structures appear to be formed by a loop extrusion mechanism mediated by cohesin complexes (Alipour and Marko, 2012; Fudenberg et al., 2016; Sanborn et al., 2015).”
BackgroundConsistencies and contradictions in different polymer models of chromatin architecture
Câmara, A. S., & Mascher, M. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.01.033 · Cited by 13
“The loop extrusion model overcomes these difficulties by considering loops that progressively grow along the chromatin fibre [41].”
BackgroundThe Accidental Ally: Nucleosome Barriers Can Accelerate Cohesin-Mediated Loop Formation in Chromatin
Maji, A., Padinhateeri, R., & Mitra, M. K. (2020) · Biophysical Journal · doi:10.1016/j.bpj.2020.10.014 · Cited by 14
Analysis of high-resolution 3D intrachromosomal interactions aided by Bayesian network modeling
Zhang, X., Branciamore, S., Gogoshin, G., Rodin, A. S., & Riggs, A. D. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1620425114 · Cited by 12
“More recently it has been proposed that the cohesin complex, containing RAD21, SMC1, and SMC3, is involved in chromosome loop formation and chromosome condensation (19, 20).”
BackgroundCatching DNA with hoops—biophysical approaches to clarify the mechanism of SMC proteins
Eeftens, J. M., & Dekker, C. (2017) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3507 · Cited by 13
One ring to bind them – Cohesin’s interaction with chromatin fibers
Gines, M. M., van Staveren, T., & Wendt, K. S. (2019) · Essays in Biochemistry · doi:10.1042/ebc20180064 · Cited by 14
Chromosome compaction and chromatin stiffness enhance diffusive loop extrusion by slip-link proteins
Bonato, A., Brackley, C. A., Johnson, J., Michieletto, D., & Marenduzzo, D. (2020) · Soft Matter · doi:10.1039/c9sm01875a · Cited by 14
TADs or no TADS: Lessons From Single-cell Imaging of Chromosome Architecture
Gizzi, A. M. C., Cattoni, D. I., & Nöllmann, M. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.12.034 · Cited by 13
Architectural proteins for the formation and maintenance of the 3D genome
Li, M., Gan, J., Sun, Y., Xu, Z., Yang, J., Sun, Y., & Li, C. (2020) · Science China Life Sciences · doi:10.1007/s11427-019-1613-3 · Cited by 15
DNA-loop extruding condensin complexes can traverse one anotherPreprint
Kim, E., Kerssemakers, J. W. J., Shaltiël, I. A., Haering, C. H., & Dekker, C. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/682864 · Cited by 13
Huang, H., Zhu, Q.-S., Jussila, A. P., Han, Y., Bintu, B., Kern, C., Conte, M., Zhang, Y.-X., Bianco, S., Chiariello, A., et al. (2020) · bioRxiv · doi:10.1101/2020.07.07.192526 · Cited by 14
“10,000 KB 1,000 KB 12,000 KB 13,000 KB 14,000 KB 15,000 KB 16,000 KB 17,000 KB 18,000 KB [0-60]”
Helical chromonema coiling is conserved in eukaryotes
Câmara, A. S., Kubalová, I., & Schubert, V. (2023) · The Plant Journal · doi:10.1111/tpj.16484 · Cited by 12
Motorized chain models of the ideal chromosome
Cao, Z., & Wolynes, P. G. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2407077121 · Cited by 11
Choppavarapu, L., Fang, K., Liu, T., Ohihoin, A. G., & Jin, V. X. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115450 · Cited by 13
“We also found a positive correlation of DLGs with HS TADs but not with differential compartments, which could be possibly explained by the model of TAD formed through a loop extrusion, 52–54 whereas compartments are formed by a distinct mechanism.”
Piveteau, V., Dupont, C., Salari, H., Dumont, A., Savocco, J., Jost, D., & Piazza, A. (2026) · The EMBO Journal · doi:10.1038/s44318-026-00748-6 · Cited by 13
“…stochastic motion of loop extruders along the chromosome into a simple polymer model to predict the impact of loop extrusion on contact frequencies, which can be compared to Hi-C contact data (Alipour and Marko, 2012; Sanborn et al, 2015; Fudenberg et al, 2016; Chan and Rubinstein, 2023).”
Sequence Ontology terminology for gene regulation
Sant, D., Sinclair, M. S., Mungall, C., Schulz, S., Zerbino, D. R., Lovering, R. C., Logie, C., & Eilbeck, K. L. (2021) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2021.194745 · Cited by 11
Predictive Polymer Models for 3D Chromosome Organization
Chiang, M., Forte, G., Gilbert, N., Marenduzzo, D., & Brackley, C. A. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-1390-0_14 · Cited by 16
TRAVERS, A. A., & Muskhelishvili, G. (2020) · EcoSal Plus · doi:10.1128/ecosalplus.esp-0016-2019 · Cited by 12
Long-Range Control of Class Switch Recombination by Transcriptional Regulatory Elements
Dauba, A., & Khamlichi, A. A. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.738216 · Cited by 12
Chromatin insulators in gene regulation and 3D genome organization
Sultana, H., Kunar, R., & Matera, A. G. (2025) · Biochemical Society Transactions · doi:10.1042/bst20253036 · Cited by 11
“This orientation of CTCF is critical in stopping the loop extrusion [45,46].”
Interplay between epigenome and 3D chromatin structure
Han, M.-H., Issagulova, D., & Park, M. (2023) · BMB Reports · doi:10.5483/bmbrep.2023-0197 · Cited by 13
“Successive loop formations dictate the chromatin structure over extended genomic regions, often spanning hundreds of kilobases (27).”
BackgroundDNA packaging by molecular motors: from bacteriophage to human chromosomes
Prevo, B., & Earnshaw, W. C. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00740-y · Cited by 11
“Indeed, several theoretical analyses have now shown that DNA loop extrusion is an efficient mechanism to drive the compaction of DNA and to form rod-shaped mitotic chromosomes 15,16,101,136,149,150 .”
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
