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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Simulations incorporating two-sided extrusion, rather than one-sided, better reproduce the juxtaposition of bacterial chromosomal arms.
“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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BackgroundThe Energetics and Physiological Impact of Cohesin Extrusion
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BackgroundCohesin-mediated interactions organize chromosomal domain architecture
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“Mitotic chromosome compaction and resolution- The SMC condensin complex in metazoan cells plays a central role in mitotic chromosome compaction and segregation (Charbin et al., 2014; Hagstrom et al., 2002; Hirano, 2016; Hirano et al., 1997; Hirano and Mitchison, 1994; Hudson et al., 2003; Nagasaka et al., 2016; Ono et…”
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“In contrast, two-sided extrusion with increased processivity generates the strong dots seen in wild-type data as well as the “extended dots” ( Figure 3 b and Figure 3 figure supplement 5 ) seen in Wapl depletion data (Gassler et al., 2017; Haarhuis et al., 2017; Wutz et al., 2017) .”
BackgroundMethodInfluentialSelf-citationWapl is an essential regulator of chromatin structure and chromosome segregation
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“Mitotic chromosome compaction and resolution- The SMC condensin complex in metazoan cells plays a central role in mitotic chromosome compaction and segregation (Charbin et al., 2014; Hagstrom et al., 2002; Hirano, 2016; Hirano et al., 1997; Hirano and Mitchison, 1994; Hudson et al., 2003; Nagasaka et al., 2016; Ono et…”
BackgroundMultiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins
Lioy, V. S., Cournac, A., Marbouty, M., Duigou, S., Mozziconacci, J., Espéli, O., Boccard, F., & Koszul, R. (2018) · Cell · doi:10.1016/j.cell.2017.12.027 · Cited by 343 · see citing works
Condensin I stabilizes chromosomes mechanically through a dynamic interaction in live cells.
Gerlich, D., Hirota, T., Koch, B., Peters, J., & Ellenberg, J. (2006) · Current Biology · doi:10.1016/j.cub.2005.12.040 · Cited by 340 · cited 3× · see citing works
“Compaction and resolution are completed within a few (~5) residence times (1/kunbind ~ 2–10 min [Gerlich et al., 2006a; Terakawa et al., 2017; Walther et al., 2018]), provided that extrusion is fast, i.”
BackgroundChromosome condensation and sister chromatid pairing in budding yeast.
Guacci, V., Hogan, E., & Koshland, D. E. (1994) · The Journal of Cell Biology · doi:10.1083/jcb.125.3.517 · Cited by 323 · cited 4× · see citing works
“This results in dramatic linear compaction of the chromatin fiber into a polymer brush with a >100-fold shorter backbone (Guacci et al., 1994; Lawrence et al., 1988; Trask et al., 1989) .”
BackgroundInfluentialHudson, D., Vagnarelli, P., Gassmann, R., & Earnshaw, W. (2003) · Developmental Cell · doi:10.1016/s1534-5807(03)00199-0 · Cited by 311 · see citing works
Architecture of metaphase chromosomes and chromosome scaffolds
Earnshaw, W. C., & Laemmli, U. K. (1983) · Journal of Cell Biology · doi:10.1083/jcb.96.1.84 · Cited by 305 · see citing works
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“Bacterial chromosome arm juxtaposition- In bacteria, SMC complexes and homologs play an important role in the maintenance of proper chromosome organization and efficient chromosomal segregation ( (Britton et al., 1998; Jensen and Shapiro, 1999; Moriya et al., 1998; Sullivan et al., 2009) and others).”
BackgroundCompaction and segregation of sister chromatids via active loop extrusion
Goloborodko, A., Imakaev, M., Marko, J., & Mirny, L. (2016) · bioRxiv · doi:10.1101/038281 · Cited by 298
Self-citationCharacterization of a prokaryotic SMC protein involved in chromosome partitioning.Preprint
Britton, R. A., Lin, D., & Grossman, A. D. (1998) · Genes & Development · doi:10.1101/gad.12.9.1254 · Cited by 298 · see citing works
Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe
Mizuguchi, T., Fudenberg, G., Mehta, S. S., Belton, J.-M., Taneja, N., Folco, H. D., FitzGerald, P. C., Dekker, J., Mirny, L. A., Barrowman, J., et al. (2014) · Nature · doi:10.1038/nature13833 · Cited by 294 · see citing works
Self-citationWang, X., Brandão, H. B., Le, T. B. K., Laub, M. T., & Rudner, D. Z. (2017) · Science · doi:10.1126/science.aai8982 · Cited by 293 · cited 9× · see citing works
“The symmetry of the juxtaposed chromosome arms implies that bSMC should be a two-sided LEF (Brandão et al., 2019; Wang et al., 2017) .”
BackgroundResultInfluentialSelf-citationOrganization and segregation of bacterial chromosomes
Wang, X.-D., Llopis, P., & Rudner, D. (2013) · Nature reviews genetics · doi:10.1038/nrg3375 · Cited by 292 · see citing works
Chromosome Compaction by Active Loop Extrusion
Goloborodko, A., Marko, J., & Mirny, L. (2016) · Biophysical Journal · doi:10.1016/j.bpj.2016.02.041 · Cited by 290 · see citing works
Self-citationEmerging Evidence of Chromosome Folding by Loop ExtrusionPreprint
Fudenberg, G., Abdennur, N. A., Imakaev, M., Goloborodko, A. A., & Mirny, L. A. (2017) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2017.82.034710 · Cited by 287 · see citing works
Self-citationMarbouty, M., Gall, A. L., Cattoni, D. I., Cournac, A., Koh, A., Fiche, J.-B., Mozziconacci, J., Murray, H. D., Koszul, R., & Nöllmann, M. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.07.020 · Cited by 272 · cited 5× · see citing works
“This signal is dependent on the bacterial SMC complex (bSMC) (Marbouty et al., 2015; Wang et al., 2015).”
BackgroundInfluentialThe condensin complex is a mechanochemical motor that translocates along DNA
Terakawa, T., Bisht, S., Eeftens, J., Dekker, C., Haering, C., & Greene, E. (2017) · Science · doi:10.1126/science.aan6516 · Cited by 269 · cited 3× · see citing works
“Compaction and resolution are completed within a few (~5) residence times (1/kunbind ~ 2–10 min [Gerlich et al., 2006a; Terakawa et al., 2017; Walther et al., 2018]), provided that extrusion is fast, i.”
BackgroundRapid movement and transcriptional re-localization of human cohesin on DNA
Davidson, I. F., Goetz, D., Zaczek, M. P., Molodtsov, M. I., Huis in 't Veld, P. J., Weissmann, F., Litos, G., Cisneros, D. A., Ocampo‐Hafalla, M., Ladurner, R., et al. (2016) · The EMBO Journal · doi:10.15252/embj.201695402 · Cited by 246 · cited 22× · see citing works
“Over time, the subunits may translocate along DNA, and the LEF eventually unbinds from DNA.”
InfluentialIn vivo Architecture and Action of Bacterial Structural Maintenance of Chromosome Proteins
Badrinarayanan, A., Reyes-Lamothe, R., Uphoff, S., Leake, M. C., & Sherratt, D. (2012) · Science · doi:10.1126/science.1227126 · Cited by 246 · cited 2× · see citing works
“Functional dimerization of bSMCs in vivo could be directly tested by photobleaching experiments with endogenous fluorescently tagged versions of bSMC , as in (Badrinarayanan et al., 2012) .”
BackgroundMitotic Transcription and Waves of Gene Reactivation During Mitotic Exit
Palozola, K. C., Donahue, G., Liu, H., Grant, G., Becker, J., Coté, A., Yu, H.-T., Raj, A., & Zaret, K. (2017) · Science · doi:10.1126/science.aal4671 · Cited by 245 · cited 1× · see citing works
“While transcription can occur during mitosis, inhibiting transcription does not visibly alter mitotic chromosome compaction (Palozola et al., 2017) .”
BackgroundCondensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilisPreprint
Wang, X.-D., Le, T., Lajoie, B., Dekker, J., Laub, M., & Rudner, D. (2015) · Genes & Development · doi:10.1101/gad.265876.115 · Cited by 236 · see citing works
Jensen, R. B., & Shapiro, L. (1999) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.96.19.10661 · Cited by 233 · cited 1× · see citing works
“Bacterial chromosome arm juxtaposition- In bacteria, SMC complexes and homologs play an important role in the maintenance of proper chromosome organization and efficient chromosomal segregation ( (Britton et al., 1998; Jensen and Shapiro, 1999; Moriya et al., 1998; Sullivan et al., 2009) and others).”
BackgroundSingle-molecule imaging reveals a collapsed conformational state for DNA-bound cohesin
Stigler, J., Çamdere, G. Ö., Koshland, D. E., & Greene, E. C. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.003 · Cited by 229 · see citing works
OpenMM: A Hardware Independent Framework for Molecular Simulations
Eastman, P., & Pande, V. (2010) · Computing in science & engineering (Print) · doi:10.1109/mcse.2010.27 · Cited by 222 · see citing works
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Cuartero, S., Weiss, F. D., Dharmalingam, G., Guo, Y., Ing-Simmons, E., Masella, S., Robles-Rebollo, I., Xiao, X., Wang, Y.-F., Barozzi, I., et al. (2018) · Nature Immunology · doi:10.1038/s41590-018-0184-1 · Cited by 210 · see citing works
A role for Drosophila SMC4 in the resolution of sister chromatids in mitosis.
Steffensen, S., Coelho, P. A., Cobbe, N., Vass, S., Costa, M., Hassan, B., Prokopenko, S. N., Bellen, H. J., Heck, M. M. S., & Sunkel, C. (2001) · Current Biology · doi:10.1016/s0960-9822(01)00096-3 · Cited by 209 · cited 3× · see citing works
“Mitotic chromosome compaction and resolution- The SMC condensin complex in metazoan cells plays a central role in mitotic chromosome compaction and segregation (Charbin et al., 2014; Hagstrom et al., 2002; Hirano, 2016; Hirano et al., 1997; Hirano and Mitchison, 1994; Hudson et al., 2003; Nagasaka et al., 2016; Ono et…”
BackgroundMazumdar, C., Shen, Y., Xavy, S., Zhao, F., Reinisch, A., Li, R., Corces, M. R., Flynn, R. A., Buenrostro, J. D., Chan, S. M., et al. (2015) · Cell stem cell · doi:10.1016/j.stem.2015.09.017 · Cited by 204 · see citing works
Moriya, S., Tsujikawa, E., Hassan, A. K. M., Asai, K., Kodama, T., & Ogasawara, N. (1998) · Molecular Microbiology · doi:10.1046/j.1365-2958.1998.00919.x · Cited by 202 · cited 1× · see citing works
“Bacterial chromosome arm juxtaposition- In bacteria, SMC complexes and homologs play an important role in the maintenance of proper chromosome organization and efficient chromosomal segregation ( (Britton et al., 1998; Jensen and Shapiro, 1999; Moriya et al., 1998; Sullivan et al., 2009) and others).”
BackgroundParB spreading requires DNA bridgingPreprint
Graham, T. G. W., Wang, X.-D., Song, D., Etson, C. M., van Oijen, A. V., Rudner, D., & Loparo, J. (2014) · Genes & Development · doi:10.1101/gad.242206.114 · Cited by 200 · see citing works
The Three-Dimensional Architecture of a Bacterial Genome
Umbarger, M., Toro, E., Wright, M. A., Porreca, G., Baù, D., Hong, S.-H., Fero, M., Zhu, L., Martí-Renom, M., McAdams, H., et al. (2011) · Molecules and Cells · doi:10.1016/j.molcel.2011.09.010 · Cited by 200 · cited 2× · see citing works
“In many bacteria, bSMCs loaded near the origin of replication (by the parABS system) generate contacts centered about the ori-ter axis, which is visible in Hi-C maps as a secondary diagonal (Böhm et al., 2020; Le et al., 2013; Marbouty et al., 2014; Umbarger et al., 2011; Wang et al., 2017, 2015) .”
BackgroundContrasting roles of condensin I and condensin II in mitotic chromosome formation
Green, L. C., Kalitsis, P., Chang, T., Cipetić, M., Kim, J. H., Marshall, O. J., Turnbull, L., Whitchurch, C., Vagnarelli, P., Samejima, K., et al. (2012) · Journal of Cell Science · doi:10.1242/jcs.097790 · Cited by 199 · cited 2× · see citing works
“, 2016) , which facilitates chromosome segregation by preventing anaphase bridge formation (Charbin et al., 2014; Green et al., 2012; Hagstrom et al., 2002; Nagasaka et al., 2016; Piskadlo et al., 2017; Steffensen et al., 2001) .”
BackgroundCohesin and condensin extrude DNA loops in a cell cycle-dependent manner
Golfier, S., Quail, T., Kimurâ, H., & Jan Brugués, A. (2020) · eLife · doi:10.7554/elife.53885 · Cited by 196 · see citing works
A handcuff model for the cohesin complex
Zhang, N., Kuznetsov, S., Sharan, S., Li, K.-Y., Rao, P., & Pati, D. (2008) · Journal of Cell Biology · doi:10.1083/jcb.200801157 · Cited by 194 · see citing works
Local nucleosome dynamics facilitate chromatin accessibility in living mammalian cells.
Hihara, S., Pack, C., Kaizu, K., Tani, T., Hanafusa, T., Nozaki, T., Takemoto, S., Yoshimi, T., Yokota, H., Imamoto, N., et al. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.11.008 · Cited by 186
A CTCF Code for 3D Genome Architecture
Nichols, M. H., & Corces, V. G. (2015) · Cell · doi:10.1016/j.cell.2015.07.053 · Cited by 186 · see citing works
A quantitative map of human Condensins provides new insights into mitotic chromosome architecture
Walther, N., Hossain, M. J., Politi, A., Koch, B., Kueblbeck, M., Ødegård-Fougner, Ø., Lampe, M., & Ellenberg, J. (2018) · bioRxiv · doi:10.1083/jcb.201801048 · Cited by 181 · cited 8× · see citing works
“, 2016a) showed that LEFs can compact and resolve metazoan chromosomes (~100 Mb in length) for physiological densities of LEFs (1 per d =10-30 kb (Fukui and Uchiyama, 2007; Takemoto et al., 2004; Walther et al., 2018) ).”
BackgroundResultInfluentialChromatin three-dimensional interactions mediate genetic effects on gene expression
Delaneau, O., Zazhytska, M., Borel, C., Giannuzzi, G., Rey, G., Howald, C., Kumar, S., Ongen, H., Popadin, K., Marbach, D., et al. (2019) · Science · doi:10.1126/science.aat8266 · Cited by 168 · see citing works
Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization
Bohn, M., & Heermann, D. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012218 · Cited by 168 · see citing works
Reconstitution of mitotic chromatids with a minimum set of purified factors
Shintomi, K., Takahashi, T. S., & Hirano, T. (2015) · Nature Cell Biology · doi:10.1038/ncb3187 · Cited by 166 · see citing works
Human condensin I and II drive extensive ATP-dependent compaction of nucleosome-bound DNA
Kong, M., Cutts, E. E., Pan, D., Beuron, F., Kaliyappan, T., Xue, C.-Y., Morris, E., Musacchio, A., Vannini, A., & Greene, E. (2019) · bioRxiv · doi:10.1101/683540 · Cited by 164 · cited 1×
“Conservatively estimating that condensin or cohesin require two ATP per extrusion step and several attempts to traverse each nucleosome (~150 bp), the ATP cost to extrude 6 Gb is of order 10 x (6 10(9)/150)~10(8) (we assume only ~5 attempts because in vitro extrusion speeds are not measurably altered by nucleosomes [K…”
BackgroundTowards a unified Model of SMC Complex Function
Hassler, M., Shaltiel, I. A., & Haering, C. (2018) · Current Biology · doi:10.1016/j.cub.2018.08.034 · Cited by 162 · see citing works
Marbouty, M., Cournac, A., Flot, J., Marie-Nelly, H., Mozziconacci, J., & Koszul, R. (2014) · eLife · doi:10.7554/elife.03318 · Cited by 160 · cited 2× · see citing works
“…et al., 2014; Wilhelm et al., 2015)), one-sided extrusion fails to yield the secondary diagonal that is characteristic of the chromosome contact maps of B. subtilis (Figure 4 a) and other bacteria (Böhm et al., 2019; Le et al., 2013; Marbouty et al., 2014; Umbarger et al., 2011; Wang et al., 2015).”
BackgroundCohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle
Lazar‐Stefanita, L., Scolari, V., Mercy, G., Muller, H., Guérin, T. M., Thierry, A., Mozziconacci, J., & Koszul, R. (2017) · EMBO Journal · doi:10.15252/embj.201797342 · Cited by 158 · see citing works
Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization
Diebold-Durand, M.-L., Lee, H., Ruiz-Ávila, L. B., Noh, H., Shin, H.-C., Im, H., Bock, F., Burmann, F., Durand, A., Basfeld, A., et al. (2017) · Molecules and Cells · doi:10.1016/j.molcel.2017.06.010 · Cited by 155 · see citing works
Hu, B., Petela, N. J., Kurze, A., Chan, K.-L., Chapard, C., & Nasmyth, K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv670 · Cited by 155 · see citing works
Structural Basis for a Safety-Belt Mechanism That Anchors Condensin to Chromosomes
Kschonsak, M., Merkel, F., Bisht, S., Metz, J., Rybin, V., Hassler, M., & Haering, C. H. (2017) · Cell · doi:10.1016/j.cell.2017.09.008 · Cited by 152 · cited 23× · see citing works
“Over time, the subunits may translocate along DNA, and the LEF eventually unbinds from DNA.”
InfluentialDNA-loop extruding condensin complexes can traverse one another
Kim, E., Kerssemakers, J., Shaltiel, I. A., Haering, C., & Dekker, C. (2019) · Nature · doi:10.1038/s41586-020-2067-5 · Cited by 145 · cited 6× · see citing works
“Experimental work on yeast condensins (Ganji et al., 2018; Kim et al., 2019) has observed that loop extrusion by yeast condensins occurs in a one-sided manner.”
BackgroundInfluentialRNA polymerases as moving barriers to condensin loop extrusion
Brandão, H. B., Paul, P., van den Berg, A. A., Rudner, D. Z., Wang, X., & Mirny, L. A. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1907009116 · Cited by 143 · cited 10× · see citing works
“The symmetry of the juxtaposed chromosome arms implies that bSMC should be a two-sided LEF (Brandão et al., 2019; Wang et al., 2017) .”
BackgroundMethodResultInfluentialSelf-citationMartin, C.-A., Murray, J. E., Carroll, P., Leitch, A., Mackenzie, K. J., Halachev, M., Fetit, A. E., Keith, C., Bicknell, L. S., Fluteau, A., et al. (2016) · Genes & Development · doi:10.1101/gad.286351.116 · Cited by 141 · cited 3× · see citing works
“, 2016) , DNA damage, aneuploidy, developmental disorders (Martin et al., 2016) , and cancer (Mazumdar et al.”
BackgroundInfluentialSub-nucleosomal Genome Structure Reveals Distinct Nucleosome Folding Motifs
Ohno, M., Ando, T., Priest, D. G., Kumar, V., Yoshida, Y., & Taniguchi, Y. (2019) · Cell · doi:10.1016/j.cell.2018.12.014 · Cited by 141 · see citing works
Wilhelm, L., Burmann, F., Minnen, A., Shin, H.-C., Toseland, C., Oh, B., & Gruber, S. (2015) · eLife · doi:10.7554/elife.06659 · Cited by 139 · cited 2× · see citing works
“As seen in Figure 4 b (right panel), with bSMC loading only at a predetermined site (with up to 30 bSMCs per origin of replication (Graham et al., 2014; Wilhelm et al., 2015) ), one-sided extrusion fails to yield the secondary diagonal that is characteristic of the chromosome contact maps of B.”
BackgroundSMC complexes differentially compact mitotic chromosomes according to genomic context
Schalbetter, S. A., Goloborodko, A. A., Fudenberg, G., Belton, J.-M., Miles, C., Yu, M., Dekker, J., Mirny, L. A., & Baxter, J. (2017) · Nature Cell Biology · doi:10.1038/ncb3594 · Cited by 137 · cited 5× · see citing works
“, ~2-fold linear compaction, Figure 2 - figure supplement 7 ) produces chromosome contact maps consistent with those obtained from Hi-C experiments (Schalbetter et al., 2017) .”
BackgroundMethodInfluentialSelf-citationCohesin acetylation and Wapl-Pds5 oppositely regulate translocation of cohesin along DNA
Kanke, M., Tahara, E., Huis in't Veld, P. J., & Nishiyama, T. (2016) · The EMBO Journal · doi:10.15252/embj.201695756 · Cited by 136 · see citing works
Determining cellular CTCF and cohesin abundances to constrain 3D genome models
Cattoglio, C., Pustova, I., Walther, N., Ho, J. J., Hantsche-Grininger, M., Inouye, C. J., Hossain, M. J., Dailey, G. M., Ellenberg, J., Darzacq, X., et al. (2019) · eLife · doi:10.7554/elife.40164 · Cited by 133 · cited 3× · see citing works
“…3 - figure supplement 1) and experimental observations, we consider a separation between loop extruders of d=200 kb and a processivity of λ=200 kb (Cattoglio et al., 2019; Fudenberg et al., 2016; Holzmann et al., 2019) in the main text, and we consider other parameter values in the…”
BackgroundMethodNonequilibrium Chromosome Looping via Molecular Slip Links
Brackley, C. A., Johnson, J., Michieletto, D., Morozov, A. N., Nicodemi, M., Cook, P. R., & Marenduzzo, D. (2017) · Physical Review Letters · doi:10.1103/physrevlett.119.138101 · Cited by 128 · see citing works
Riggs, A. D. (1990) · Philosophical Transactions of the Royal Society of London. B, Biological Sciences · doi:10.1098/rstb.1990.0012 · Cited by 126 · cited 2× · see citing works
“The SMC complex progressively enlarges the loop by reeling chromatin from outside the loop into the growing loop (Alipour and Marko, 2012; Nasmyth, 2001; Riggs, 1990).”
BackgroundTran, N., Laub, M., & Le, T. (2017) · bioRxiv · doi:10.1101/125344 · Cited by 125 · see citing works
Chromosomes progress to metaphase in multiple discrete steps via global compaction/expansion cycles
Liang, Z., Zickler, D., Prentiss, M., Chang, F., Witz, G., Maeshima, K., & Kleckner, N. (2015) · Cell · doi:10.1016/j.cell.2015.04.030 · Cited by 122 · cited 1× · see citing works
“We measure the resulting 3D compaction by computing chromosome volume, V , which is expected to decrease by >2-fold during mitotic compaction (Daban, 2003; Hihara et al., 2012; Liang et al., 2015; Nagasaka et al., 2016; Sumner, 1991) .”
MethodThe SMC condensin complex is required for origin segregation in Bacillus subtilis
Wang, X.-D., Tang, O., Riley, E. P., & Rudner, D. (2014) · Current Biology · doi:10.1016/j.cub.2013.11.050 · Cited by 121 · see citing works
Marko, J., Rios, P. D. L., Barducci, A., & Gruber, S. (2018) · bioRxiv · doi:10.1093/nar/gkz497 · Cited by 116 · cited 4× · see citing works
“Such a switching mechanism could be achieved in vivo by a stochastic strand switching mechanism in which both upstream and downstream DNA can be captured by the loop extruder (Hassler et al., 2018; Marko et al., 2019) .”
BackgroundResultInfluentialSelf-citationAbsolute quantification of cohesin, CTCF and their regulators in human cells
Holzmann, J., Politi, A. Z., Nagasaka, K., Hantsche-Grininger, M., Walther, N., Koch, B., Fuchs, J., Dürnberger, G., Tang, W., Ladurner, R., et al. (2019) · eLife · doi:10.7554/elife.46269 · Cited by 109 · cited 3× · see citing works
“We perform polymer simulations for each model, sweeping λ and d (Cattoglio et al., 2019; Fudenberg et al., 2016; Holzmann et al., 2019) , as well as model-specific parameters.”
BackgroundMethodInfluentialCondensin-Dependent Chromatin Compaction Represses Transcription Globally during Quiescence
Swygert, S. G., Kim, S., Wu, X., Fu, T., Hsieh, T.-H. S., Rando, O. J., Eisenman, R. N., Shendure, J., McKnight, J. N., & Tsukiyama, T. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.11.020 · Cited by 107 · cited 3× · see citing works
“In quiescent cells, condensins generate dots at the corners of small (10-60 kb), transcription-silencing domains in micro-C maps (Swygert et al., 2019) .”
BackgroundRegulation of Cohesin-Mediated Chromosome Folding by Eco1 and Other Partners
Dauban, L., Montagne, R., Thierry, A., Lazar‐Stefanita, L., Bastié, N., Gadal, O., Cournac, A., Koszul, R., & Beckouët, F. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.01.019 · Cited by 104 · cited 5× · see citing works
“However, pure one-sided extrusion alone is insufficient to form dots in Hi-C and micro-C (Dauban et al., 2020; Ohno et al., 2019; Swygert et al., 2019) .”
BackgroundInfluentialMitotic chromosome assembly despite nucleosome depletion in Xenopus egg extracts
Shintomi, K., Inoue, F., Watanabe, H., Ohsumi, K., Ohsugi, M., & Hirano, T. (2017) · Science · doi:10.1126/science.aam9702 · Cited by 98 · see citing works
Scanning electron microscopy of mammalian chromosomes from prophase to telophase
Sumner, A. (1991) · Chromosoma · doi:10.1007/bf00337519 · Cited by 98 · cited 1× · see citing works
“We measure the resulting 3D compaction by computing chromosome volume, V, which is expected to decrease by >2-fold during mitotic compaction (Daban, 2003; Hihara et al., 2012; Liang et al., 2015; Nagasaka et al., 2016; Sumner, 1991).”
MethodA simple biophysical model emulates budding yeast chromosome condensation
Cheng, T. M. K., Heeger, S., Chaleil, R. A. G., Matthews, N., Stewart, A., Wright, J. D., Lim, C., Bates, P., & Uhlmann, F. (2015) · eLife · doi:10.7554/elife.05565 · Cited by 97 · cited 2× · see citing works
“It has previously been suggested that 3D attractive interactions between LEFs could facilitate compaction of mitotic chromosomes (Cheng et al., 2015; Sakai et al., 2018) .”
BackgroundCondensin aids sister chromatid decatenation by topoisomerase II
Charbin, A., Bouchoux, C., & Uhlmann, F. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt882 · Cited by 93 · see citing works
Studies of metaphase and interphase chromosomes using fluorescence in situ hybridization.
Trask, B., Allen, S., Massa, H., Fertitta, A., Sachs, R. K., van den Engh, G. J., & Wu, M. (1993) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1993.058.01.084 · Cited by 92 · cited 1×
“Fluorescence imaging and Hi-C show that these loops maintain the linear ordering of the genome (Gibcus et al., 2018; Naumova et al., 2013; Strukov and Belmont, 2009; Trask et al., 1993) .”
BackgroundSister chromatid resolution is an intrinsic part of chromosome organization in prophase
Nagasaka, K., Hossain, M. J., Roberti, M. J., Ellenberg, J., & Hirota, T. (2016) · Nature Cell Biology · doi:10.1038/ncb3353 · Cited by 89
Condensin-mediated remodeling of the mitotic chromatin landscape in fission yeast
Kakui, Y., Rabinowitz, A., Barry, D., & Uhlmann, F. (2017) · Nature Genetics · doi:10.1038/ng.3938 · Cited by 86 · cited 2× · see citing works
“, 2017) and formation of chromatin domains without dots (Kakui et al., 2017; Lazar Stefanita et al., 2017; Mizuguchi et al., 2014; Schalbetter et al., 2017; Tanizawa et al., 2017) is consistent with one-sided extrusion by yeast SMC complexes.”
BackgroundMinnen, A., Burmann, F., Wilhelm, L., Anchimiuk, A., Diebold-Durand, M.-L., & Gruber, S. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.01.066 · Cited by 82 · cited 2× · see citing works
“Experiments show that bSMC is loaded at a bacterial parS site near the origin of replication, and then, while bridging the two arms, actively and processively moves along the chromosome, thus juxtaposing or “zipping” the arms together (Minnen et al., 2016; Tran et al., 2017; Wang et al., 2018, 2017) .”
BackgroundKim, K.-D., Tanizawa, H., Iwasaki, O., & Noma, K.-I. (2016) · Nature Genetics · doi:10.1038/ng.3647 · Cited by 80 · see citing works
Real‐time detection of condensin‐driven DNA compaction reveals a multistep binding mechanism
Eeftens, J., Bisht, S., Kerssemakers, J., Kschonsak, M., Haering, C., & Dekker, C. (2017) · bioRxiv · doi:10.15252/embj.201797596 · Cited by 79 · cited 1× · see citing works
“Although not yet observed experimentally, we hypothesize that switching activity of SMC complexes could potentially be induced by exchange of subunits within the SMC complex, different solution conditions, or post-translational or genetic modifications, all of which can alter SMC complex behavior in experiments (Eefte…”
BackgroundMetaphase chromosome structure is dynamically maintained by condensin I-directed DNA (de)catenation
Piskadlo, E., Tavares, A., & Oliveira, R. A. (2017) · eLife · doi:10.7554/elife.26120 · Cited by 77 · cited 5× · see citing works
“Median distance and overlap are expected to contribute to the disentanglement of chromatids (Piskadlo et al., 2017; Sen et al., 2016), which facilitates chromosome segregation by preventing anaphase bridge formation (Charbin et al., 2014; Green et al., 2012; Hagstrom et al., 2002; Nagasaka et al.,…”
BackgroundInfluentialInterallelic complementation provides functional evidence for cohesin–cohesin interactions on DNA
Eng, T., Guacci, V., & Koshland, D. (2015) · Molecular Biology of the Cell · doi:10.1091/mbc.e15-06-0331 · Cited by 76 · see citing works
Böhm, K., Giacomelli, G., Schmidt, A., Imhof, A., Koszul, R., Marbouty, M., & Bramkamp, M. (2019) · Nature Communications · doi:10.1038/s41467-020-15238-4 · Cited by 75 · cited 2× · see citing works
“In many bacteria, bSMCs loaded near the origin of replication (by the parABS system) generate contacts centered about the ori-ter axis, which is visible in Hi-C maps as a secondary diagonal (Böhm et al., 2020; Le et al., 2013; Marbouty et al., 2014; Umbarger et al., 2011; Wang et al., 2017, 2015) .”
BackgroundWang, X.-D., Hughes, A. C., Brandão, H. B., Walker, B. C., Lierz, C., Cochran, J. C., Oakley, M. G., Kruse, A., & Rudner, D. (2018) · Molecules and Cells · doi:10.1016/j.molcel.2018.07.006 · Cited by 71 · see citing works
Self-citationOcampo-Hafalla, M. T., & Uhlmann, F. (2011) · Journal of Cell Science · doi:10.1242/jcs.073866 · Cited by 68 · cited 1× · see citing works
“While such dots can be explained by two-sided extrusion, we also considered the possibility that one-sided extrusion assisted by RNA polymerases that can push one side of an SMC complex (Lengronne et al., 2004; Ocampo-Hafalla and Uhlmann, 2011) .”
BackgroundHigh concentration of DNA in condensed chromatin.
Daban, J. (2003) · Biochemistry and cell biology = Biochimie et biologie cellulaire · doi:10.1139/o03-037 · Cited by 68 · cited 1× · see citing works
“We measure the resulting 3D compaction by computing chromosome volume, V, which is expected to decrease by >2-fold during mitotic compaction (Daban, 2003; Hihara et al., 2012; Liang et al., 2015; Nagasaka et al., 2016; Sumner, 1991).”
MethodCell Cycle-dependent Phosphorylation, Nuclear Localization, and Activation of Human Condensin*
Takemoto, A., Kimura, K., Yokoyama, S., & Hanaoka, F. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m310925200 · Cited by 66 · cited 1×
“, 2016a) showed that LEFs can compact and resolve metazoan chromosomes (~100 Mb in length) for physiological densities of LEFs (1 per d = 10–30 kb [Fukui and Uchiyama, 2007; Takemoto et al., 2004; Walther et al., 2018]).”
BackgroundFlamholz, A. I., Phillips, R., & Milo, R. (2014) · Molecular Biology of the Cell · doi:10.1091/mbc.e14-09-1347 · Cited by 66 · cited 1× · see citing works
“This upper limit estimate is still less than the ~10 9 ATP present in the cell (Traut, 1994) and less than the ~10 9 ATP/s that the cell produces (Flamholz et al., 2014) .”
BackgroundArchitectural alterations of the fission yeast genome during the cell cycle
Tanizawa, H., Kim, K.-D., Iwasaki, O., & Noma, K.-I. (2017) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3482 · Cited by 65 · see citing works
Chromosome structure: improved immunolabeling for electron microscopy
Maeshima, K., Eltsov, M., & Laemmli, U. K. (2005) · Chromosoma · doi:10.1007/s00412-005-0023-7 · Cited by 62 · cited 1×
“, [Maeshima et al., 2005]), as has been observed in previous simulations (Goloborodko et al.”
ResultMultistep assembly of DNA condensation clusters by SMC
Kim, H., & Loparo, J. (2016) · Nature Communications · doi:10.1038/ncomms10200 · Cited by 59 · see citing works
Barysz, H., Kim, J. H., Chen, Z., Hudson, D., Rappsilber, J., Gerloff, D., & Earnshaw, W. (2015) · Open Biology · doi:10.1098/rsob.150005 · Cited by 59 · cited 1× · see citing works
“In eukaryotes, in situ amino acid crosslinking (Barysz et al., 2015) and in vitro gel filtration (Keenholtz et al., 2017) suggest that condensins can oligomerize.”
BackgroundMarko, J. (2009) · Physical review. E, Statistical, nonlinear, and soft matter physics · doi:10.1103/physreve.79.051905 · Cited by 57 · cited 1×
“…the packaging, resolution, and segregation of chromosomes during mitosis by effectively shortening and disentangling chromatids (Brahmachari and Marko, 2019; Eykelenboom et al., 2019; Goloborodko et al., 2016a; Green et al., 2012; Marko, 2009; Nagasaka et al., 2016; Sakai et al., 2018, 2016).”
BackgroundSelf-citationMultilayer chromosome organization through DNA bending, bridging and extrusion.
Gruber, S. (2014) · Current Opinion in Microbiology · doi:10.1016/j.mib.2014.09.018 · Cited by 55 · cited 1× · see citing works
“These diverse chromosome phenomena are hypothesized to be driven by a common underlying physical mechanism by which SMC complexes processively extrude chromatin or DNA loops (Alipour and Marko, 2012; Bürmann and Gruber, 2015; Fudenberg et al., 2017, 2016; Goloborodko et al., 2016a, 2016b; Gruber, 2014; Nasmyth, 2001;…”
BackgroundChromosome disentanglement driven via optimal compaction of loop-extruded brush structures
Brahmachari, S., & Marko, J. F. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1906355116 · Cited by 54 · see citing works
Self-citationSheiko, S., Borisov, O. V., Prokhorova, S., & Möller, M. (2004) · The European Physical Journal E : Soft matter · doi:10.1140/epje/e2004-00049-8 · Cited by 53 · cited 2×
“For mitotic chromosomes, our results, along with previous work on polymer combs suggests otherwise (Fytas and Theodorakis, 2013; Sheiko et al., 2004) .”
ResultPhysical Proximity of Sister Chromatids Promotes Top2-Dependent Intertwining
Sen, N., Leonard, J., Torres, R., García-Luis, J., Palou-Marin, G., & Aragón, L. (2016) · Molecules and Cells · doi:10.1016/j.molcel.2016.09.007 · Cited by 52 · see citing works
HTLV‐I‐associated myelopathy and polymyositis in a US native
Evans, B., Gore, I., Harrell, L., Arnold, T., & Oh, S. (1989) · Neurology · doi:10.1212/wnl.39.12.1572 · Cited by 52
Effect of geometrical rotation on conductance fluctuations in graphene quantum dots
Ying, L., Huang, L., Lai, Y., & Zhang, Y. (2013) · Journal of Physics: Condensed Matter · doi:10.1088/0953-8984/25/10/105802 · Cited by 50 · cited 2× · see citing works
“These findings are consistent with previous theoretical and computational work on polymer combs (Fytas and Theodorakis, 2013; Sheiko et al., 2004), showing that 3D attractive interactions lead to a coil-globule transition.”
ResultCondensin II mutation causes T-cell lymphoma through tissue-specific genome instabilityPreprint
Woodward, J., Taylor, G., Soares, D., Boyle, S., Sie, D., Read, D., Chathoth, K. T., Vukovic, M., Tarrats, N., Jamieson, D., et al. (2016) · Genes & Development · doi:10.1101/gad.284562.116 · Cited by 47 · see citing works
Chromatin topology in development and disease
Bompadre, O., & Andrey, G. (2019) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2019.04.007 · Cited by 46 · see citing works
MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin
Zawadzka, K., Zawadzki, P., Baker, R. A., Rajasekar, K., Wagner, F., Sherratt, D., & Arciszewska, L. (2018) · eLife · doi:10.7554/elife.31522 · Cited by 44 · cited 2× · see citing works
“, 2012) linked by the kleisin molecule, MukF (Zawadzka et al., 2018) .”
BackgroundRepulsive Forces Between Looping Chromosomes Induce Entropy-Driven Segregation
Bohn, M., & Heermann, D. (2011) · PLoS ONE · doi:10.1371/journal.pone.0014428 · Cited by 43 · see citing works
Benedetti, F., Račko, D., Dorier, J., Burnier, Y., & Stasiak, A. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx716 · Cited by 42 · see citing works
Distinct Roles for Condensin’s Two ATPase Sites in Chromosome Condensation
Elbatsh, A., Kim, E., Eeftens, J., Raaijmakers, J., van der Weide, R. H., García-Nieto, A., Bravo, S., Ganji, M., de Bos, J. U., Teunissen, H., et al. (2019) · Molecules and Cells · doi:10.1016/j.molcel.2019.09.020 · Cited by 40 · see citing works
Mitotic chromosome structure: reproducibility of folding and symmetry between sister chromatids.
Strukov, Y., & Belmont, A. S. (2009) · Biophysical Journal · doi:10.1016/j.bpj.2008.10.051 · Cited by 40 · see citing works
Oligomerization and ATP stimulate condensin-mediated DNA compaction
Keenholtz, R. A., Dhanaraman, T., Palou, R., Yu, J., D'Amours, D., & Marko, J. (2017) · Scientific Reports · doi:10.1038/s41598-017-14701-5 · Cited by 39 · cited 2× · see citing works
“Although not yet observed experimentally, we hypothesize that switching activity of SMC complexes could potentially be induced by exchange of subunits within the SMC complex, different solution conditions, or post-translational or genetic modifications, all of which can alter SMC complex behavior in experiments (Eefte…”
BackgroundSelf-citationLimits of chromosome compaction by loop-extruding motors
Banigan, E., & Mirny, L. (2018) · bioRxiv · doi:10.1101/476424 · Cited by 37
Self-citationCentromeres License the Mitotic Condensation of Yeast Chromosome Arms
Kruitwagen, T., Chymkowitch, P., Denoth-Lippuner, A., Enserink, J., & Barral, Y. (2018) · Cell · doi:10.1016/j.cell.2018.09.012 · Cited by 36
Chromosome protein framework from proteome analysis of isolated human metaphase chromosomes.
Fukui, K., & Uchiyama, S. (2007) · The chemical record · doi:10.1002/tcr.20120 · Cited by 35
N. Institute (2020) · Definitions · doi:10.32388/wre023 · Cited by 33 · cited 4×
“…phenomena are driven by the condensin complex (Eykelenboom et al., 2019; Hagstrom et al., 2002; Hirano, 2016; Hirano et al., 1997; Hirano and Mitchison, 1994; Hudson et al., 2003; Nagasaka et al., 2016; Ono et al., 2003; Piskadlo et al., 2017; Shintomi et al., 2017, 2015; Steffensen et al., 2001).”
BackgroundInfluentialNagy, G., Czipa, E., Steiner, L., Nagy, T., Pongor, S., Nagy, L., & Barta, E. (2016) · BMC Genomics · doi:10.1186/s12864-016-2940-7 · Cited by 27 · see citing works
SMC condensin: promoting cohesion of replicon arms
Burmann, F., & Gruber, S. (2015) · Nature Structural &Molecular Biology · doi:10.1038/nsmb.3082 · Cited by 26 · cited 1× · see citing works
“These diverse chromosome phenomena are hypothesized to be driven by a common underlying physical mechanism by which SMC complexes processively extrude chromatin or DNA loops (Alipour and Marko, 2012; Bürmann and Gruber, 2015; Fudenberg et al., 2017, 2016; Goloborodko et al., 2016a, 2016b; Gruber, 2014; Nasmyth, 2001;…”
BackgroundLive imaging of marked chromosome regions reveals their dynamic resolution and compaction in mitosis
Eykelenboom, J. K., Gierliński, M., Yue, Z.-J., Hégarat, N., Pollard, H., Fukagawa, T., Hochegger, H., & Tanaka, T. U. (2019) · Journal of Cell Biology · doi:10.1083/jcb.201807125 · Cited by 24 · cited 3× · see citing works
“Experimentally, it has been shown that these phenomena are driven by the condensin complex (Eykelenboom et al., 2019; Hagstrom et al., 2002; Hirano, 2016; Hirano et al., 1997; Hirano and Mitchison, 1994; Hudson et al., 2003; Nagasaka et al., 2016; Ono et al., 2003; Piskadlo et al., 2017; Shintomi et al., 2017, 2015; S…”
BackgroundModeling 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 · cited 2× · see citing works
“It has previously been suggested that 3D attractive interactions between LEFs could facilitate compaction of mitotic chromosomes (Cheng et al., 2015; Sakai et al., 2018) .”
BackgroundBacterial 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 · see citing works
Osmotic mechanism of the loop extrusion process.
Yamamoto, T., & Schiessel, H. (2017) · Physical Review E · doi:10.1103/physreve.96.030402 · Cited by 20 · cited 17× · see citing works
“Dots are foci on Hi-C maps that reflect enriched contact frequency between specific loci, often found at the corners of TADs and/or between proximal (<1-2 Mb) CTCF sites (Krietenstein et al., 2019; Rao et al., 2014).”
BackgroundInfluentialSMC Condensation Centers in Bacillus subtilis Are Dynamic Structures
Borgmann, L. A. K. K., Hummel, H., Ulbrich, M. H., & Graumann, P. (2013) · Journal of Bacteriology · doi:10.1128/jb.02097-12 · Cited by 19 · see citing works
Paschal, B., Mcreynolds, L., Noren, C., & Nichols, N. (2008) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb0308s84 · Cited by 17 · cited 7×
“Two-sided loop extrusion models (Brandão et al., 2019; Fudenberg et al., 2017, 2016; Goloborodko et al., 2016a, 2016b; Sanborn et al., 2015) can account for the various chromosome organization phenomena described above, but in vitro single-molecule experiments suggest that at least some SMC…”
BackgroundMethodResultInfluentialCohesin and condensin extrude loops in a cell-cycle dependent manner
Golfier, S., Quail, T., Kimura, H., & Brugués, J. (2019) · bioRxiv · doi:10.1101/821306 · Cited by 10
Choreography of budding yeast chromosomes during the cell cycle
Lazar‐Stefanita, L., Scolari, V., Mercy, G., Thierry, A., Muller, H., Mozziconacci, J., & Koszul, R. (2016) · bioRxiv · doi:10.1101/096826 · Cited by 5
Sakai, Y., Tachikawa, M., & Mochizuki, A. (2016) · Physical Review E · doi:10.1103/physreve.94.042403 · Cited by 3
Nucleosome Curtains and their application to the study of DNA condensation by condensin
Moevus, C. J. (2019) · doi:10.7916/d8-zcrc-2f56 · Cited by 1 · cited 2×
“Indeed, recent experimental evidence suggests that pairs of yeast condensins may be able to cooperatively grow loops bidirectionally (Kim et al., 2019), while human condensins can perform either one- or two-sided loop extrusion (Kong et al., 2019; Moevus, 2019).”
Background
Flagged first, then by citations
7 of the 182 references couldn’t be matched to a known paper.
Research works printed but not linked: 5
- Banigan E van den Berg AA Brandão HB 2020 Codes relevant for "Chromosome organization by one-sided and two-sided loop extrusion" GitHub 01af355 https://github.com/mirnylab/one_sided_extrusion PMC7295573 32250245
- Fytas NG Theodorakis PE 2013 Molecular dynamics simulations of single-component bottle-brush polymers with flexible backbones under poor solvent conditions Journal of Physics: Condensed Matter 25 285105 10.1088/0953-8984/25/28/285105 23765452 · DOI
- Glynn EF Megee PC Yu HG Mistrot C Unal E Koshland DE DeRisi JL Gerton JL 2004 Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae PLOS Biology 2 E259 10.1371/journal.pbio.0020259 15309048 PMC490026 · DOI
- Kerpedjiev P Abdennur N Lekschas F McCallum C Dinkla K Strobelt H Luber JM Ouellette SB Azhir A Kumar N Hwang J Lee S Alver BH Pfister H Mirny LA Park PJ Gehlenborg N 2018 HiGlass: web-based visual exploration and analysis of genome interaction maps Genome Biology 19 125 10.1186/s13059-018-1486-1 30143029 PMC6109259 · DOI
- Seitan VC Faure AJ Zhan Y McCord RP Lajoie BR Ing-Simmons E Lenhard B Giorgetti L Heard E Fisher AG Flicek P Dekker J Merkenschlager M 2013 Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments Genome Research 23 2066 2077 10.1101/gr.161620.113 24002784 PMC3847776 · DOI · Paper page
Cited by
Sorted by citations
Transcription shapes 3D chromatin organization by interacting with loop extrusion
Banigan, E. J., Tang, W., van den Berg, A. A., Stocsits, R. R., Wutz, G., Brandão, H. B., Busslinger, G. A., Peters, J., & Mirny, L. A. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2210480120 · Cited by 216 · see citing works
“For active extrusion, τ=100 for CTCF KO and τ=1000 for DKO simulations, giving mean LEF processivities of λ=200 kb and 2000 kb, respectively, similar to previous studies (Banigan et al., 2020; Nuebler et al., 2018).”
BackgroundMethodResultInfluentialSelf-citationCohesin and condensin extrude DNA loops in a cell cycle-dependent manner
Golfier, S., Quail, T., Kimurâ, H., & Jan Brugués, A. (2020) · eLife · doi:10.7554/elife.53885 · Cited by 196 · see citing works
“The cell cycle-dependent activities of con- densin and cohesin could account for the transition between symmetric and non-symmetric loop extrusion (Banigan et al., 2019; Abramo et al., Figure 1 continued https://elifesciences.org/articles/53885#fig1video8 Figure 1—video 9.”
BackgroundResultInfluentialLoop extrusion: theory meets single-molecule experiments
Banigan, E. J., & Mirny, L. A. (2020) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2020.04.011 · Cited by 160 · see citing works
Self-citationMCM complexes are barriers that restrict cohesin-mediated loop extrusion
Dequeker, B. J. H., Scherr, M. J., Brandão, H. B., Gassler, J., Powell, S. T., Gáspár, I., Flyamer, I. M., Lalic, A., Tang, W., Stocsits, R. R., et al. (2022) · Nature · doi:10.1038/s41586-022-04730-0 · Cited by 149 · see citing works
Self-citationLooping the Genome with SMC Complexes
Kim, E., Barth, R., & Dekker, C. (2023) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-032620-110506 · Cited by 96 · see citing works
CTCF as a boundary factor for cohesin-mediated loop extrusion: evidence for a multi-step mechanism
Hansen, A. S. (2020) · Nucleus · doi:10.1080/19491034.2020.1782024 · Cited by 101 · see citing works
“Polymer simulations of the simple loop extrusion model with just cohesin and CTCF generate contact maps similar to experimental maps at the level of TADs and loop domains [17,18,38,44,77].”
MethodDNA-loop-extruding SMC complexes can traverse one another in vivo
Brandão, H. B., Ren, Z., Karaboja, X., Mirny, L. A., & Wang, X. (2021) · Nature Structural & Molecular Biology · doi:10.1038/s41594-021-00626-1 · Cited by 90 · see citing works
“In eukaryotes, bypassing can help promote chromosome compaction and sister-chromatid segregation 30,36 .”
BackgroundMethodInfluentialSelf-citationChromatin architecture transitions from zebrafish sperm through early embryogenesisPreprint
Wike, C. L., Guo, Y., Tan, M., Nakamura, R., Shaw, D. K., Díaz, N., Whittaker-Tademy, A. F., Durand, N. C., Aiden, E. L., Vaquerizas, J. M., et al. (2021) · Genome Research · doi:10.1101/gr.269860.120 · Cited by 87 · see citing works
Tracking and interpreting long-range chromatin interactions with super-resolution live-cell imaging
Brandão, H. B., Gabriele, M., & Hansen, A. S. (2021) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2020.11.002 · Cited by 77 · see citing works
Self-citationChromatin jets define the properties of cohesin-driven in vivo loop extrusion.
Guo, Y., Al-Jibury, E., Garcia-Millan, R., Ntagiantas, K., King, J. W. D., Nash, A. J., Galjart, N., Lenhard, B., Rueckert, D., Fisher, A., et al. (2022) · Molecules and Cells · doi:10.1016/j.molcel.2022.09.003 · Cited by 69 · see citing works
Spatial Organization of Chromatin: Emergence of Chromatin Structure During Development
Ghosh, R. P., & Meyer, B. J. (2021) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-032321-035734 · Cited by 56 · see citing works
“Polymer simulations showed that stochastic strand switching can efficiently recapitulate chromosome compaction levels achieved through a two-sided extrusion model (Banigan et al. 2020) (Figure 1c–f).”
BackgroundVos, E. S. M., Valdes‐Quezada, C., Huang, Y., Allahyar, A., Verstegen, M. J. A. M., Felder, A.-K., van der Vegt, F., Uijttewaal, E. C. H., Krijger, P. H. L., & de Laat, W. L. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.06.008 · Cited by 61 · see citing works
Nomidis, S. K., Carlon, E., Gruber, S., & Marko, J. (2022) · bioRxiv · doi:10.1093/nar/gkac268 · Cited by 48 · see citing works
Self-citationSuper-Enhancers, Phase-Separated Condensates, and 3D Genome Organization in Cancer
Tang, S., Vijayakumar, U., Zhang, Y., & Fullwood, M. (2022) · Cancers · doi:10.3390/cancers14122866 · Cited by 46 · see citing works
“This is explained by the loop extrusion model in which frequent transient loops are organised by structural maintenance of chromosomes (SMC) complexes that reel in chromatin, forming growing loops that stop at CCCTC-binding factor (CTCF) boundaries [14,15].”
BackgroundSMC complexes: Lifting the lid on loop extrusion
Higashi, T. L., & Uhlmann, F. (2022) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2021.12.003 · Cited by 56 · see citing works
Bringing the genetically minimal cell to life on a computer in 4D
Thornburg, Z. R., Maytin, A., Kwon, J., Brier, T. A., Gilbert, B. R., Fu, E., Gao, Y.-L., Quenneville, J., Wu, T., Li, H., et al. (2026) · Cell · doi:10.1016/j.cell.2026.02.009 · Cited by 44 · see citing works
SMC motor proteins extrude DNA asymmetrically and can switch directions
Barth, R., Davidson, I. F., van der Torre, J., Taschner, M., Gruber, S., Peters, J.-M., & Dekker, C. (2025) · Cell · doi:10.1016/j.cell.2024.12.020 · Cited by 40 · see citing works
“Close inspection of their loop extrusion dynamics revealed that cohesin and SMC5/6 undergo short phases of active extrusion, characterized by loop growth, which are interspersed by diffusion 3 of the loop and SMC across the DNA, and loop slipping, the gradual loss of the previously extruded loop.”
InfluentialCondensin DC loads and spreads from recruitment sites to create loop-anchored TADs in C. elegans
Kim, J., Jimenez, D., Ragipani, B., Zhang, B., Street, L., Kramer, M., Albritton, S., Winterkorn, L., Morao, A., & Ercan, S. (2022) · bioRxiv · doi:10.1101/2021.03.23.436694 · Cited by 38
“As randomly distributed LEFs track along DNA, pairs of increasingly distant genomic loci are looped in 3-dimensional space except when LEFs encounter a barrier.”
BackgroundInfluentialPredicting Genome Architecture: Challenges and Solutions
Belokopytova, P., & Fishman, V. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2020.617202 · Cited by 38 · see citing works
“A recent preprint from Banigan et al. (2020) shows another impressive application of polymer modeling in which it helps to investigate if a one-or two-sided loop extrusion model works in the cell and to identify a class of one-sided extrusion models that can reproduce in vivo experiments.”
BackgroundStefano, M. D., Paulsen, J., Jost, D., & Martí-Renom, M. (2020) · Current Opinion in Genetics and Development · doi:10.1016/j.gde.2020.10.004 · Cited by 38 · see citing works
Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation
Galitsyna, A. A., Ulianov, S. V., Bazarevich, M., Bykov, N. S., Veil, M., Gao, M., Perevoschikova, K., Gelfand, M. S., Razin, S. V., Mirny, L. A., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-69105-9 · Cited by 40 · see citing works
Self-citationDNA double-strand break end synapsis by DNA loop extrusion
Yang, J. H., Brandão, H. B., & Hansen, A. S. (2023) · Nature Communications · doi:10.1038/s41467-023-37583-w · Cited by 36 · see citing works
Self-citationLocal chromatin fiber folding represses transcription and loop extrusion in quiescent cells
Swygert, S. G., Lin, D., Portillo‐Ledesma, S., Lin, P.-Y., Hunt, D. R., Kao, C.-F., Tamar Schlick, A., Noble, W. S., & Tsukiyama, T. (2021) · eLife · doi:10.7554/elife.72062 · Cited by 41 · see citing works
Rapid depletion of CTCF and cohesin proteins reveals dynamic features of chromosome architecturePreprint
Liu, N.-Q., Magnitov, M. D., Schijns, M. M. G. A., van Schaik, T., van der Weide, R. H., Teunissen, H., van Steensel, B., & de Wit, E. (2021) · bioRxiv · doi:10.1101/2021.08.27.457977 · Cited by 34 · see citing works
“In Bacillus subtilis, SMC complexes, which are related to cohesin, can be coordinately loaded at the origin of replication using a temperature sensitive mutant (Banigan et al., 2020; Wang et al., 2017, 2018).”
BackgroundCohesin organizes 3D DNA contacts surrounding active enhancers in C. elegansPreprint
Kim, J., Wang, H., & Ercan, S. (2025) · Genome Research · doi:10.1101/gr.279365.124 · Cited by 31 · see citing works
“In simulation, cohesin was inferred to be an effectively two-sided loop-extruding factor (Banigan et al. 2020).”
A comparison of topologically associating domain callers over mammals at high resolution
Sefer, E. (2022) · BMC Bioinformatics · doi:10.1186/s12859-022-04674-2 · Cited by 34 · see citing works
“The loop extrusion is thought to be a viable chromatin organization mechanism according to [48, 102].”
BackgroundChan, B., & Rubinstein, M. (2024) · bioRxiv · doi:10.1073/pnas.2401494121 · Cited by 29 · see citing works
“Compaction on longer contour length scales extends within topologically associated domains (TADs), facilitating gene regulation by distal elements.”
Liu, Y., Zhao, N., Kanemaki, M. T., Yamamoto, Y., Sadamura, Y., Ito, Y., Tokunaga, M., Stasevich, T., & Kimura, H. (2021) · bioRxiv · doi:10.1111/gtc.12893 · Cited by 29 · see citing works
“First, the ZF target sequence should be within 10 kb from the chromatin contact sites considering the resolution of light microscopy (Banigan et al., 2020; Brandão et al., 2021).”
A Lamin Associated Chromatin Model for Chromosome Organization
Maji, A., Ahmed, J., Roy, S., Chakrabarti, B., & Mitra, M. K. (2019) · bioRxiv · doi:10.1101/788497 · Cited by 28
Loop 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 · see citing works
Nanoscale DNA tracing reveals the self-organization mechanism of mitotic chromosomes
Beckwith, K., Brunner, A., Morero, N., Jungmann, R., & Ellenberg, J. (2025) · Cell · doi:10.1016/j.cell.2025.02.028 · Cited by 26 · see citing works
“41,42 Both one-and two-sided extrusion modes have been reported for human condensin.”
All eukaryotic SMC proteins induce a twist of −0.6 at each DNA loop extrusion step
Janissen, R., Barth, R., Davidson, I., Taschner, M., Gruber, S., Peters, J.-M., & Dekker, C. (2024) · bioRxiv · doi:10.1126/sciadv.adt1832 · Cited by 26 · see citing works
“…contribute to the appearance of characteristic CTCF-dependent TAD corner dots in high-throughput chromosome conformation capture (Hi-C) maps ( 59 , 74 , 75 ) since those depend on a fraction of TADs whose DNA is completely contained in SMC-mediated loops ( 76 ) as observed in vivo ( 77 , 78 ).”
Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers
Liu, N.-Q., Magnitov, M. D., Schijns, M. M. G. A., van Schaik, T., Teunissen, H., van Steensel, B., & de Wit, E. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf549 · Cited by 23 · see citing works
Predicting genome organisation and function with mechanistic modelling.
Chiang, M., Brackley, C., Marenduzzo, D., & Gilbert, N. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.11.001 · Cited by 23 · see citing works
“This finding led to more theoretical work examining the impact of one-sided versus two-sided extrusion on the resulting domain architecture [54,55].”
Bendandi, A., Dante, S., Zia, S. R., Diaspro, A., & Rocchia, W. (2020) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2020.00015 · Cited by 23 · see citing works
“In addition to the “one-sided” loop extrusion mechanism described above, recent research indicates that “two-sided” loop extrusion might prove to be more robust in explaining experimental data (Banigan et al., 2019).”
BackgroundGenome-wide absolute quantification of chromatin looping
Jusuf, J. M., Yang, J. H., Toppen, J., Grosse-Holz, S., Gabriele, M., Mach, P., Flyamer, I. M., Zechner, C., Giorgetti, L., Mirny, L. A., et al. (2026) · Nature Structural & Molecular Biology · doi:10.1038/s41594-026-01819-2 · Cited by 22 · see citing works
Self-citationFunction and Evolution of the Loop Extrusion Machinery in Animals
Kabirova, E., Nurislamov, A. R., Shadskiy, A., Smirnov, A. V., Popov, A., Salnikov, P., Баттулин, Н. Р., & Fishman, V. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24055017 · Cited by 25 · see citing works
“The other one, one-sided loop extrusion, suggests that a fraction of SMC complexes reel in DNA from only one side, while the other side remains anchored to its DNA loading site [30].”
BackgroundNicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolutionPreprint
Luo, Z.-Y., Zhang, R., Hu, T.-F., Zhu, Y.-T., Wu, Y.-M., Li, W.-F., Zhang, Z., Yao, X.-B., Liang, H.-Y., & Song, X.-Y. (2022) · Genome Research · doi:10.1101/gr.275986.121 · Cited by 20 · see citing works
“A stripe emerges when one side of extruding is stalled by CTCF while the other side continues extruding (Banigan et al. 2020).”
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 · see citing works
“…Giorgetti, 2019) are required to solve the inverse problem of determining 3D genome organization (Di Pierro et al., 2017; Messelink et al., 2021; Shi and Thirumalai, 2023) and provide mechanistic insights (Sanborn et al., 2015; Fudenberg et al., 2016; Banigan et al., 2020; Fiorillo et al., 2021).”
A low Smc flux avoids collisions and facilitates chromosome organization in Bacillus subtilis
Anchimiuk, A., Lioy, V., Bock, F., Minnen, A., Boccard, F., & Gruber, S. (2021) · eLife · doi:10.7554/elife.65467 · Cited by 19 · see citing works
“undesirable DNA entanglements (such as pseudoknots) (Banigan et al., 2020).”
Decoding the organization, dynamics, and function of the 4D genome
Aboelnour, E., & Bonev, B. (2021) · Developmental Cell · doi:10.1016/j.devcel.2021.04.023 · Cited by 21 · see citing works
The interplay between asymmetric and symmetric DNA loop extrusion
Banigan, E., & Mirny, L. (2020) · bioRxiv · doi:10.7554/elife.63528 · Cited by 19 · see citing works
Self-citationMatityahu, A., & Onn, I. (2021) · Journal of Cell Science · doi:10.1242/jcs.247577 · Cited by 17 · see citing works
“Loop extrusion suppression in condensin and Smc5/6 Loop extrusion is also considered a component of the mitotic chromosome assembly mechanism by the cohesin-related SMC complex condensin (Banigan et al., 2020; Ganji et al., 2018; Kim et al., 2020; Terakawa et al., 2017).”
BackgroundFob1-dependent condensin recruitment and loop extrusion on yeast chromosome III
Dinda, M., Fine, R. D., Saha, S., Wang, Z., Zang, C., Li, M., & Smith, J. S. (2022) · bioRxiv · doi:10.1371/journal.pgen.1010705 · Cited by 15 · see citing works
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 18 · see citing works
“LEF simulations further demonstrate that the dynamic extrusion of loops by SMC complexes combined with the existence of boundary elements encoded in the DNA (for example, sequence-specific binding of CTCF, which is enriched at boundaries and physically interacts with cohesin (Parelho et al., 2008; Wendt et al., 2008))…”
BackgroundInfluentialDynamics of microcompartment formation at the mitosis-to-G1 transition
Goel, V. Y., Aboreden, N. G., Jusuf, J. M., Zhang, H.-Y., Mori, L. P., Mirny, L., Blobel, G. A., Banigan, E., & Hansen, A. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01687-2 · Cited by 14 · see citing works
“6a, top) 37,48–50 .”
Self-citationDNA 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 14 · see citing works
“This ‘switching model’ was found to be the only one-sided extruder model capable of achieving proper chromosome compaction 137 .”
SMC motor proteins extrude DNA asymmetrically and contain a direction switchPreprint
Barth, R., Davidson, I., van der Torre, J., Taschner, M., Gruber, S., Peters, J.-M., & Dekker, C. (2023) · bioRxiv · doi:10.1101/2023.12.21.572892 · Cited by 14 · see citing works
“…the experimentally observed interphase chromosome organization, in particular the formation of TADs, even if the anchor site is only diffusively bound to DNA 56 , while asymmetric extrusion with Z-loop formation and direction switching could recapitulate mitotic chromosome formation 56,57 .”
BackgroundMoDLE: 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 · see citing works
“assessed the level of DNA compaction that can be achieved by different loop extrusion mechanisms and concluded that one-sided loop extrusion alone fails to achieve the level of compaction observed in large metazoan genomes [36].”
BackgroundMethodDrosophila insulator proteins exhibit in vivo liquid–liquid phase separation properties
Amankwaa, B., Schoborg, T. A., & Labrador, M. (2022) · Life Science Alliance · doi:10.26508/lsa.202201536 · Cited by 17 · see citing works
“Insulator and cohesin proteins synergistically mediate the formation of TADs through a chromatin looping process known as loop extrusion in mammals (8, 9).”
BackgroundMultiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila
Götz, M., Messina, O., Espinola, S., Fiche, J., & Nollmann, M. (2022) · Nature Communications · doi:10.1038/s41467-022-32973-y · Cited by 14 · see citing works
“In contrast, chromatin behaves as a random-coil polymer in the absence of cohesin or in absence of monomer-monomer interactions 40,63,64 .”
Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging
Sabaté, T., Lelandais, B., Bertrand, E., & Zimmer, C. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad034 · Cited by 13 · see citing works
“To model loop extrusion, we assumed that a single loop extrusion complex was loaded on the polymer at a random position between the two anchors, whereafter both sides of the polymer chain were extruded simultaneously (bidirectional extrusion (26,71)).”
Vinayak, V., Basir, R., Golloshi, R., Toth, J. M., Sant'Anna, L. E., Lakadamyali, M., McCord, R. P., & Shenoy, V. B. (2025) · Nature Communications · doi:10.1038/s41467-025-59001-z · Cited by 13 · see citing works
“…approaches have provided insight into the dynamic reorganization of chromatin during the transition from interphase to mitosis 101 , revealing the crucial roles of looping motors 48 and transcription-driven supercoiling dynamics in chromatin compaction and recon fi guration 11,102,103 .”
The “Genomic Code”: DNA Pervasively Moulds Chromatin Structures Leaving no Room for “Junk”
Bernardi, G. (2021) · Life · doi:10.3390/life11040342 · Cited by 13 · see citing works
“Extrusion has, however, several problems: (1) removal of cohesin and CTCF from chromosomes showed limited effects on steady-state transcription [85–87]; (2) extrusion does not appear to be a general phenomenon in chromatin domains; indeed, it is “malleable and variable between individual cells” [88] and absent in Dros…”
BackgroundZabolotnaya, E., Mela, I., Henderson, R. M., & Robinson, N. P. (2020) · Biochemical Society Transactions · doi:10.1042/bst20170168 · Cited by 12 · see citing works
Two CTCF motifs impede cohesin-mediated DNA loop extrusion
Barth, R., Janissen, R., Muras, L., van der Torre, J., Litos, G., van der Sluis, E. O., van den Berg, A., Davidson, I., Peters, J.-M., & Dekker, C. (2025) · bioRxiv · doi:10.1101/2025.01.26.634934 · Cited by 12
“…to what extent stalling of cohesin, rather than direction reversal, can explain Hi-C maps, we performed 3D polymer simulations (STAR Methods), 69,70 varying two key parameters: (1) the probability of CTCF stalling cohesin and (2) the likelihood that this stalling also prevents extrusion away…”
Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness
Chowdhury, H. M. A. M., Boult, T. E., & Oluwadare, O. (2023) · bioRxiv · doi:10.1186/s12859-024-05713-w · Cited by 12 · see citing works
“These loops and peaks are important regions from which we can answer questions about chromatin interaction and conformation [6, 9].”
BackgroundAbdulla, A. Z., Salari, H., Tortora, M. M. C., Vaillant, C., & Jost, D. (2023) · Current Opinion in Genetics and Development · doi:10.1016/j.gde.2023.102033 · Cited by 12 · see citing works
Yin, S., NandyMazumdar, M., Paranjapye, A., & Harris, A. (2022) · Genomics · doi:10.1016/j.ygeno.2022.110350 · Cited by 13 · see citing works
Câmara, A. S., Schubert, V., Mascher, M., & Houben, A. (2021) · bioRxiv · doi:10.1093/nar/gkab648 · Cited by 12 · see citing works
“We adopted two-sided LEs because (34) showed that one-sided LEs could not reproduce alone some biological phenomena.”
MethodRNA polymerase backtracking results in the accumulation of fission yeast condensin at active genes
Rivosecchi, J., Jost, D., Vachez, L., Gautier, F., Bernard, P., & Vanoosthuyse, V. (2021) · Life Science Alliance · doi:10.26508/lsa.202101046 · Cited by 12 · see citing works
“An inability to bypass obstacles might result in the formation of unlooped chromatin gaps within mitotic chromosomes (Banigan et al, 2020).”
Rusková, R., & Račko, D. (2021) · Biology · doi:10.3390/biology10020130 · Cited by 12 · see citing works
“Today, the role of SMCs in loop formation and chromosome organization in organisms from bacteria to humans is generally accepted [11].”
BackgroundMaji, A., Padinhateeri, R., & Mitra, M. K. (2019) · bioRxiv · doi:10.1101/861161 · Cited by 12
The physical chemistry of interphase loop extrusion
Tortora, M. M. C., & Fudenberg, G. (2024) · bioRxiv · doi:10.1101/2024.08.23.609419 · Cited by 11
“…et al., 2023) , a dependence of the loop extrusion rate on chromatin tension (Nomidis et al., 2022) and/or local conformation (Conforto et al., 2024) , cohesin backtracking and bypassing (Banigan and Mirny, 2020) or capture of spatially proximal chromatin in trans (Bonato and Michieletto, 2021) .”
Meiotic chromosome organization and crossover patterns
Shang, Y.-L., Tan, T.-C., Fan, C., Nie, H., Wang, Y., Yang, X., Zhai, B., Wang, S., & Zhang, L.-R. (2022) · Biology of Reproduction · doi:10.1093/biolre/ioac040 · Cited by 11 · see citing works
Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C
Liu, N., Low, W. Y., Alinejad‐Rokny, H., Pederson, S., Sadlon, T. J., Barry, S. C., & Breen, J. (2021) · Epigenetics & Chromatin · doi:10.1186/s13072-021-00417-4 · Cited by 14 · see citing works
Cohesin and condensin extrude loops in a cell-cycle dependent manner
Golfier, S., Quail, T., Kimura, H., & Brugués, J. (2019) · bioRxiv · doi:10.1101/821306 · Cited by 10
Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure
(2025) · doi:10.1038/s41467-025-56197-y · Cited by 10 · see citing works
“A simulation study showed that, if a loop-extruding factor shapes a boundary at its loading site as postulated above, it must perform asymmetric loop extrusion combined with one-dimensional diffusion along DNA 83 .”
LoopSage: An Energy-Based Monte Carlo approach for the Loop Extrusion Modelling of Chromatin
Korsak, S., & Plewczynski, D. (2024) · bioRxiv · doi:10.1101/2024.01.10.574968 · Cited by 9
“…how loop extrusion impacts chromatin folding and the global chromatin structure, examining the effects of different types of LE (one-sided, two-sided, symmetrical, asymmetrical) [16, 18, 20] and exploring the influence of other protein remodelers, such as RNApII, on cohesin dynamics [21–24].”
BackgroundMolecular dynamics simulations for the study of chromatin biology.
Brandani, G., Gopi, S., Yamauchi, M., & Takada, S. (2022) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2022.102485 · Cited by 9 · see citing works
Landscape of the Epstein-Barr virus-host chromatin interactome and gene regulation
Tian, S., Yang, Y., Ning, D., Yu, T., Gao, T., Deng, Y., Fang, K., Xu, Y., Jing, K., Huang, G., et al. (2025) · EMBO Journal · doi:10.1038/s44318-025-00466-5 · Cited by 8 · see citing works
“5P), differing from the asymmetric DNA loop extrusion commonly driven by RNAPII or CTCF (Banigan et al, 2020; Zheng et al, 2019).”
Interactions Between Nucleosomes: From Atomistic Simulation to Polymer Model
Zhang, C., & Huang, J. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.624679 · Cited by 8 · see citing works
“, 2016), and shed light on the mechanisms underlying the folding and organization of chromatin (Gibcus et al., 2018; Mirny et al., 2019; Stam et al., 2019; Banigan et al., 2020).”
BackgroundLocus architecture and RAG scanning determine antibody diversity
Kenter, A., Priyadarshi, S., & Drake, E. B. (2023) · Trends in immunology · doi:10.1016/j.it.2022.12.005 · Cited by 7 · see citing works
Belan, S., & Parfenyev, V. (2023) · Journal of Chemical Physics · doi:10.1063/5.0199573 · Cited by 7 · see citing works
Keeping intracellular DNA untangled: A new role for condensin?
Roca, J., Dyson, S., Segura, J., Valdés, A., & Martínez-García, B. (2021) · Bioessays · doi:10.1002/bies.202100187 · Cited by 7 · see citing works
PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes.
Wutz, G., Davidson, I., Banigan, E., Stocsits, R. R., Kawasumi, R., Tang, W., Nagasaka, K., Costantino, L., Jansen, R.-P., Hirota, K., et al. (2026) · Molecules and Cells · doi:10.1016/j.molcel.2026.03.025 · Cited by 6 · see citing works
Self-citationReplisomes restrict SMC translocation in vivo
Liao, Q., Brandão, H. B., Ren, Z., & Wang, X.-D. (2025) · Nature Communications · doi:10.1038/s41467-025-62596-y · Cited by 6 · see citing works
“1 dynamics, we adapted a framework based on previous measurements and simulations 37,39,45 and included parameters speci fi c to this study (see details in Supplementary Methods).”
Self-citationWang, J., Cheng, K.-K., Yan, C.-K., Luo, H., & Luo, J.-W. (2025) · BMC Bioinformatics · doi:10.1186/s12859-025-06092-6 · Cited by 6 · see citing works
Dynamical properties of chromatin provide insights into key folding principles
Kadam, S., Sahoo, S., Kumar, P. B. S., & Padinhateeri, R. (2025) · bioRxiv · doi:10.1101/2024.05.07.592992 · Cited by 5
Loop-extruder mediated rigidity can globally order bacterial chromosomes
Harju, J., Armbruster, T., & Broedersz, C. P. (2024) · bioRxiv · doi:10.1101/2024.10.10.617531 · Cited by 5
“To develop a computational model for our system, we adapt a previously used simulation scheme [42], where 1D simulations of loop extrusion are used to dynamically constrain 3D polymer simulations.”
Yuan, T., Yan, H., Li, K. C., Surovtsev, I., King, M., & Mochrie, S. (2024) · bioRxiv · doi:10.1186/s13059-024-03432-2 · Cited by 5 · see citing works
Buka, K., Parteka-Tojek, Z., Agarwal, A., Denkiewicz, M., Korsak, S., Chiliński, M., Banecki, K. H., & Plewczynski, D. (2024) · bioRxiv · doi:10.1038/s42003-025-07847-w · Cited by 4 · see citing works
“…loop extrusion process for an exemplary region on chromosome 1 ( Figure 3C ), Usually, to simulate loop extrusion, stochastic models are used (16, 28, 48–50), where the cohesin proteins on the chromatin fibre perform one-dimensional random walk motion, and they may unload or load in different…”
Spectral-based detection of chromatin loops in multiplexed super-resolution FISH data
Liefsoens, M., Földes, T., & Barbi, M. (2023) · bioRxiv · doi:10.1038/s41467-024-51650-w · Cited by 4 · see citing works
“As insulator proteins, CTCF and cohesin regulate chromatin loop stability, probably as a ’ dynamic complex ’ that frequently breaks and reforms throughout the cell cycle 12 .”
StripeDiff: Model-based algorithm for differential analysis of chromatin stripe
Gupta, K., Wang, G., Zhang, S., Gao, X.-L., Zheng, R., Zhang, Y., Meng, Q., Zhang, L.-L., Cao, Q., & Chen, K.-F. (2022) · Science Advances · doi:10.1126/sciadv.abk2246 · Cited by 4 · see citing works
DNA sliding and loop formation by E. coli SMC complex: MukBEF
Zhou, M. (2021) · bioRxiv · doi:10.1016/j.bbrep.2022.101297 · Cited by 4 · see citing works
Starkov, D., Parfenyev, V., & Belan, S. (2021) · Journal of Chemical Physics · doi:10.1063/5.0048942 · Cited by 4 · see citing works
Exploring the energy landscape of bacterial chromosome segregation
Brahmachari, S., Oliveira, A. B., Mello, M. F., Contessoto, V. G., & Onuchic, J. (2026) · bioRxiv · doi:10.1101/2024.07.27.604869 · Cited by 3
DNA actively regulates the “safety-belt” dynamics of condensin during loop extrusion
Chen, J.-Y., Feng, C.-B., Wang, Y., & Chu, X.-K. (2025) · bioRxiv · doi:10.1038/s41467-025-68239-6 · Cited by 3 · see citing works
“6 as the optimal interaction strength between DNA and Ycg1 (see Methods for details).”
InfluentialIrvin, E. M., & Wang, H. (2023) · DNA Repair · doi:10.1016/j.dnarep.2023.103528 · Cited by 3 · see citing works
Franek, M., Kilar, A. M., Fojtík, P., Olšinová, M., Benda, A., Rotrekl, V., Dvořáčková, M., & Fajkus, J. (2021) · Journal of Cell Science · doi:10.1242/jcs.258374 · Cited by 3 · see citing works
Fine-tuning of the Smc flux facilitates chromosome organization in B. subtilis
Anchimiuk, A., Lioy, V., Minnen, A., Boccard, F., & Gruber, S. (2020) · bioRxiv · doi:10.1101/2020.12.04.411900 · Cited by 3
Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent Cells
Swygert, S. G., Lin, D., Portillo-Ledesma, S., Lin, P.-Y., Hunt, D. R., Kao, C., Schlick, T., Noble, W. S., & Tsukiyama, T. (2020) · bioRxiv · doi:10.1101/2020.11.24.396713 · Cited by 3
RNA polymerase backtracking drives the accumulation of fission yeast condensin at active genes
Rivosecchi, J., Vachez, L., Gautier, F., Bernard, P., & Vanoosthuyse, V. (2020) · bioRxiv · doi:10.1101/2020.11.13.381434 · Cited by 3
A comparative analysis of topological domain callers over RNA-associated interactome
Alaygut, T., & Sefer, E. (2026) · BMC Bioinformatics · doi:10.1186/s12859-026-06432-0 · Cited by 2 · see citing works
“Loop extrusion is regarded as a likely mechanism for chromatin organization within DNA domains, according to studies such as [96, 100].”
The physical chemistry of interphase loop extrusion
Tortora, M. M. C., & Fudenberg, G. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.101098 · Cited by 2 · see citing works
“Many alternatives and elaborations are likely, including asymmetric extrusion with switching, 40,69 a dependence of the loop-extru-sion rate on local conformation, 70 cohesin backtracking and by-passing, 71 or capture of spatially proximal chromatin in trans .”
Zhegalova, I., Ulianov, S., Galitsyna, A., Pletenev, I., Tsoy, O., Luzhin, A. V., Vasiluev, P., Bulavko, E. S., Ivankov, D., Gavrilov, A., et al. (2024) · bioRxiv · doi:10.1101/2024.06.12.598618 · Cited by 2 · see citing works
“This is likely caused by the high density of TSSs: 72, 51, 11, and 1 TSSs per 100 kb on average for Dicty, budding yeast, fruit fly, and human cells, respectively.”
BackgroundNature of barriers determines first passage times in heterogeneous media.
Dasgupta, M., Guha, S., Armbruster, L., Das, D., & Mitra, M. K. (2022) · Soft Matter · doi:10.1039/d4sm00908h · Cited by 2 · see citing works
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Chromatin dynamics are constrained by loops and driven by the INO80 nucleosome remodelerPreprint
Bailey, M. L. P., Surovtsev, I., Williams, J. F., Yan, H., Yuan, T.-Y., Mochrie, S., & King, M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.29.969683 · Cited by 2 · see citing works
D'Asaro, D., Arbona, J., Vaillant, C., & Jost, D. (2026) · bioRxiv · doi:10.1093/nar/gkag731 · Cited by 1
“Note that our model for loop extrusion is minimal and does not account for extra processes, such as stalling at and by-passing barriers that may lead to slight corrections to our predictions [ 57 , 59 , 60 ].”
- Authors
- Banigan, E. J., van den Berg, A. A., Brandão, H. B., Marko, J. F., & Mirny, L. A.
- Affiliations
- Massachusetts Institute of Technology (US)
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, United States
- 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 · 2018: 1
- 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
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 ›
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