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Chromosome organization by one-sided and two-sided loop extrusion
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Abstract
SMC complexes, such as condensin or cohesin, organize chromatin throughout the cell cycle by a process known as loop extrusion. SMC complexes reel in DNA, extruding and progressively growing DNA loops. Modeling assuming two-sided loop extrusion reproduces key features of chromatin organization across different organisms. In vitro single-molecule experiments confirmed that yeast condensins extrude loops, however, they remain anchored to their loading sites and extrude loops in a ‘one-sided’ manner. We therefore simulate one-sided loop extrusion to investigate whether ‘one-sided’ complexes can compact mitotic chromosomes, organize interphase domains, and juxtapose bacterial chromosomal arms, as can be done by ‘two-sided’ loop extruders. While one-sided loop extrusion cannot reproduce these phenomena, variants can recapitulate in vivo observations. We predict that SMC complexes in vivo constitute effectively two-sided motors or exhibit biased loading and propose relevant experiments. Our work suggests that loop extrusion is a viable general mechanism of chromatin organization.
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“and simulations incorporating two-sided extrusion, rather than one-sided, better reproduce the juxtaposition of bacterial chromosomal arms.78”
From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [78]
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BackgroundWutz, G., Várnai, C., Nagasaka, K., Cisneros, D. A., Stocsits, R. R., Tang, W., Schoenfelder, S., Jessberger, G., Muhar, M., Hossain, M. J., et al. (2017) · The EMBO Journal · doi:10.15252/embj.201798004 · Cited by 864
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“Over time, the subunits may translocate along DNA, and the LEF eventually unbinds from DNA.”
BackgroundResultInfluentialA pathway for mitotic chromosome formation
Gibcus, J. H., Samejima, K., Goloborodko, A. A., Samejima, I., Naumova, N., Nuebler, J., Kanemaki, M. T., Xie, L., Paulson, J. R., Earnshaw, W. C., et al. (2018) · Science · doi:10.1126/science.aao6135 · Cited by 744 · cited 5×
“SMC complexes linearly compact mitotic chromosomes in metazoan cells (Gibcus et al., 2018; Hirano et al., 1997; Hirano and Mitchison, 1994; Ono et al., 2003; Shintomi et al., 2017, 2015) , maintain topologically associated domains (TADs) in interphase vertebrate cells (Gassler et al.”
BackgroundInfluentialSelf-citationHuman cohesin compacts DNA by loop extrusion
Kim, Y., Shi, Z., Zhang, H., Finkelstein, I. J., & Yu, H. (2019) · Science · doi:10.1126/science.aaz4475 · Cited by 701 · cited 1×
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BackgroundEastman, P. K., Friedrichs, M. S., Chodera, J. D., Radmer, R. J., Bruns, C. M., Ku, J. P., Beauchamp, K. A., Lane, T. J., Wang, L., Shukla, D., et al. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300857j · Cited by 695
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CTCF Binding Polarity Determines Chromatin Looping
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BackgroundMethodSelf-citationWapl controls the dynamic association of cohesin with chromatin
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ResultUltrastructural Details of Mammalian Chromosome Architecture
Krietenstein, N., Abraham, S., Venev, S. V., Abdennur, N., Gibcus, J., Hsieh, T.-H. S., Parsi, K. M., Yang, L., Maehr, R., Mirny, L. A., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.003 · Cited by 622
Self-citationHigh-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome
Le, T. B. K., Imakaev, M., Mirny, L. A., & Laub, M. T. (2013) · Science · doi:10.1126/science.1242059 · Cited by 614
Self-citationCTCF and cohesin regulate chromatin loop stability with distinct dynamics
Hansen, A. S., Pustova, I., Cattoglio, C., Tjian, R., & Darzacq, X. (2017) · eLife · doi:10.7554/elife.25776 · Cited by 613 · cited 3×
“For typical cohesin residence times (Gerlich et al., 2006b; Hansen et al., 2017; Kueng et al., 2006; Tedeschi et al., 2013; Wutz et al., 2017) , this model suggests that small loops of 10-60 kb (Dauban et al.”
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“SMC complexes linearly compact mitotic chromosomes in metazoan cells (Gibcus et al., 2018; Hirano et al., 1997; Hirano and Mitchison, 1994; Ono et al., 2003; Shintomi et al., 2017, 2015) , maintain topologically associated domains (TADs) in interphase vertebrate cells (Gassler et al.”
BackgroundCohesin relocation from sites of chromosomal loading to places of convergent transcription
Lengronne, A., Katou, Y., Mori, S., Yokobayashi, S., Kelly, G. P., Itoh, T., Watanabe, Y., Shirahige, K., & Uhlmann, F. (2004) · Nature · doi:10.1038/nature02742 · Cited by 588 · cited 2×
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“SMC complexes linearly compact mitotic chromosomes in metazoan cells (Gibcus et al., 2018; Hirano et al., 1997; Hirano and Mitchison, 1994; Ono et al., 2003; Shintomi et al., 2017, 2015) , maintain topologically associated domains (TADs) in interphase vertebrate cells (Gassler et al.”
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Ultrastructural details of mammalian chromosome architecture
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“Next, we considered variations of the model in which one-sided LEFs are loaded nonuniformly, with increased probability of loading at barriers (Nichols and Corces, 2015; Rubio et al., 2008) ( Figure 3 d ).”
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BackgroundInfluentialTranscription Elongation Can Affect Genome 3D Structure
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BackgroundThe Energetics and Physiological Impact of Cohesin Extrusion
Vian, L., Pękowska, A., Rao, S. S. P., Kieffer-Kwon, K.-R., Jung, S., Baranello, L., Huang, S.-C., Khattabi, L., Dose, M., Pruett, N., et al. (2018) · Cell · doi:10.1016/j.cell.2018.09.002 · Cited by 435 · cited 1×
“We found that one-sided extrusion with uniform association and dissociation of LEFs can generate TADs ( Figure 3 b, right) and “stripes” (or “flames,” “tracks,” or “lines”) (Fudenberg et al., 2017, 2016; Vian et al., 2018) on Hi-C maps ( Figure 3 a ).”
BackgroundCohesin-mediated interactions organize chromosomal domain architecture
Sofueva, S., Yaffe, E., Chan, W., Georgopoulou, D., Vietri Rudan, M., Mira‐Bontenbal, H., Pollard, S. M., Schroth, G. P., Tanay, A., & Hadjur, S. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.237 · Cited by 394
Condensin-based chromosome organization from bacteria to vertebrates
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“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…”
BackgroundInfluentialA mechanism of cohesin‐dependent loop extrusion organizes zygotic genome architecture
Gassler, J., Brandão, H. B., Imakaev, M., Flyamer, I. M., Ladstätter, S., Bickmore, W. A., Peters, J., Mirny, L. A., & Tachibana, K.-E. K. (2017) · The EMBO Journal · doi:10.15252/embj.201798083 · Cited by 382 · cited 4×
“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) .”
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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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Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins
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Wapl is an essential regulator of chromatin structure and chromosome segregation
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“, Wapl depletion [Tedeschi et al., 2013]) interphase chromosomes, which have linearly dense arrays of chromatin loops.”
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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…”
BackgroundCondensin I stabilizes chromosomes mechanically through a dynamic interaction in live cells.
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“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×
“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) .”
BackgroundInfluentialHagstrom, K., Holmes, V. F., Cozzarelli, N. R., & Meyer, B. J. (2002) · Genes & Development · doi:10.1101/gad.968302 · Cited by 323
Organization and segregation of bacterial chromosomes
Wang, X., Llopis, P. D. L. M. M., & Rudner, D. Z. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3375 · Cited by 323
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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
Sullivan, N., Marquis, K. A., & Rudner, D. (2009) · Cell · doi:10.1016/j.cell.2009.04.044 · Cited by 299 · cited 1×
“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
Emerging Evidence of Chromosome Folding by Loop ExtrusionPreprint
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Self-citationCohesin-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
Self-citationBacillus subtilis SMC complexes juxtapose chromosome arms as they travel from origin to terminus
Wang, 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×
“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-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 292 · cited 5×
“This signal is dependent on the bacterial SMC complex (bSMC) (Marbouty et al., 2015; Wang et al., 2015).”
BackgroundInfluentialChromosome 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
Self-citationThe Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation
Umbarger, M. A., Toro, E., Wright, M. A., Porreca, G. J., Baù, D., Hong, S., Fero, M. J., Zhu, L. J., Martı́-Renom, M. A., McAdams, H. H., et al. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.09.010 · Cited by 274 · cited 2×
“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) .”
BackgroundThe 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×
“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×
“Over time, the subunits may translocate along DNA, and the LEF eventually unbinds from DNA.”
InfluentialMitotic 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×
“While transcription can occur during mitosis, inhibiting transcription does not visibly alter mitotic chromosome compaction (Palozola et al., 2017) .”
BackgroundIn Vivo Architecture and Action of Bacterial Structural Maintenance of Chromosome Proteins
Badrinarayanan, A., Reyes‐Lamothe, R., Uphoff, S., Leake, M. C., & Sherratt, D. J. (2012) · Science · doi:10.1126/science.1227126 · Cited by 241 · cited 2×
“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) .”
BackgroundCondensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilisPreprint
Wang, X., Le, T. B. K., Lajoie, B. R., Dekker, J., Laub, M. T., & Rudner, D. Z. (2015) · Genes & Development · doi:10.1101/gad.265876.115 · Cited by 236
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×
“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
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
Trask, B., Pinkel, D., & van den Engh, G. J. (1989) · Genomics · doi:10.1016/0888-7543(89)90112-2 · Cited by 221
Chromatin three-dimensional interactions mediate genetic effects on gene expression
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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×
“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
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×
“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).”
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 201
ParB 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
Contrasting 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×
“, 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) .”
BackgroundA CTCF Code for 3D Genome Architecture
Nichols, M. H., & Corces, V. G. (2015) · Cell · doi:10.1016/j.cell.2015.07.053 · Cited by 195
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
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
Marbouty, M., Cournac, A., Flot, J., Marie-Nelly, H., Mozziconacci, J., & Koszul, R. (2014) · eLife · doi:10.7554/elife.03318 · Cited by 186 · cited 2×
“…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).”
BackgroundA 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×
“, 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) ).”
BackgroundResultInfluentialCohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle
Lazar‐Stefanita, L., Scolari, V. F., Mercy, G., Muller, H., Guérin, T. M., Thierry, A., Mozziconacci, J., & Koszul, R. (2017) · The EMBO Journal · doi:10.15252/embj.201797342 · Cited by 177
Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization
Diebold, M.-L., Lee, H., Avila, L. B. R., Noh, H., Shin, H., Im, H., Bock, F. P., Bürmann, F., Durand, A., Basfeld, A., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.06.010 · Cited by 173
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
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…”
BackgroundDiffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization
Bohn, M., & Heermann, D. W. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012218 · Cited by 163
Hu, B., Petela, N. J., Kurze, A., Chan, K., Chapard, C., & Nasmyth, K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv670 · Cited by 162
Towards a Unified Model of SMC Complex Function
Hassler, M., Shaltiël, I. A., & Haering, C. H. (2018) · Current Biology · doi:10.1016/j.cub.2018.08.034 · Cited by 161
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×
“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×
“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×
“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×
“, 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
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×
“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×
“, ~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
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×
“…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 131
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×
“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
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×
“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
Marko, J., Rios, P. D. L., Barducci, A., & Gruber, S. (2018) · bioRxiv · doi:10.1093/nar/gkz497 · Cited by 116 · cited 4×
“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-citationRegulation 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 116 · cited 5×
“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) .”
BackgroundInfluentialAbsolute 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 113 · cited 3×
“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 113 · cited 3×
“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) .”
BackgroundMitotic 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
Scanning electron microscopy of mammalian chromosomes from prophase to telophase
Sumner, A. (1991) · Chromosoma · doi:10.1007/bf00337519 · Cited by 98 · cited 1×
“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×
“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
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×
“, 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.”
BackgroundKim, K.-D., Tanizawa, H., Iwasaki, O., & Noma, K.-I. (2016) · Nature Genetics · doi:10.1038/ng.3647 · Cited by 86
Böhm, K., Giacomelli, G., Schmidt, A., Imhof, A., Koszul, R., Marbouty, M., & Bramkamp, M. (2020) · Nature Communications · doi:10.1038/s41467-020-15238-4 · Cited by 83 · cited 2×
“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) .”
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×
“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) .”
BackgroundReal‐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×
“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×
“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
Ocampo-Hafalla, M. T., & Uhlmann, F. (2011) · Journal of Cell Science · doi:10.1242/jcs.073866 · Cited by 72 · cited 1×
“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) .”
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
Self-citationFlamholz, A. I., Phillips, R., & Milo, R. (2014) · Molecular Biology of the Cell · doi:10.1091/mbc.e14-09-1347 · Cited by 71 · cited 1×
“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 69
High 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×
“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]).”
BackgroundChromosome 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.”
ResultMultilayer 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 62 · cited 1×
“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;…”
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-citationDistinct Roles for Condensin’s Two ATPase Sites in Chromosome Condensation
Elbatsh, A. M. O., Kim, E., Eeftens, J. M., Raaijmakers, J. A., van der Weide, R. H., García-Nieto, A., Bravo, S., Ganji, M., de Bos, J. U., Teunissen, H., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.09.020 · Cited by 57
Multistep assembly of DNA condensation clusters by SMC
Kim, H., & Loparo, J. J. (2016) · Nature Communications · doi:10.1038/ncomms10200 · Cited by 55
Chromosome 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
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) .”
ResultBarysz, H. M., Kim, J. H., Chen, Z. A., Hudson, D. F., Rappsilber, J., Gerloff, D. L., & Earnshaw, W. C. (2015) · Open Biology · doi:10.1098/rsob.150005 · Cited by 52 · cited 1×
“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.”
BackgroundPhysical 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
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×
“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. C. A., Soares, D. C., 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 48
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 47
MukB ATPases are regulated independently by the N- and C-terminal domains of MukF kleisin
Zawadzka, K., Zawadzki, P., Baker, R., Rajasekar, K. V., Wagner, F., Sherratt, D. J., & Arciszewska, L. K. (2018) · eLife · doi:10.7554/elife.31522 · Cited by 46 · cited 2×
“, 2012) linked by the kleisin molecule, MukF (Zawadzka et al., 2018) .”
BackgroundBenedetti, F., Račko, D., Dorier, J., Burnier, Y., & Stasiak, A. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx716 · Cited by 42
Repulsive Forces Between Looping Chromosomes Induce Entropy-Driven Segregation
Bohn, M., & Heermann, D. W. (2011) · PLoS ONE · doi:10.1371/journal.pone.0014428 · Cited by 40
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
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×
“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
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×
“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., Hégarat, N., Pollard, H. J., Fukagawa, T., Hochegger, H., & Tanaka, T. U. (2019) · The Journal of Cell Biology · doi:10.1083/jcb.201807125 · Cited by 26 · cited 3×
“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×
“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
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×
“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
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
- de Lange, 1933, Sur un type nouveau de dégénération (typus amstelodamensis), Arch Méd Enfants, 36, 713
- Fytas, 2013, Molecular dynamics simulations of single-component bottle-brush polymers with flexible backbones under poor solvent conditions, Journal of Physics: Condensed Matter, 25, 10.1088/0953-8984/25/28/285105 · DOI
- Glynn, 2004, Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae, PLOS Biology, 2, 10.1371/journal.pbio.0020259 · DOI
- Kerpedjiev, 2018, HiGlass: web-based visual exploration and analysis of genome interaction maps, Genome Biology, 19, 10.1186/s13059-018-1486-1 · DOI
- Seitan, 2013, Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments, Genome Research, 23, 2066, 10.1101/gr.161620.113 · 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 238
“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 201
“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 169
Self-citationMCM complexes are barriers that restrict cohesin-mediated loop extrusion
Dequeker, B., 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. (2020) · Nature · doi:10.1038/s41586-022-04730-0 · Cited by 132
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
Metadata
- Authors
- Banigan, E. J., van den Berg, A. A., Brandão, H. B., Marko, J. F., & Mirny, L. A.
- Affiliations
- Massachusetts Institute of Technology (US)
- Harvard University (US)
- Northwestern University (US)
- Corresponding author
- Mirny, Leonid A
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2020-04-06
- Volume
- 9
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC7295573
- OpenAlex
- W3014551288
- Cited by
- 146
- References
- 182
- Citations by year
- 2026: 21 · 2025: 26 · 2024: 16 · 2023: 15 · 2022: 28 · 2021: 26 · 2020: 13
- FWCI
- 6.65
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Funders
- National Institutes of Health (U54DK107980, U54CA193419, GM114190)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Keywords
- loop extrusion, SMC complex, condensin, cohesin, chromatin organization
- MeSH terms
- Bacterial Proteins, Chromatin, Chromosomes, Chromosomes, Bacterial, Interphase, Models, Molecular, Molecular Conformation, Cell Cycle Proteins, Molecular Dynamics Simulation
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