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Volumn 22, Issue 7, 2012, Pages 1295-1305

Physical tethering and volume exclusion determine higher-order genome organization in budding yeast

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL INTERACTION; CELLULAR DISTRIBUTION; CENTROMERE; CHROMOSOME 1; CHROMOSOME 12; CHROMOSOME 3; CHROMOSOME 4; CHROMOSOME 5; CHROMOSOME 6; CHROMOSOME 7; CHROMOSOME 8; CHROMOSOME 9; CONTROLLED STUDY; FUNGAL GENETICS; GENE CLUSTER; GENE INTERACTION; GENE LOCUS; GENE REPLICATION; GENE STRUCTURE; GENETIC ASSOCIATION; GENOME ANALYSIS; HETEROCHROMATIN; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; TELOMERE;

EID: 84863540362     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.129437.111     Document Type: Article
Times cited : (177)

References (66)
  • 3
    • 48749103296 scopus 로고    scopus 로고
    • Integrating diverse data for structure determination of macromolecular assemblies
    • Alber F, Forster F, Korkin D, Topf M, Sali A. 2008. Integrating diverse data for structure determination of macromolecular assemblies. Annu Rev Biochem 77: 443-477.
    • (2008) Annu Rev Biochem , vol.77 , pp. 443-477
    • Alber, F.1    Forster, F.2    Korkin, D.3    Topf, M.4    Sali, A.5
  • 5
    • 77957867310 scopus 로고    scopus 로고
    • Diffusion-driven looping provides a consistent framework for chromatin organization
    • doi: 10.1371/journal.pone.0012218
    • Bohn M, Heermann DW. 2010. Diffusion-driven looping provides a consistent framework for chromatin organization. PLoS ONE 5: e12218. doi: 10.1371/journal.pone.0012218.
    • (2010) PLoS ONE , vol.5
    • Bohn, M.1    Heermann, D.W.2
  • 6
    • 0031437119 scopus 로고    scopus 로고
    • Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin
    • Brown KE, Guest SS, Smale ST, Hahm K, Merkenschlager M, Fisher AG. 1997. Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 91: 845-854.
    • (1997) Cell , vol.91 , pp. 845-854
    • Brown, K.E.1    Guest, S.S.2    Smale, S.T.3    Hahm, K.4    Merkenschlager, M.5    Fisher, A.G.6
  • 7
    • 9344239339 scopus 로고    scopus 로고
    • Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques
    • Bystricky K, Heun P, Gehlen L, Langowski J, Gasser SM. 2004. Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques. Proc Natl Acad Sci 101: 16495-16500.
    • (2004) Proc Natl Acad Sci , vol.101 , pp. 16495-16500
    • Bystricky, K.1    Heun, P.2    Gehlen, L.3    Langowski, J.4    Gasser, S.M.5
  • 8
    • 13444257509 scopus 로고    scopus 로고
    • Chromosome looping in yeast: Telomere pairing and coordinated movement reflect anchoring efficiency and territorial organization
    • Bystricky K, Laroche T, van Houwe G, Blaszczyk M, Gasser SM. 2005. Chromosome looping in yeast: telomere pairing and coordinated movement reflect anchoring efficiency and territorial organization. J Cell Biol 168: 375-387.
    • (2005) J Cell Biol , vol.168 , pp. 375-387
    • Bystricky, K.1    Laroche, T.2    Van Houwe, G.3    Blaszczyk, M.4    Gasser, S.M.5
  • 10
    • 2342501365 scopus 로고    scopus 로고
    • Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization
    • Casolari JM, Brown CR, Komili S, West J, Hieronymus H, Silver PA. 2004. Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell 117: 427-439.
    • (2004) Cell , vol.117 , pp. 427-439
    • Casolari, J.M.1    Brown, C.R.2    Komili, S.3    West, J.4    Hieronymus, H.5    Silver, P.A.6
  • 11
    • 0037459063 scopus 로고    scopus 로고
    • Considering nuclear compartmentalization in the light of nuclear dynamics
    • Chubb JR, Bickmore WA. 2003. Considering nuclear compartmentalization in the light of nuclear dynamics. Cell 112: 403-406.
    • (2003) Cell , vol.112 , pp. 403-406
    • Chubb, J.R.1    Bickmore, W.A.2
  • 12
    • 0033118342 scopus 로고    scopus 로고
    • Nuclear compartments and gene regulation
    • Cockell M, Gasser SM. 1999. Nuclear compartments and gene regulation. Curr Opin Genet Dev 9: 199-205.
    • (1999) Curr Opin Genet Dev , vol.9 , pp. 199-205
    • Cockell, M.1    Gasser, S.M.2
  • 13
    • 70349944662 scopus 로고    scopus 로고
    • Entropic organization of interphase chromosomes
    • Cook PR, Marenduzzo D. 2009. Entropic organization of interphase chromosomes. J Cell Biol 186: 825-834.
    • (2009) J Cell Biol , vol.186 , pp. 825-834
    • Cook, P.R.1    Marenduzzo, D.2
  • 14
    • 0029937208 scopus 로고    scopus 로고
    • Genetic modification of heterochromatic association and nuclear organization in Drosophila
    • Csink AK, Henikoff S. 1996. Genetic modification of heterochromatic association and nuclear organization in Drosophila. Nature 381: 529-531.
    • (1996) Nature , vol.381 , pp. 529-531
    • Csink, A.K.1    Henikoff, S.2
  • 15
    • 0032487506 scopus 로고    scopus 로고
    • Large-scale chromosomal movements during interphase progression in Drosophila
    • Csink AK, Henikoff S. 1998. Large-scale chromosomal movements during interphase progression in Drosophila. J Cell Biol 143: 13-22.
    • (1998) J Cell Biol , vol.143 , pp. 13-22
    • Csink, A.K.1    Henikoff, S.2
  • 16
    • 0034602688 scopus 로고    scopus 로고
    • Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure
    • Cui Y, Bustamante C. 2000. Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure. Proc Natl Acad Sci 97: 127-132.
    • (2000) Proc Natl Acad Sci , vol.97 , pp. 127-132
    • Cui, Y.1    Bustamante, C.2
  • 17
    • 58049192401 scopus 로고    scopus 로고
    • Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction
    • Dekker J. 2008. Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction. J Biol Chem 283: 34532-34540.
    • (2008) J Biol Chem , vol.283 , pp. 34532-34540
    • Dekker, J.1
  • 19
    • 67649873461 scopus 로고    scopus 로고
    • Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei
    • de Nooijer S, Wellink J, Mulder B, Bisseling T. 2009. Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei. Nucleic Acids Res 37: 3558-3568.
    • (2009) Nucleic Acids Res , vol.37 , pp. 3558-3568
    • De Nooijer, S.1    Wellink, J.2    Mulder, B.3    Bisseling, T.4
  • 22
    • 78649902376 scopus 로고    scopus 로고
    • The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture
    • Dorier J, Stasiak A. 2010. The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture. Nucleic Acids Res 38: 7410-7421.
    • (2010) Nucleic Acids Res , vol.38 , pp. 7410-7421
    • Dorier, J.1    Stasiak, A.2
  • 24
    • 0025917415 scopus 로고
    • Ultrastructural localization of nucleic acid sequences in Saccharomyces cerevisiae nucleoli
    • Dvorkin N, Clark MW, Hamkalo BA. 1991. Ultrastructural localization of nucleic acid sequences in Saccharomyces cerevisiae nucleoli. Chromosoma 100: 519-523.
    • (1991) Chromosoma , vol.100 , pp. 519-523
    • Dvorkin, N.1    Clark, M.W.2    Hamkalo, B.A.3
  • 26
    • 0026759324 scopus 로고
    • Cell cycle dependent chromosomal movement in pre-mitotic human T-lymphocyte nuclei
    • Ferguson M, Ward DC. 1992. Cell cycle dependent chromosomal movement in pre-mitotic human T-lymphocyte nuclei. Chromosoma 101: 557-565.
    • (1992) Chromosoma , vol.101 , pp. 557-565
    • Ferguson, M.1    Ward, D.C.2
  • 27
    • 0037165965 scopus 로고    scopus 로고
    • Visualizing chromatin dynamics in interphase nuclei
    • Gasser SM. 2002. Visualizing chromatin dynamics in interphase nuclei. Science 296: 1412-1416.
    • (2002) Science , vol.296 , pp. 1412-1416
    • Gasser, S.M.1
  • 28
    • 0023447159 scopus 로고
    • Chromatin higher-order structure studied by neutron scattering and scanning transmission electron microscopy
    • Gerchman SE, Ramakrishnan V. 1987. Chromatin higher-order structure studied by neutron scattering and scanning transmission electron microscopy. Proc Natl Acad Sci 84: 7802-7806.
    • (1987) Proc Natl Acad Sci , vol.84 , pp. 7802-7806
    • Gerchman, S.E.1    Ramakrishnan, V.2
  • 29
    • 0029820640 scopus 로고    scopus 로고
    • The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae
    • Gotta M, Laroche T, Formenton A, Maillet L, Scherthan H, Gasser SM. 1996. The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae. J Cell Biol 134: 1349-1363.
    • (1996) J Cell Biol , vol.134 , pp. 1349-1363
    • Gotta, M.1    Laroche, T.2    Formenton, A.3    Maillet, L.4    Scherthan, H.5    Gasser, S.M.6
  • 30
    • 0037164718 scopus 로고    scopus 로고
    • Live imaging of telomeres: YKu and Sir proteins define redundant telomere-anchoring pathways in yeast
    • Hediger F, Neumann FR, Van Houwe G, Dubrana K, Gasser SM. 2002. Live imaging of telomeres: yKu and Sir proteins define redundant telomere-anchoring pathways in yeast. Curr Biol 12: 2076-2089.
    • (2002) Curr Biol , vol.12 , pp. 2076-2089
    • Hediger, F.1    Neumann, F.R.2    Van Houwe, G.3    Dubrana, K.4    Gasser, S.M.5
  • 31
  • 32
    • 80052767367 scopus 로고    scopus 로고
    • Ribosome biogenesis factors bind a nuclear envelope SUN domain protein to cluster yeast telomeres
    • Horigome C, Okada T, Shimazu K, Gasser SM, Mizuta K. 2011. Ribosome biogenesis factors bind a nuclear envelope SUN domain protein to cluster yeast telomeres. EMBO J 30: 3799-3811.
    • (2011) EMBO J , vol.30 , pp. 3799-3811
    • Horigome, C.1    Okada, T.2    Shimazu, K.3    Gasser, S.M.4    Mizuta, K.5
  • 33
    • 0034041633 scopus 로고    scopus 로고
    • Centromere clustering is a major determinant of yeast interphase nuclear organization
    • Jin QW, Fuchs J, Loidl J. 2000. Centromere clustering is a major determinant of yeast interphase nuclear organization. J Cell Sci 113: 1903-1912.
    • (2000) J Cell Sci , vol.113 , pp. 1903-1912
    • Jin, Q.W.1    Fuchs, J.2    Loidl, J.3
  • 34
    • 84862917808 scopus 로고    scopus 로고
    • Genome architectures revealed by tethered chromosome conformation capture and population-based modeling
    • Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L. 2012. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol 30: 90-98.
    • (2012) Nat Biotechnol , vol.30 , pp. 90-98
    • Kalhor, R.1    Tjong, H.2    Jayathilaka, N.3    Alber, F.4    Chen, L.5
  • 36
    • 33645286183 scopus 로고    scopus 로고
    • Polymer chain models of DNA and chromatin
    • Langowski J. 2006. Polymer chain models of DNA and chromatin. Eur Phys J E Soft Matter 19: 241-249.
    • (2006) Eur Phys J e Soft Matter , vol.19 , pp. 241-249
    • Langowski, J.1
  • 38
    • 0029746494 scopus 로고    scopus 로고
    • Evidence for silencing compartments within the yeast nucleus: A role for telomere proximity and Sir protein concentration in silencer-mediated repression
    • Maillet L, Boscheron C, Gotta M, Marcand S, Gilson E, Gasser SM. 1996. Evidence for silencing compartments within the yeast nucleus: a role for telomere proximity and Sir protein concentration in silencer-mediated repression. Genes Dev 10: 1796-1811.
    • (1996) Genes Dev , vol.10 , pp. 1796-1811
    • Maillet, L.1    Boscheron, C.2    Gotta, M.3    Marcand, S.4    Gilson, E.5    Gasser, S.M.6
  • 43
    • 77951616674 scopus 로고    scopus 로고
    • The nuclear envelope in genome organization, expression and stability
    • Mekhail K, Moazed D. 2010. The nuclear envelope in genome organization, expression and stability. Nat Rev Mol Cell Biol 11: 317-328.
    • (2010) Nat Rev Mol Cell Biol , vol.11 , pp. 317-328
    • Mekhail, K.1    Moazed, D.2
  • 44
    • 57349093701 scopus 로고    scopus 로고
    • Role for perinuclear chromosome tethering inmaintenance of genome stability
    • Mekhail K, Seebacher J, Gygi SP, Moazed D. 2008. Role for perinuclear chromosome tethering inmaintenance of genome stability. Nature 456: 667-670.
    • (2008) Nature , vol.456 , pp. 667-670
    • Mekhail, K.1    Seebacher, J.2    Gygi, S.P.3    Moazed, D.4
  • 45
    • 33847077659 scopus 로고    scopus 로고
    • Beyond the sequence: Cellular organization of genome function
    • Misteli T. 2007. Beyond the sequence: cellular organization of genome function. Cell 128: 787-800.
    • (2007) Cell , vol.128 , pp. 787-800
    • Misteli, T.1
  • 46
    • 84855543588 scopus 로고    scopus 로고
    • Parallel genome universes
    • Misteli T. 2012. Parallel genome universes. Nat Biotechnol 30: 55-56.
    • (2012) Nat Biotechnol , vol.30 , pp. 55-56
    • Misteli, T.1
  • 47
    • 0033053359 scopus 로고    scopus 로고
    • High-voltage electron tomography of spindle pole bodies and early mitotic spindles in the yeast Saccharomyces cerevisiae
    • O'Toole ET, Winey M, McIntosh JR. 1999. High-voltage electron tomography of spindle pole bodies and early mitotic spindles in the yeast Saccharomyces cerevisiae. Mol Biol Cell 10: 2017-2031.
    • (1999) Mol Biol Cell , vol.10 , pp. 2017-2031
    • O'Toole, E.T.1    Winey, M.2    McIntosh, J.R.3
  • 48
    • 70149094741 scopus 로고    scopus 로고
    • Global identification of yeast chromosome interactions using genome conformation capture
    • Rodley CD, Bertels F, Jones B, O'Sullivan JM. 2009. Global identification of yeast chromosome interactions using genome conformation capture. Fungal Genet Biol 46: 879-886.
    • (2009) Fungal Genet Biol , vol.46 , pp. 879-886
    • Rodley, C.D.1    Bertels, F.2    Jones, B.3    O'Sullivan, J.M.4
  • 49
    • 77953012431 scopus 로고    scopus 로고
    • Looping probabilities in model interphase chromosomes
    • Rosa A, Becker NB, Everaers R. 2010. Looping probabilities in model interphase chromosomes. Biophys J 98: 2410-2419.
    • (2010) Biophys J , vol.98 , pp. 2410-2419
    • Rosa, A.1    Becker, N.B.2    Everaers, R.3
  • 50
    • 84856497340 scopus 로고    scopus 로고
    • Putting the pieces together: Integrative modeling platform software for structure determination of macromolecular assemblies
    • doi: 10.1371/journal.pbio.1001244
    • Russel D, Lasker K, Webb B, Velazquez-Muriel J, Tjioe E, Schneidman-Duhovny D, Peterson B, Sali A. 2012. Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol 10: e1001244. doi: 10.1371/journal.pbio. 1001244.
    • (2012) PLoS Biol , vol.10
    • Russel, D.1    Lasker, K.2    Webb, B.3    Velazquez-Muriel, J.4    Tjioe, E.5    Schneidman-Duhovny, D.6    Peterson, B.7    Sali, A.8
  • 52
    • 77949368063 scopus 로고    scopus 로고
    • GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome
    • doi: 10.1038/msb.2010.8
    • Sekedat MD, Fenyo D, Rogers RS, Tackett AJ, Aitchison JD, Chait BT. 2010. GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome. Mol Syst Biol 6: 353. doi: 10.1038/msb.2010.8.
    • (2010) Mol Syst Biol , vol.6 , pp. 353
    • Sekedat, M.D.1    Fenyo, D.2    Rogers, R.S.3    Tackett, A.J.4    Aitchison, J.D.5    Chait, B.T.6
  • 54
    • 1942503933 scopus 로고    scopus 로고
    • Separation of silencing from perinuclear anchoring functions in yeast Ku80, Sir4 and Esc1 proteins
    • Taddei A, Hedinger F, Neumann FR, Bauer C, Gasser SM. 2004. Separation of silencing from perinuclear anchoring functions in yeast Ku80, Sir4 and Esc1 proteins. EMBO J 23: 1301-1312.
    • (2004) EMBO J , vol.23 , pp. 1301-1312
    • Taddei, A.1    Hedinger, F.2    Neumann, F.R.3    Bauer, C.4    Gasser, S.M.5
  • 55
    • 63849287611 scopus 로고    scopus 로고
    • The functional importance of telomere clustering: Global changes in gene expression result from SIR factor dispersion
    • Taddei A, Van Houwe G, Nagai S, Erb I, van Nimwegen E, Gasser SM. 2009. The functional importance of telomere clustering: Global changes in gene expression result from SIR factor dispersion. Genome Res 19: 611-625.
    • (2009) Genome Res , vol.19 , pp. 611-625
    • Taddei, A.1    Van Houwe, G.2    Nagai, S.3    Erb, I.4    Van Nimwegen, E.5    Gasser, S.M.6
  • 57
    • 52949133457 scopus 로고    scopus 로고
    • The meaning of gene positioning
    • Takizawa T, Meaburn KJ, Misteli T. 2008. The meaning of gene positioning. Cell 135: 9-13.
    • (2008) Cell , vol.135 , pp. 9-13
    • Takizawa, T.1    Meaburn, K.J.2    Misteli, T.3
  • 58
    • 78650458168 scopus 로고    scopus 로고
    • Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation
    • Tanizawa H, Iwasaki O, Tanaka A, Capizzi JR, Wickramasinghe P, Lee M, Fu Z, Noma K. 2010. Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation. Nucleic Acids Res 38: 8164-8177.
    • (2010) Nucleic Acids Res , vol.38 , pp. 8164-8177
    • Tanizawa, H.1    Iwasaki, O.2    Tanaka, A.3    Capizzi, J.R.4    Wickramasinghe, P.5    Lee, M.6    Fu, Z.7    Noma, K.8
  • 59
    • 76649101456 scopus 로고    scopus 로고
    • Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres
    • Therizols P, Duong T, Dujon B, Zimmer C, Fabre E. 2010. Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres. Proc Natl Acad Sci 107: 2025-2030.
    • (2010) Proc Natl Acad Sci , vol.107 , pp. 2025-2030
    • Therizols, P.1    Duong, T.2    Dujon, B.3    Zimmer, C.4    Fabre, E.5
  • 60
    • 0018581187 scopus 로고
    • Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin
    • Thoma F, Koller T, Klug A. 1979. Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin. J Cell Biol 83: 403-427.
    • (1979) J Cell Biol , vol.83 , pp. 403-427
    • Thoma, F.1    Koller, T.2    Klug, A.3
  • 63
    • 80054984337 scopus 로고    scopus 로고
    • Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture
    • Yaffe E, Tanay A. 2011. Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet 43: 1059-1065.
    • (2011) Nat Genet , vol.43 , pp. 1059-1065
    • Yaffe, E.1    Tanay, A.2
  • 64
    • 0024708867 scopus 로고
    • Higher order structure is present in the yeast nucleus: Autoantibody probes demonstrate that the nucleolus lies opposite the spindle pole body
    • Yang CH, Lambie EJ, Hardin J, Craft J, Snyder M. 1989. Higher order structure is present in the yeast nucleus: autoantibody probes demonstrate that the nucleolus lies opposite the spindle pole body. Chromosoma 98: 123-128.
    • (1989) Chromosoma , vol.98 , pp. 123-128
    • Yang, C.H.1    Lambie, E.J.2    Hardin, J.3    Craft, J.4    Snyder, M.5
  • 66
    • 79952403632 scopus 로고    scopus 로고
    • Principles of chromosomal organization: Lessons from yeast
    • Zimmer C, Fabre E. 2011. Principles of chromosomal organization: Lessons from yeast. J Cell Biol 192: 723-733.
    • (2011) J Cell Biol , vol.192 , pp. 723-733
    • Zimmer, C.1    Fabre, E.2


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