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Volumn 99, Issue 3, 2010, Pages 179-191

Chromatin remodeling in silico: A stochastic model for SWI/SNF

Author keywords

Chromatin remodeling; Discrete event simulation; Stochastic modeling; SWI SNF

Indexed keywords

HISTONE;

EID: 77649272093     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2009.11.001     Document Type: Article
Times cited : (2)

References (36)
  • 1
    • 0036091330 scopus 로고    scopus 로고
    • Nucleosome remodeling by humans SWI/SNF complex requires transient global disruption of histone-DNA interaction
    • Aoyagi S., Narlikar G., Zheng C., Sif S., Kingston R., Hayes J. Nucleosome remodeling by humans SWI/SNF complex requires transient global disruption of histone-DNA interaction. Mol. Cell Biol. 2002, 22:3653-3662.
    • (2002) Mol. Cell Biol. , vol.22 , pp. 3653-3662
    • Aoyagi, S.1    Narlikar, G.2    Zheng, C.3    Sif, S.4    Kingston, R.5    Hayes, J.6
  • 2
    • 0018036889 scopus 로고
    • Mobility of histones on the chromosome of simian virus 40
    • Beard P. Mobility of histones on the chromosome of simian virus 40. Cell 1978, 15:955-967.
    • (1978) Cell , vol.15 , pp. 955-967
    • Beard, P.1
  • 5
    • 0037388372 scopus 로고    scopus 로고
    • Mechanism for nucleosome mobilization
    • Flaus A., Owen-Hughes T. Mechanism for nucleosome mobilization. J. Biopolym. 2003, 66:563-578.
    • (2003) J. Biopolym. , vol.66 , pp. 563-578
    • Flaus, A.1    Owen-Hughes, T.2
  • 6
    • 65649085971 scopus 로고    scopus 로고
    • Antagonistic roles for BRM and BRG1 SWI/SNF complexes in differentiation
    • Flowers S., Nagl N., Beck G., Moran E. Antagonistic roles for BRM and BRG1 SWI/SNF complexes in differentiation. J. Biol. Chem. 2009, 15:10067-10075.
    • (2009) J. Biol. Chem. , vol.15 , pp. 10067-10075
    • Flowers, S.1    Nagl, N.2    Beck, G.3    Moran, E.4
  • 7
    • 55249100077 scopus 로고    scopus 로고
    • Holding time estimation for reactions in stochastic event-based simulation of complex biological systems
    • Ghosh P., Ghosh S., Basu K., Das S. Holding time estimation for reactions in stochastic event-based simulation of complex biological systems. Els. Sim. Model. Pract. Theory 2007, 16:1615-1639.
    • (2007) Els. Sim. Model. Pract. Theory , vol.16 , pp. 1615-1639
    • Ghosh, P.1    Ghosh, S.2    Basu, K.3    Das, S.4
  • 8
    • 37549021369 scopus 로고    scopus 로고
    • Collision Theory
    • ISBN-13: 978-0486435077.
    • Goldberger, M., Watson, K., 2004. Collision Theory. Dover Pub., ISBN-13: 978-0486435077.
    • (2004) Dover Pub.
    • Goldberger, M.1    Watson, K.2
  • 9
    • 43549092406 scopus 로고    scopus 로고
    • Role of the mammalian SWI/SNF chromatin remodeling complex in the cellular response to UV damage
    • Gong F., Fahy D., Wang H.L.W., Smerdon M. Role of the mammalian SWI/SNF chromatin remodeling complex in the cellular response to UV damage. J. Cell Cycle 2008, 7:1067-1074.
    • (2008) J. Cell Cycle , vol.7 , pp. 1067-1074
    • Gong, F.1    Fahy, D.2    Wang, H.L.W.3    Smerdon, M.4
  • 10
    • 0027182114 scopus 로고
    • Helicase: amino acid sequence comparisons and structure-function relationships
    • Gorbalenya A., Koonin E. Helicase: amino acid sequence comparisons and structure-function relationships. Curr. Opin. Struct. Biol. 1993, 3:419-429.
    • (1993) Curr. Opin. Struct. Biol. , vol.3 , pp. 419-429
    • Gorbalenya, A.1    Koonin, E.2
  • 12
    • 59649116298 scopus 로고    scopus 로고
    • SWI/SNF: a chromatin remodeling complex with a role in carcinogenesis
    • Halliday G., Bock V., Moloney F., Lyons J. SWI/SNF: a chromatin remodeling complex with a role in carcinogenesis. Int. J. Biochem. Cell Biol. 2009, 41:725-728.
    • (2009) Int. J. Biochem. Cell Biol. , vol.41 , pp. 725-728
    • Halliday, G.1    Bock, V.2    Moloney, F.3    Lyons, J.4
  • 13
    • 0034704235 scopus 로고    scopus 로고
    • Generation of superhelical torsion by ATP-dependent chromatin remodeling activities
    • Havas K., Flaus A., Phelan M., Kingston R., Wade P., Lilley D., Owen-Hughes T. Generation of superhelical torsion by ATP-dependent chromatin remodeling activities. Cell 2000, 103:1133-1142.
    • (2000) Cell , vol.103 , pp. 1133-1142
    • Havas, K.1    Flaus, A.2    Phelan, M.3    Kingston, R.4    Wade, P.5    Lilley, D.6    Owen-Hughes, T.7
  • 14
    • 56049099516 scopus 로고    scopus 로고
    • Human SWI/SNF directs sequence specific chromatin changes on promoter polynucleosomes
    • Hillel S., Cassandra B., Gavin S. Human SWI/SNF directs sequence specific chromatin changes on promoter polynucleosomes. Nucl. Acids Res. 2008, 36:6118-6131.
    • (2008) Nucl. Acids Res. , vol.36 , pp. 6118-6131
    • Hillel, S.1    Cassandra, B.2    Gavin, S.3
  • 15
    • 66349130703 scopus 로고    scopus 로고
    • Chromatin dynamics coupled to DNA repair
    • Huertas D., Sendra R., Muoz P. Chromatin dynamics coupled to DNA repair. Epigenetics 2009, 4:31-42.
    • (2009) Epigenetics , vol.4 , pp. 31-42
    • Huertas, D.1    Sendra, R.2    Muoz, P.3
  • 16
    • 60349089645 scopus 로고    scopus 로고
    • Nucleosome positioning and gene regulation: advances through genomics
    • Jiang C., Pugh B. Nucleosome positioning and gene regulation: advances through genomics. Nat. Rev. Genet. 2009, 10:161-172.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 161-172
    • Jiang, C.1    Pugh, B.2
  • 17
    • 0037292355 scopus 로고    scopus 로고
    • SWI/SNF unwraps, slides and rewraps the nucleosome
    • Kassabov B., Zheng B., Persinger J., Bartholomew SWI/SNF unwraps, slides and rewraps the nucleosome. Mol. Cell 2003, 11:391-403.
    • (2003) Mol. Cell , vol.11 , pp. 391-403
    • Kassabov, B.1    Zheng, B.2    Persinger, J.3    Bartholomew4
  • 18
    • 63249087504 scopus 로고    scopus 로고
    • SWI/SNF regulates the cellular response to hypoxia
    • Kenneth N., Mudie S., van Uden P., Rocha S. SWI/SNF regulates the cellular response to hypoxia. J. Biol. Chem. 2009, 284:4123-4131.
    • (2009) J. Biol. Chem. , vol.284 , pp. 4123-4131
    • Kenneth, N.1    Mudie, S.2    van Uden, P.3    Rocha, S.4
  • 19
    • 0038298709 scopus 로고    scopus 로고
    • Nucleosome repositioning via loop formation
    • Kulic I., Schiessel H. Nucleosome repositioning via loop formation. J. Biophys. 2003, 84:3197-3211.
    • (2003) J. Biophys. , vol.84 , pp. 3197-3211
    • Kulic, I.1    Schiessel, H.2
  • 20
    • 33646782953 scopus 로고    scopus 로고
    • Brownian dynamics simulation of directional sliding of histone octamers caused by DNA bending
    • 51909
    • Li W., Dou S., Xie P., Wang P. Brownian dynamics simulation of directional sliding of histone octamers caused by DNA bending. Phys. Rev. 2006, 51909:1-7.
    • (2006) Phys. Rev. , pp. 1-7
    • Li, W.1    Dou, S.2    Xie, P.3    Wang, P.4
  • 22
    • 47149101636 scopus 로고    scopus 로고
    • Involvement of the chromatin remodeling factor BRG1/SMARCA4 in human cancer
    • Medina P., Sanchez-Cespedes M. Involvement of the chromatin remodeling factor BRG1/SMARCA4 in human cancer. Epigenetics 2008, 3:64-88.
    • (2008) Epigenetics , vol.3 , pp. 64-88
    • Medina, P.1    Sanchez-Cespedes, M.2
  • 23
    • 7044220398 scopus 로고    scopus 로고
    • Theory of nucleosome corkscrew sliding in the presence of synthetic DNA ligands
    • Mohammad-Rafiee F., Kulic I., Schiessel H. Theory of nucleosome corkscrew sliding in the presence of synthetic DNA ligands. J. Mol. Biol. 2004, 344:47-58.
    • (2004) J. Mol. Biol. , vol.344 , pp. 47-58
    • Mohammad-Rafiee, F.1    Kulic, I.2    Schiessel, H.3
  • 24
    • 0037154963 scopus 로고    scopus 로고
    • Cooperation between complexes that regulate chromatin structure and transcription
    • Narlikar G., Fan H., Kingston R. Cooperation between complexes that regulate chromatin structure and transcription. Cell 2002, 108:475.
    • (2002) Cell , vol.108 , pp. 475
    • Narlikar, G.1    Fan, H.2    Kingston, R.3
  • 25
    • 56549100855 scopus 로고    scopus 로고
    • Mammalian SWI/SNF chromatin remodeling complexes are required to prevent apoptosis after DNA damage
    • Park J., Park E., Hur S., Kim S., Kwon J. Mammalian SWI/SNF chromatin remodeling complexes are required to prevent apoptosis after DNA damage. J. DNA Repair 2009, 8:29-39.
    • (2009) J. DNA Repair , vol.8 , pp. 29-39
    • Park, J.1    Park, E.2    Hur, S.3    Kim, S.4    Kwon, J.5
  • 26
    • 21744434032 scopus 로고    scopus 로고
    • Conserved Swi2/Snf2 ATPase motif couples ATP hydrolysis to chromatin remodeling
    • Peterson C., Smith C. Conserved Swi2/Snf2 ATPase motif couples ATP hydrolysis to chromatin remodeling. Mol. Cell Biol. 2005, 25:5880-5892.
    • (2005) Mol. Cell Biol. , vol.25 , pp. 5880-5892
    • Peterson, C.1    Smith, C.2
  • 27
    • 64949113367 scopus 로고    scopus 로고
    • The SWI/SNF complex and cancer
    • Reisman D., Glaros S., Thompson E. The SWI/SNF complex and cancer. Oncogene 2009, 28:1653-1668.
    • (2009) Oncogene , vol.28 , pp. 1653-1668
    • Reisman, D.1    Glaros, S.2    Thompson, E.3
  • 28
    • 26944461283 scopus 로고    scopus 로고
    • Chromatin remodeling through directional DNA translocation from an internal nucleosomal site
    • Saha A., Wittmeyer J., Cairns B. Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nat. Struct. Mol. Biol. 2005, 12:744-757.
    • (2005) Nat. Struct. Mol. Biol. , vol.12 , pp. 744-757
    • Saha, A.1    Wittmeyer, J.2    Cairns, B.3
  • 29
    • 33745790132 scopus 로고    scopus 로고
    • Chromatin remodeling: the industrial revolution of DNA around histones
    • Saha A., Wittmeyer J., Cairns B. Chromatin remodeling: the industrial revolution of DNA around histones. Nat. Rev. Mol. Cell Biol. 2006, 7:437-447.
    • (2006) Nat. Rev. Mol. Cell Biol. , vol.7 , pp. 437-447
    • Saha, A.1    Wittmeyer, J.2    Cairns, B.3
  • 31
    • 85194544768 scopus 로고    scopus 로고
    • Functional and structural analysis of the yeast SWI/SNF complex, Ph.D. Dissertation
    • Smith, S., 2004. Functional and structural analysis of the yeast SWI/SNF complex, Ph.D. Dissertation, Univ. of Mass. Med. School.
    • (2004) Univ. of Mass. Med. School.
    • Smith, S.1
  • 32
    • 28544438953 scopus 로고    scopus 로고
    • Human SWI/SNF generates abundant, structurally altered dinucleosomes on polynucleosomal templates
    • Ulyanova N., Schnitzler G. Human SWI/SNF generates abundant, structurally altered dinucleosomes on polynucleosomal templates. Mol. Cell. Biol. 2005, 25:11156-11170.
    • (2005) Mol. Cell. Biol. , vol.25 , pp. 11156-11170
    • Ulyanova, N.1    Schnitzler, G.2
  • 36
    • 33744916194 scopus 로고    scopus 로고
    • Chromatin remodeling by ISWI2 and SWI/SNF requires DNA translocation inside the nucleosome
    • Zofall M., Persinger J., Kassabov S., Bartholomew B. Chromatin remodeling by ISWI2 and SWI/SNF requires DNA translocation inside the nucleosome. Nat. Struct. Mol. Biol. 2006, 13:339-346.
    • (2006) Nat. Struct. Mol. Biol. , vol.13 , pp. 339-346
    • Zofall, M.1    Persinger, J.2    Kassabov, S.3    Bartholomew, B.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.