메뉴 건너뛰기




Volumn 4, Issue 3, 2012, Pages 171-178

Insights into gene expression and packaging from computer simulations

Author keywords

Chromatin; DNA looping; Histone tails; Monte Carlo simulations; Protein communication

Indexed keywords


EID: 84873129269     PISSN: 18672450     EISSN: 18672469     Source Type: Journal    
DOI: 10.1007/s12551-012-0093-8     Document Type: Review
Times cited : (11)

References (32)
  • 1
    • 33750807408 scopus 로고    scopus 로고
    • Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model
    • Arya G, Schlick T (2006) Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model. Proc Natl Acad Sci USA 103: 16236-16241.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 16236-16241
    • Arya, G.1    Schlick, T.2
  • 3
    • 33749243974 scopus 로고    scopus 로고
    • Sequence-dependent effects in the cyclization of short DNA
    • doi:10.1021/ct060025+
    • Czapla L, Swigon D, Olson WK (2006) Sequence-dependent effects in the cyclization of short DNA. J Chem Theor Comp 2: 685-695. doi: 10. 1021/ct060025+.
    • (2006) J Chem Theor Comp , vol.2 , pp. 685-695
    • Czapla, L.1    Swigon, D.2    Olson, W.K.3
  • 4
    • 50249126024 scopus 로고    scopus 로고
    • Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte-Carlo simulations
    • Czapla L, Swigon D, Olson WK (2008) Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte-Carlo simulations. J Mol Biol 382: 353-370.
    • (2008) J Mol Biol , vol.382 , pp. 353-370
    • Czapla, L.1    Swigon, D.2    Olson, W.K.3
  • 5
    • 79955907601 scopus 로고    scopus 로고
    • Understanding apparent DNA flexibility enhancement by HU and HMGB proteins: experiment and simulation
    • Czapla L, Peters JP, Rueter EM, Olson WK, Maher LJ III (2011) Understanding apparent DNA flexibility enhancement by HU and HMGB proteins: experiment and simulation. J Mol Biol 409: 278-289.
    • (2011) J Mol Biol , vol.409 , pp. 278-289
    • Czapla, L.1    Peters, J.P.2    Rueter, E.M.3    Olson, W.K.4    Maher III, L.J.5
  • 6
    • 0036307707 scopus 로고    scopus 로고
    • Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution
    • Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ (2002) Solvent mediated interactions in the structure of the nucleosome core particle at 1. 9 Å resolution. J Mol Biol 319: 1097-1113.
    • (2002) J Mol Biol , vol.319 , pp. 1097-1113
    • Davey, C.A.1    Sargent, D.F.2    Luger, K.3    Maeder, A.W.4    Richmond, T.J.5
  • 7
    • 33744780177 scopus 로고    scopus 로고
    • The structural basis for regulated assembly and function of the transcriptional activator NtrC
    • De Carlo S, Chen B, Hoover TR, Kondrashkina E, Nogales E, Nixon T (2006) The structural basis for regulated assembly and function of the transcriptional activator NtrC. Genes Dev 20: 1485-1495.
    • (2006) Genes Dev , vol.20 , pp. 1485-1495
    • De Carlo, S.1    Chen, B.2    Hoover, T.R.3    Kondrashkina, E.4    Nogales, E.5    Nixon, T.6
  • 9
    • 0037436410 scopus 로고    scopus 로고
    • Chromatin fiber folding: requirement for the histone H4 N-terminal tail
    • Dorigo B, Schalch T, Bystricky K, Richmond TJ (2003) Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J Mol Biol 327: 85-96.
    • (2003) J Mol Biol , vol.327 , pp. 85-96
    • Dorigo, B.1    Schalch, T.2    Bystricky, K.3    Richmond, T.J.4
  • 10
    • 0000323202 scopus 로고
    • Macrocyclization equilibria. 1. Theory
    • doi:10.1021/ja00435a001
    • Flory PJ, Suter UW, Mutter M (1976) Macrocyclization equilibria. 1. Theory. J Am Chem Soc 98: 5733-5739. doi: 10. 1021/ja00435a001.
    • (1976) J Am Chem Soc , vol.98 , pp. 5733-5739
    • Flory, P.J.1    Suter, U.W.2    Mutter, M.3
  • 11
    • 0025135578 scopus 로고
    • The size of chromatin loops in HeLa cells
    • Jackson DA, Dickinson P, Cook PR (1990) The size of chromatin loops in HeLa cells. EMBO J 9: 567-57.
    • (1990) EMBO J , vol.9 , pp. 557-567
    • Jackson, D.A.1    Dickinson, P.2    Cook, P.R.3
  • 12
    • 3843114319 scopus 로고
    • Intramolecular reaction in polycondensations. I. The theory of linear systems
    • doi: 10. 1063/1. 1747547
    • Jacobson H, Stockmayer WH (1950) Intramolecular reaction in polycondensations. I. The theory of linear systems. J Chem Phys 18: 1600-1606. doi: 10. 1063/1. 1747547.
    • (1950) J Chem Phys , vol.18 , pp. 1600-1606
    • Jacobson, H.1    Stockmayer, W.H.2
  • 15
    • 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
  • 16
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    • Lu XJ, Olson WK (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31: 5108-5121.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5108-5121
    • Lu, X.J.1    Olson, W.K.2
  • 17
    • 50349085962 scopus 로고    scopus 로고
    • 3DNA: a versatile, integrated software system for the analysis, rebuilding, and visualization of three-dimensional nucleic-acid structures
    • Lu X-J, Olson WK (2008) 3DNA: a versatile, integrated software system for the analysis, rebuilding, and visualization of three-dimensional nucleic-acid structures. Nature Protoc 3: 1213-1227.
    • (2008) Nature Protoc , vol.3 , pp. 1213-1227
    • Lu, X.-J.1    Olson, W.K.2
  • 18
    • 0017895903 scopus 로고
    • The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
    • Manning GS (1978) The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q Rev Biophys 11: 179-246.
    • (1978) Q Rev Biophys , vol.11 , pp. 179-246
    • Manning, G.S.1
  • 20
    • 0037123659 scopus 로고    scopus 로고
    • Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution
    • Murakami KS, Masuda S, Darst SA (2002) Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution. Science 296: 1280-1284.
    • (2002) Science , vol.296 , pp. 1280-1284
    • Murakami, K.S.1    Masuda, S.2    Darst, S.A.3
  • 21
    • 0032530555 scopus 로고    scopus 로고
    • DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
    • Olson WK, Gorin AA, Lu X-J, Hock LM, Zhurkin VB (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci USA 95: 11163-11168.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 11163-11168
    • Olson, W.K.1    Gorin, A.A.2    Lu, X.-J.3    Hock, L.M.4    Zhurkin, V.B.5
  • 22
    • 67649119962 scopus 로고    scopus 로고
    • Analysis of distant communication on defined chromatin templates in vitro
    • Polikanov YS, Studitsky VM (2009) Analysis of distant communication on defined chromatin templates in vitro. Methods Mol Biol 543: 563-576.
    • (2009) Methods Mol Biol , vol.543 , pp. 563-576
    • Polikanov, Y.S.1    Studitsky, V.M.2
  • 23
    • 33847077618 scopus 로고    scopus 로고
    • Biochemical analysis of enhancer-promoter communication in chromatin
    • Polikanov YS, Rubtsov MA, Studitsky VM (2007) Biochemical analysis of enhancer-promoter communication in chromatin. Methods 41: 250-258.
    • (2007) Methods , vol.41 , pp. 250-258
    • Polikanov, Y.S.1    Rubtsov, M.A.2    Studitsky, V.M.3
  • 24
    • 0030956032 scopus 로고    scopus 로고
    • Histone structure and the organization of the nucleosome
    • doi:10.1146/annurev.biophys.26.1.83
    • Ramakrishnan V (1997) Histone structure and the organization of the nucleosome. Annu Rev Biophys Biomol Struct 26: 83-112. doi: 10. 1146/annurev. biophys. 26. 1. 83.
    • (1997) Annu Rev Biophys Biomol Struct , vol.26 , pp. 83-112
    • Ramakrishnan, V.1
  • 28
    • 0000545475 scopus 로고
    • Ring-closure probabilities for twisted wormlike chains. Application to DNA
    • doi:10.1021/ma00134a028
    • Shimada J, Yamakawa H (1984) Ring-closure probabilities for twisted wormlike chains. Application to DNA. Macromolecules 17: 689-698. doi: 10. 1021/ma00134a028.
    • (1984) Macromolecules , vol.17 , pp. 689-698
    • Shimada, J.1    Yamakawa, H.2
  • 29
    • 56949101883 scopus 로고    scopus 로고
    • Mesoscale modeling of multi-protein-DNA assemblies: the role of the catabolic activator protein in Lac-repressor-mediated looping
    • doi: 10. 1016/j. ijnonlinmec. 2008. 07. 003
    • Swigon D, Olson WK (2008) Mesoscale modeling of multi-protein-DNA assemblies: the role of the catabolic activator protein in Lac-repressor-mediated looping. Intl J Non-linear Mechanics 43: 1082-1093. doi: 10. 1016/j. ijnonlinmec. 2008. 07. 003.
    • (2008) Intl J Non-linear Mechanics , vol.43 , pp. 1082-1093
    • Swigon, D.1    Olson, W.K.2
  • 30
    • 33745595880 scopus 로고    scopus 로고
    • Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation
    • Swigon D, Coleman BD, Olson WK (2006) Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation. Proc Natl Acad Sci USA 103: 9879-9884.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 9879-9884
    • Swigon, D.1    Coleman, B.D.2    Olson, W.K.3
  • 31
    • 77953320684 scopus 로고    scopus 로고
    • DNA architecture, deformability, and nucleosome positioning
    • Xu F, Olson WK (2010) DNA architecture, deformability, and nucleosome positioning. J Biomol Struct Dyn 27: 725-739.
    • (2010) J Biomol Struct Dyn , vol.27 , pp. 725-739
    • Xu, F.1    Olson, W.K.2
  • 32
    • 35848931678 scopus 로고    scopus 로고
    • The nucleosome surface regulates chromatin compaction and couples it with transcriptional repression
    • Zhou J, Fan JY, Rangasamy D, Tremethick DJ (2007) The nucleosome surface regulates chromatin compaction and couples it with transcriptional repression. Nat Struct Mol Biol 14: 1070-1076.
    • (2007) Nat Struct Mol Biol , vol.14 , pp. 1070-1076
    • Zhou, J.1    Fan, J.Y.2    Rangasamy, D.3    Tremethick, D.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.