메뉴 건너뛰기




Volumn 27, Issue 6, 2015, Pages

The effect of DNA supercoiling on nucleosome structure and stability

Author keywords

atomic force spectroscopy; fluorescence correlation spectroscopy; histone; supercoiled DNA

Indexed keywords

FLUORESCENCE; FLUORESCENCE SPECTROSCOPY; SCANNING TUNNELING MICROSCOPY; SPECTROSCOPIC ANALYSIS; TRANSCRIPTION;

EID: 84921672969     PISSN: 09538984     EISSN: 1361648X     Source Type: Journal    
DOI: 10.1088/0953-8984/27/6/064105     Document Type: Article
Times cited : (14)

References (36)
  • 2
    • 0037992395 scopus 로고    scopus 로고
    • The structure of DNA in the nucleosome core
    • Richmon T J and Davey C A 2003 The structure of DNA in the nucleosome core Nature 423 145-50
    • (2003) Nature , vol.423 , pp. 145-150
    • Richmon, T.J.1    Davey, C.A.2
  • 4
    • 33847070442 scopus 로고    scopus 로고
    • The role of chromatin during transcription
    • Li B, Carey M and Workman J L 2007 The role of chromatin during transcription Cell 128 707-19
    • (2007) Cell , vol.128 , pp. 707-719
    • Li, B.1    Carey, M.2    Workman, J.L.3
  • 5
    • 84857430552 scopus 로고    scopus 로고
    • Chromatin replication and epigenome maintenance
    • Alabert C and Groth A 2012 Chromatin replication and epigenome maintenance Nat. Rev. Mol. Cell Biol. 13 153-67
    • (2012) Nat. Rev. Mol. Cell Biol. , vol.13 , pp. 153-167
    • Alabert, C.1    Groth, A.2
  • 6
    • 35348910082 scopus 로고    scopus 로고
    • Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in xenopus egg extracts
    • Ranjith P, Yan J and Marko J F 2007 Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in xenopus egg extracts Proc. Natl Acad. Sci. USA 104 13649-54
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 13649-13654
    • Ranjith, P.1    Yan, J.2    Marko, J.F.3
  • 7
    • 79955811415 scopus 로고    scopus 로고
    • Nucleosome structure (s) and stability: Variations on a theme
    • Andrews A J and Luger K 2011 Nucleosome structure (s) and stability: variations on a theme Ann. Rev. Biophys. 40 99-117
    • (2011) Ann. Rev. Biophys. , vol.40 , pp. 99-117
    • Andrews, A.J.1    Luger, K.2
  • 11
    • 65249169329 scopus 로고    scopus 로고
    • Forces and torques in the nucleus: Chromatin under mechanical constraints
    • Lavelle C 2009 Forces and torques in the nucleus: chromatin under mechanical constraints Biochem. Cell Biol. 87 307-22
    • (2009) Biochem. Cell Biol. , vol.87 , pp. 307-322
    • Lavelle, C.1
  • 12
    • 0018962604 scopus 로고
    • Torsional tension in the DNA double helix measured with trimethylpsoralen in living e. Coli cells: Analogous measurements in insect and human cells
    • Sinden R R, Carlson J O and Pettijohn D E 1980 Torsional tension in the DNA double helix measured with trimethylpsoralen in living e. Coli cells: analogous measurements in insect and human cells Cell 21 773-83
    • (1980) Cell , vol.21 , pp. 773-783
    • Sinden, R.R.1    Carlson, J.O.2    Pettijohn, D.E.3
  • 13
    • 4444234129 scopus 로고    scopus 로고
    • Visualization of unconstrained negative supercoils of DNA on polytene chromosomes of drosophila
    • Matsumoto K and Hirose S 2004 Visualization of unconstrained negative supercoils of DNA on polytene chromosomes of drosophila J. Cell Sci. 117 3797-805
    • (2004) J. Cell Sci. , vol.117 , pp. 3797-3805
    • Matsumoto, K.1    Hirose, S.2
  • 16
    • 0023433855 scopus 로고
    • Supercoiling of the DNA template during transcription
    • Liu L F and Wang J C 1987 Supercoiling of the DNA template during transcription Proc. Natl Acad. Sci. USA 84 7024-7
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 7024-7027
    • Liu, L.F.1    Wang, J.C.2
  • 19
    • 68149120313 scopus 로고    scopus 로고
    • Nucleosomal fluctuations govern the transcription dynamics of rna polymerase ii
    • Hodges C, Bintu L, Lubkowska L, Kashlev M and Bustamante C 2009 Nucleosomal fluctuations govern the transcription dynamics of rna polymerase ii Science 325 626-8
    • (2009) Science , vol.325 , pp. 626-628
    • Hodges, C.1    Bintu, L.2    Lubkowska, L.3    Kashlev, M.4    Bustamante, C.5
  • 20
    • 65249149694 scopus 로고    scopus 로고
    • Brownian dynamics simulation of DNA unrolling from the nucleosome
    • Wocjan T, Klenin K and Langowski J 2008 Brownian dynamics simulation of DNA unrolling from the nucleosome J. Phys. Chem. B 113 2639-46
    • (2008) J. Phys. Chem. , vol.113 , pp. 2639-2646
    • Wocjan, T.1    Klenin, K.2    Langowski, J.3
  • 21
    • 22044436367 scopus 로고    scopus 로고
    • Forced unraveling of nucleosomes assembled on heterogeneous DNA using core histones, nap-1, and acf
    • Gemmen G J, Sim R, Haushalter K A, Ke P C, Kadonaga J T and Smith D E 2005 Forced unraveling of nucleosomes assembled on heterogeneous DNA using core histones, nap-1, and acf J. Mol. Biol. 351 89-99
    • (2005) J. Mol. Biol. , vol.351 , pp. 89-99
    • Gemmen, G.J.1    Sim, R.2    Haushalter, K.A.3    Ke, P.C.4    Kadonaga, J.T.5    Smith, D.E.6
  • 22
    • 84885660614 scopus 로고    scopus 로고
    • Torque modulates nucleosome stability and facilitates h2a/h2b dimer loss
    • Sheinin M Y, Li M, Soltani M, Luger K and Wang M D 2013 Torque modulates nucleosome stability and facilitates h2a/h2b dimer loss Nat. Commun. 4 2579
    • (2013) Nat. Commun. , vol.4 , pp. 2579
    • Sheinin, M.Y.1    Li, M.2    Soltani, M.3    Luger, K.4    Wang, M.D.5
  • 23
    • 0026479071 scopus 로고
    • Preparation of DNA topoisomers by RP-18 high-performacne liquid chromatography
    • Kapp U and Langowski J 1992 Preparation of DNA topoisomers by RP-18 high-performacne liquid chromatography Anal. Biochem. 206 293-9
    • (1992) Anal. Biochem. , vol.206 , pp. 293-299
    • Kapp, U.1    Langowski, J.2
  • 24
    • 0030817948 scopus 로고    scopus 로고
    • Winding of the DNA helix by divalent metal ions
    • Xu Y C and Bremer H 1997 Winding of the DNA helix by divalent metal ions Nucl. Acids Res. 25 4067-71
    • (1997) Nucl. Acids Res. , vol.25 , pp. 4067-4071
    • Xu, Y.C.1    Bremer, H.2
  • 25
    • 0001074488 scopus 로고
    • Determination of the number of superhelical turns in simian virus 40 DNA by gel electrophoresis
    • Keller W 1975 Determination of the number of superhelical turns in simian virus 40 DNA by gel electrophoresis Proc. Natl Acad. Sci. USA 72 4876-80
    • (1975) Proc. Natl Acad. Sci. USA , vol.72 , pp. 4876-4880
    • Keller, W.1
  • 27
    • 2142855641 scopus 로고    scopus 로고
    • Polylysine-coated mica can be used to observe systematic changes in the supercoiled DNA conformation by scanning force microscopy in solution
    • Bussiek M, Muecke N and Langowski J 2003 Polylysine-coated mica can be used to observe systematic changes in the supercoiled DNA conformation by scanning force microscopy in solution Nucl. Acids Res. 31 e137
    • (2003) Nucl. Acids Res. , vol.31 , pp. 137
    • Bussiek, M.1    Muecke, N.2    Langowski, J.3
  • 28
    • 0016379116 scopus 로고
    • Fluorescence correlation spectroscopy I: Conceptual basis and theory
    • Magde D, Elson E L and Webb W W 1974 Fluorescence correlation spectroscopy I: conceptual basis and theory Biopolymers 13 1-27
    • (1974) Biopolymers , vol.13 , pp. 1-27
    • Magde, D.1    Elson, E.L.2    Webb, W.W.3
  • 29
    • 0016366591 scopus 로고
    • Fluorescence correlation spectroscopy II: An experimental realization
    • Magde D, Elson E L and Webb W W 1974 Fluorescence correlation spectroscopy II: an experimental realization Biopolymers 13 29-61
    • (1974) Biopolymers , vol.13 , pp. 29-61
    • Magde, D.1    Elson, E.L.2    Webb, W.W.3
  • 30
    • 0036175642 scopus 로고    scopus 로고
    • Fluorescence correlation spectroscopy: The technique and its applications
    • Krichevsky O and Bonnet G 2002 Fluorescence correlation spectroscopy: the technique and its applications Rep. Prog. Phys. 65 251-97
    • (2002) Rep. Prog. Phys. , vol.65 , Issue.2 , pp. 251-297
    • Krichevsky, O.1    Bonnet, G.2
  • 31
    • 84921642176 scopus 로고    scopus 로고
    • Krieger J W and Langowski J 2014 QuickFit 3.0 (status: beta, compiled: 25.06.2014, SVN: 3292): a data evaluation application for biophysics (web page) www.dkfz.de/Macromol/quickfit/ (Accessed on 25.06.2014)
    • (2014)
    • Krieger, J.W.1    Langowski, J.2
  • 32
    • 1042278772 scopus 로고    scopus 로고
    • Maximum-entropy decomposition of fluorescence correlation spectroscopy data: Application to liposome-human serum albumin association
    • Módos K, Galántai R, Bárdos-Nagy I, Wachsmuth M, Tóth K, Fidy J and Langowski J 2004 Maximum-entropy decomposition of fluorescence correlation spectroscopy data: application to liposome-human serum albumin association Eur. Biophys. J. 33 59-67
    • (2004) Eur. Biophys. J. , vol.33 , pp. 59-67
    • Módos, K.1    Galántai, R.2    Bárdos-Nagy, I.3    Wachsmuth, M.4    Tóth, K.5    Fidy, J.6    Langowski, J.7
  • 33
    • 0000431384 scopus 로고
    • Maximum entropy image reconstruction - General algorithm
    • Skilling J and Bryan R K 1984 Maximum entropy image reconstruction - general algorithm Mon. Not. R. Astron. Soc. 211 111
    • (1984) Mon. Not. R. Astron. Soc. , vol.211 , pp. 111
    • Skilling, J.1    Bryan, R.K.2
  • 34
    • 38949147878 scopus 로고    scopus 로고
    • Precise measurement of diffusion coefficients using scanning fluorescence correlation spectroscopy
    • Petrásek Z and Schwille P 2008 Precise measurement of diffusion coefficients using scanning fluorescence correlation spectroscopy Biophys. J. 94 1437-48
    • (2008) Biophys. J. , vol.94 , pp. 1437-1448
    • Petrásek, Z.1    Schwille, P.2
  • 35
    • 84861531483 scopus 로고    scopus 로고
    • Overcoming the nucleosome barrier during transcript elongation
    • Petesch S J and Lis J T 2012 Overcoming the nucleosome barrier during transcript elongation Trends Genet. 28 285-94
    • (2012) Trends Genet. , vol.28 , pp. 285-294
    • Petesch, S.J.1    Lis, J.T.2
  • 36
    • 0035954427 scopus 로고    scopus 로고
    • Kinetics of core histones in living human cells little exchange of H3 and H4 and some rapid exchange of H2B
    • Kimura H and Cook P R 2001 Kinetics of core histones in living human cells little exchange of H3 and H4 and some rapid exchange of H2B J. Cell Biol. 153 1341-54
    • (2001) J. Cell Biol. , vol.153 , pp. 1341-1354
    • Kimura, H.1    Cook, P.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.