The effect of DNA CpG methylation on the dynamic conformation of a nucleosome

Biophysical Journal

Volumn 103, Issue 12, 2012, Pages 2502-2512

  Jimenez Useche, Isabel ^a   Yuan, Chongli ^a  

^a PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MAGNESIUM; S ADENOSYLMETHIONINE;

ARTICLE; CHEMISTRY; CPG ISLAND; DNA METHYLATION; DRUG EFFECT; GENETICS; METABOLISM; MOLECULAR GENETICS; MOVEMENT (PHYSIOLOGY); NUCLEOSOME; NUCLEOTIDE SEQUENCE; PROTEIN CONFORMATION;

BASE SEQUENCE; CPG ISLANDS; DNA; DNA METHYLATION; MAGNESIUM; MOLECULAR SEQUENCE DATA; MOVEMENT; NUCLEOSOMES; PROTEIN CONFORMATION; S-ADENOSYLMETHIONINE;

EID: 84871346683     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2012.11.012     Document Type: Article

References (50)

1. T.J. Richmond, and C.A. Davey The structure of DNA in the nucleosome core Nature 423 2003 145 150 (Pubitemid 36569532)
2. R.D. Kornberg, and Y.L. Lorch Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome Cell 98 1999 285 294 (Pubitemid 29380564)
3. K. Luger Structure and dynamic behavior of nucleosomes Curr. Opin. Genet. Dev. 13 2003 127 135 (Pubitemid 36369736)
4. K. Luger Dynamic nucleosomes Chromosome Res. 14 2006 5 16
5. T. Jenuwein, and C.D. Allis Translating the histone code Science 293 2001 1074 1080 (Pubitemid 32758077)
6. T.H. Bestor, and B. Tycko Creation of genomic methylation patterns Nat. Genet. 12 1996 363 367 (Pubitemid 126510021)
7. S.B. Baylin DNA methylation and gene silencing in cancer Nat. Clin. Pract. Oncol. 2 Suppl 1 2005 S4 S11
8. K.D. Robertson DNA methylation and human disease Nat. Rev. Genet. 6 2005 597 610 (Pubitemid 41044297)
9. A. Razin CpG methylation, chromatin structure and gene silencing-a three-way connection EMBO J. 17 1998 4905 4908 (Pubitemid 28408457)
10. H. Cedar, and Y. Bergman Linking DNA methylation and histone modification: patterns and paradigms Nat. Rev. Genet. 10 2009 295 304
11. S.U. Kass, D. Pruss, and A.P. Wolffe How does DNA methylation repress transcription? Trends Genet. 13 1997 444 449 (Pubitemid 27479903)
12. J.S. Choy, and S. Wei T.H. Lee DNA methylation increases nucleosome compaction and rigidity J. Am. Chem. Soc. 132 2010 1782 1783
13. C.S. Davey, and S. Pennings J. Allan A determining influence for CpG dinucleotides on nucleosome positioning in vitro Nucleic Acids Res. 32 2004 4322 4331 (Pubitemid 39232304)
14. J.S. Godde, and S.U. Kass A.P. Wolffe Nucleosome assembly on methylated CGG triplet repeats in the fragile X mental retardation gene 1 promoter J. Biol. Chem. 271 1996 24325 24328 (Pubitemid 26333159)
15. P.T. Lowary, and J. Widom New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning J. Mol. Biol. 276 1998 19 42 (Pubitemid 28085408)
16. A. Gansen, and A. Valeri C.A. Seidel Nucleosome disassembly intermediates characterized by single-molecule FRET Proc. Natl. Acad. Sci. USA 106 2009 15308 15313
17. L. Kelbauskas, and N. Chan D. Lohr Sequence-dependent variations associated with H2A/H2B depletion of nucleosomes Biophys. J. 94 2008 147 158
18. W.J.A. Koopmans, and R. Buning J. van Noort spFRET using alternating excitation and FCS reveals progressive DNA unwrapping in nucleosomes Biophys. J. 97 2009 195 204
19. K. Luger, T.J. Rechsteiner, and T.J. Richmond Preparation of nucleosome core particle from recombinant histones Methods Enzymol. 304 1999 3 19 (Pubitemid 29268874)
20. B. Dorigo, and T. Schalch T.J. Richmond Chromatin fiber folding: requirement for the histone H4 N-terminal tail J. Mol. Biol. 327 2003 85 96 (Pubitemid 36293304)
21. A. Bertin, and S. Mangenot F. Livolant Structure and phase diagram of nucleosome core particles aggregated by multivalent cations Biophys. J. 93 2007 3652 3663 (Pubitemid 350190827)
22. G.S. Bassi, and A.I.H. Murchie D.M. Lilley Ion-induced folding of the hammerhead ribozyme: a fluorescence resonance energy transfer study EMBO J. 16 1997 7481 7489 (Pubitemid 28010507)
23. D. Klostermeier, and D.P. Millar Time-resolved fluorescence resonance energy transfer: a versatile tool for the analysis of nucleic acids Biopolymers 61 2001-2002 159 179 (Pubitemid 34496055)
24. N.G. Walter Structural dynamics of catalytic RNA highlighted by fluorescence resonance energy transfer Methods 25 2001 19 30 (Pubitemid 32905285)
25. C. Claudet, and D. Angelov J. Bednar Histone octamer instability under single molecule experiment conditions J. Biol. Chem. 280 2005 19958 19965 (Pubitemid 41379524)
26. J.S. Godde, and A.P. Wolffe Disruption of reconstituted nucleosomes. The effect of particle concentration, MgCl2 and KCl concentration, the histone tails, and temperature J. Biol. Chem. 270 1995 27399 27402
27. M. Chabbert, and W. Hillen J.A. Bousquet Structural analysis of the operator binding domain of Tn10-encoded Tet repressor: a time-resolved fluorescence and anisotropy study Biochemistry 31 1992 1951 1960
28. A. Grinvald, and I.Z. Steinberg On the analysis of fluorescence decay kinetics by the method of least-squares Anal. Biochem. 59 1974 583 598
29. C.L. Yuan, and E. Rhoades L.A. Archer Mismatch-induced DNA unbending upon duplex opening Biophys. J. 89 2005 2564 2573 (Pubitemid 41401045)
30. G. Li, and J. Widom Nucleosomes facilitate their own invasion Nat. Struct. Mol. Biol. 11 2004 763 769 (Pubitemid 39014502)
31. K. Tóth, N. Brun, and J. Langowski Chromatin compaction at the mononucleosome level Biochemistry 45 2006 1591 1598 (Pubitemid 43222103)
32. V. Böhm, and A.R. Hieb J. Langowski Nucleosome accessibility governed by the dimer/tetramer interface Nucleic Acids Res. 39 2011 3093 3102
33. M.G. Poirier, and E. Oh J. Widom Dynamics and function of compact nucleosome arrays Nat. Struct. Mol. Biol. 16 2009 938 944
34. P.M. Schwarz, and A. Felthauser J.C. Hansen Reversible oligonucleosome self-association: dependence on divalent cations and core histone tail domains Biochemistry 35 1996 4009 4015 (Pubitemid 26113457)
35. R.A. Waterland Assessing the effects of high methionine intake on DNA methylation J. Nutr. 136 6, Suppl 2006 1706S 1710S (Pubitemid 43765384)
36. Y.J. Park, and P.N. Dyer K. Luger A new fluorescence resonance energy transfer approach demonstrates that the histone variant H2AZ stabilizes the histone octamer within the nucleosome J. Biol. Chem. 279 2004 24274 24282 (Pubitemid 38725289)
37. A. Miyagi, T. Ando, and Y.L. Lyubchenko Dynamics of nucleosomes assessed with time-lapse high-speed atomic force microscopy Biochemistry 50 2011 7901 7908
38. L.S. Shlyakhtenko, A.Y. Lushnikov, and Y.L. Lyubchenko Dynamics of nucleosomes revealed by time-lapse atomic force microscopy Biochemistry 48 2009 7842 7848
39. K. Voltz, and J. Trylska J. Langowski Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study Biophys. J. 102 2012 849 858
40. M.T. Record Jr., M.L. Lohman, and P. De Haseth Ion effects on ligand-nucleic acid interactions J. Mol. Biol. 107 1976 145 158
41. B. Luan, and A. Aksimentiev DNA attraction in monovalent and divalent electrolytes J. Am. Chem. Soc. 130 2008 15754 15755
42. X.Y. Qiu, and K. Andresen L. Pollack Inter-DNA attraction mediated by divalent counterions Phys. Rev. Lett. 99 2007 038104
43. D. Nathan, and D.M. Crothers Bending and flexibility of methylated and unmethylated EcoRI DNA J. Mol. Biol. 316 2002 7 17 (Pubitemid 34729262)
44. C.G. Baumann, and S.B. Smith C. Bustamante Ionic effects on the elasticity of single DNA molecules Proc. Natl. Acad. Sci. USA 94 1997 6185 6190 (Pubitemid 27270659)
45. L.M. Edelman, R. Cheong, and J.D. Kahn Fluorescence resonance energy transfer over approximately 130 basepairs in hyperstable lac repressor-DNA loops Biophys. J. 84 2003 1131 1145 (Pubitemid 36133436)
46. Y. You, A.V. Tataurov, and R. Owczarzy Measuring thermodynamic details of DNA hybridization using fluorescence Biopolymers 95 2011 472 486
47. E. Haas, E. Katchalski-Katzir, and I.Z. Steinberg Effect of the orientation of donor and acceptor on the probability of energy transfer involving electronic transitions of mixed polarization Biochemistry 17 1978 5064 5070
48. J. Sambrook, and D.W. Russell Methods in Molecular Cloning 2001 Cold Spring Harbor Laboratory Press NY
49. F. Stühmeier, and J.B. Welch R.M. Clegg Global structure of three-way DNA junctions with and without additional unpaired bases: a fluorescence resonance energy transfer analysis Biochemistry 36 1997 13530 13538 (Pubitemid 27481599)
50. L. Stryer Fluorescence energy transfer as a spectroscopic ruler Annu. Rev. Biochem. 47 1978 819 846