Subnucleosomal structures and nucleosome asymmetry across a genome

Cell

Volumn 159, Issue 6, 2014, Pages 1377-1388

  Rhee, Ho Sung ^a,b   Bataille, Alain R ^a   Zhang, Liye ^a,c   Pugh, B Franklin ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b Department of Medicine   (United States)

^c BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ENZYME VARIANT; EXONUCLEASE; HISTONE H1; HISTONE H2AZ; HISTONE; NUCLEOSOME; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; CELL BUDDING; CELL STRUCTURE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; DNA CROSS LINKING; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HISTONE ACETYLATION; HISTONE METHYLATION; HISTONE MODIFICATION; HISTONE UBIQUITINATION; IN VIVO STUDY; MOLECULAR BEACON; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN INTERACTION; SUBNUCLEOSOMAL STRUCTURE; YEAST; CHEMISTRY; FUNGAL GENOME; GENETICS; HISTONE CODE; METABOLISM; SACCHAROMYCES CEREVISIAE;

GENOME, FUNGAL; HISTONE CODE; HISTONES; NUCLEOSOMES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC;

EID: 84923596623     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2014.10.054     Document Type: Article

References (52)

1. I. Albert, T.N. Mavrich, L.P. Tomsho, J. Qi, S.J. Zanton, S.C. Schuster, and B.F. Pugh Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome Nature 446 2007 572 576
2. A.T. Annunziato Split decision: what happens to nucleosomes during DNA replication? J. Biol. Chem. 280 2005 12065 12068
3. K. Batta, Z. Zhang, K. Yen, D.B. Goffman, and B.F. Pugh Genome-wide function of H2B ubiquitylation in promoter and genic regions Genes Dev. 25 2011 2254 2265
4. B.E. Black, and D.W. Cleveland Epigenetic centromere propagation and the nature of CENP-a nucleosomes Cell 144 2011 471 479
5. C. Bönisch, and S.B. Hake Histone H2A variants in nucleosomes and chromatin: more or less stable? Nucleic Acids Res. 40 2012 10719 10741
6. K. Brogaard, L. Xi, J.P. Wang, and J. Widom A map of nucleosome positions in yeast at base-pair resolution Nature 486 2012 496 501
7. B.D. Brower-Toland, C.L. Smith, R.C. Yeh, J.T. Lis, C.L. Peterson, and M.D. Wang Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA Proc. Natl. Acad. Sci. USA 99 2002 1960 1965
8. M.J. Carrozza, B. Li, L. Florens, T. Suganuma, S.K. Swanson, K.K. Lee, W.J. Shia, S. Anderson, J. Yates, M.P. Washburn, and J.L. Workman Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription Cell 123 2005 581 592
9. T.A. Chen, M.M. Smith, S.Y. Le, R. Sternglanz, and V.G. Allfrey Nucleosome fractionation by mercury affinity chromatography. Contrasting distribution of transcriptionally active DNA sequences and acetylated histones in nucleosome fractions of wild-type yeast cells and cells expressing a histone H3 gene altered to encode a cysteine 110 residue J. Biol. Chem. 266 1991 6489 6498
10. Y. Dalal, T. Furuyama, D. Vermaak, and S. Henikoff Structure, dynamics, and evolution of centromeric nucleosomes Proc. Natl. Acad. Sci. USA 104 2007 15974 15981
11. M.F. Dion, T. Kaplan, M. Kim, S. Buratowski, N. Friedman, and O.J. Rando Dynamics of replication-independent histone turnover in budding yeast Science 315 2007 1405 1408
12. H. Ferreira, J. Somers, R. Webster, A. Flaus, and T. Owen-Hughes Histone tails and the H3 alphaN helix regulate nucleosome mobility and stability Mol. Cell. Biol. 27 2007 4037 4048
13. A.B. Fleming, C.F. Kao, C. Hillyer, M. Pikaart, and M.A. Osley H2B ubiquitylation plays a role in nucleosome dynamics during transcription elongation Mol. Cell 31 2008 57 66
14. T. Furuyama, C.A. Codomo, and S. Henikoff Reconstitution of hemisomes on budding yeast centromeric DNA Nucleic Acids Res. 41 2013 5769 5783
15. S. Henikoff Nucleosome destabilization in the epigenetic regulation of gene expression Nat. Rev. Genet. 9 2008 15 26
16. J.G. Henikoff, J.A. Belsky, K. Krassovsky, D.M. MacAlpine, and S. Henikoff Epigenome characterization at single base-pair resolution Proc. Natl. Acad. Sci. USA 108 2011 18318 18323
17. F.C. Holstege, E.G. Jennings, J.J. Wyrick, T.I. Lee, C.J. Hengartner, M.R. Green, T.R. Golub, E.S. Lander, and R.A. Young Dissecting the regulatory circuitry of a eukaryotic genome Cell 95 1998 717 728
18. K.L. Huisinga, and B.F. Pugh A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae Mol. Cell 13 2004 573 585
19. C. Jiang, and B.F. Pugh Nucleosome positioning and gene regulation: advances through genomics Nat. Rev. Genet. 10 2009 161 172
20. N. Kaplan, I.K. Moore, Y. Fondufe-Mittendorf, A.J. Gossett, D. Tillo, Y. Field, E.M. LeProust, T.R. Hughes, J.D. Lieb, J. Widom, and E. Segal The DNA-encoded nucleosome organization of a eukaryotic genome Nature 458 2009 362 366
21. M.C. Keogh, S.K. Kurdistani, S.A. Morris, S.H. Ahn, V. Podolny, S.R. Collins, M. Schuldiner, K. Chin, T. Punna, and N.J. Thompson Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex Cell 123 2005 593 605
22. R.D. Kornberg, and Y. Lorch Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome Cell 98 1999 285 294
23. K. Krassovsky, J.G. Henikoff, and S. Henikoff Tripartite organization of centromeric chromatin in budding yeast Proc. Natl. Acad. Sci. USA 109 2012 243 248
24. K. Luger, A.W. Mäder, R.K. Richmond, D.F. Sargent, and T.J. Richmond Crystal structure of the nucleosome core particle at 2.8 A resolution Nature 389 1997 251 260
25. K. Luger, M.L. Dechassa, and D.J. Tremethick New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? Nat. Rev. Mol. Cell Biol. 13 2012 436 447
26. T.N. Mavrich, I.P. Ioshikhes, B.J. Venters, C. Jiang, L.P. Tomsho, J. Qi, S.C. Schuster, I. Albert, and B.F. Pugh A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome Genome Res. 18 2008 1073 1083
27. B.A. Morgan, B.A. Mittman, and M.M. Smith The highly conserved N-terminal domains of histones H3 and H4 are required for normal cell cycle progression Mol. Cell. Biol. 11 1991 4111 4120
28. R. Pavri, B. Zhu, G. Li, P. Trojer, S. Mandal, A. Shilatifard, and D. Reinberg Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II Cell 125 2006 703 717
29. O.J. Rando, and K. Ahmad Rules and regulation in the primary structure of chromatin Curr. Opin. Cell Biol. 19 2007 250 256
30. A. Ranjan, G. Mizuguchi, P.C. FitzGerald, D. Wei, F. Wang, Y. Huang, E. Luk, C.L. Woodcock, and C. Wu Nucleosome-free region dominates histone acetylation in targeting SWR1 to promoters for H2A.Z replacement Cell 154 2013 1232 1245
31. H.S. Rhee, and B.F. Pugh Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution Cell 147 2011 1408 1419
32. H.S. Rhee, and B.F. Pugh ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy Curr. Protoc. Mol. Biol. Chapter 21 2012 Unit21 24
33. H.S. Rhee, and B.F. Pugh Genome-wide structure and organization of eukaryotic pre-initiation complexes Nature 483 2012 295 301
34. E. Segal, and J. Widom What controls nucleosome positions? Trends Genet. 25 2009 335 343
35. M.S. Shukla, S.H. Syed, D. Goutte-Gattat, J.L. Richard, F. Montel, A. Hamiche, A. Travers, C. Faivre-Moskalenko, J. Bednar, and J.J. Hayes The docking domain of histone H2A is required for H1 binding and RSC-mediated nucleosome remodeling Nucleic Acids Res. 39 2011 2559 2570
36. M. Smolle, S. Venkatesh, M.M. Gogol, H. Li, Y. Zhang, L. Florens, M.P. Washburn, and J.L. Workman Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange Nat. Struct. Mol. Biol. 19 2012 884 892
37. D. Tillo, and T.R. Hughes G+C content dominates intrinsic nucleosome occupancy BMC Bioinformatics 10 2009 442
38. I. Tirosh, and N. Barkai Two strategies for gene regulation by promoter nucleosomes Genome Res. 18 2008 1084 1091
39. S.I. Usachenko, S.G. Bavykin, I.M. Gavin, and E.M. Bradbury Rearrangement of the histone H2A C-terminal domain in the nucleosome Proc. Natl. Acad. Sci. USA 91 1994 6845 6849
40. C.M. Weber, S. Ramachandran, and S. Henikoff Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase Mol. Cell 53 2014 819 830
41. H. Weintraub, K. Palter, and F. Van Lente Histones H2a, H2b, H3, and H4 form a tetrameric complex in solutions of high salt Cell 6 1975 85 110
42. H. Weintraub, A. Worcel, and B. Alberts A model for chromatin based upon two symmetrically paired half-nucleosomes Cell 9 1976 409 417
43. K. Yen, V. Vinayachandran, and B.F. Pugh SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes Cell 154 2013 1246 1256
44. L. Zhang, H. Ma, and B.F. Pugh Stable and dynamic nucleosome states during a meiotic developmental process Genome Res. 21 2011 875 884
45. Z. Zhang, C.J. Wippo, M. Wal, E. Ward, P. Korber, and B.F. Pugh A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome Science 332 2011 977 980
46. J. Zhang, K.A. McCabe, and C.E. Bell Crystal structures of lambda exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity Proc. Natl. Acad. Sci. USA 108 2011 11872 11877
47. C. Zheng, X. Lu, J.C. Hansen, and J.J. Hayes Salt-dependent intra- and internucleosomal interactions of the H3 tail domain in a model oligonucleosomal array J. Biol. Chem. 280 2005 33552 33557
48. J. Zlatanova, T.C. Bishop, J.M. Victor, V. Jackson, and K. van Holde The nucleosome family: dynamic and growing Structure 17 2009 160 171
49. I. Albert, S. Wachi, C. Jiang, and B.F. Pugh GeneTrack - a genomic data processing and visualization framework Bioinformatics 24 2008 1305 1306
50. H. Huang, and P.B. Hopkins DNA interstrand cross-linking by formaldehyde: nucleotide sequence preference and covalent structure of the predominant cross-link formed in synthetic oligonucleotides J. Am. Chem. Soc. 115 1993 9402 9408
51. J.D. McGhee, and P.H. von Hippel Formaldehyde as a probe of DNA structure. I. Reaction with exocyclic amino groups of DNA bases Biochemistry 14 1975 1281 1296
52. H. Utiyama, and P. Doty Kinetic studies of denaturation and reaction with formaldehyde on polydeoxyribonucleotides Biochemistry 10 1971 1254 1264