Histone structure and nucleosome stability

Expert Review of Proteomics

Volumn 2, Issue 5, 2005, Pages 719-729

  Mariño Ramírez, Leonardo ^a   Kann, Maricel G ^a   Shoemaker, Benjamin A ^a   Landsman, David ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Chromatin structure; Historic variants; Nucleosomes

Indexed keywords

HISTONE; HISTONE H2A; HISTONE H2B; HISTONE H3; HISTONE H4;

CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN STRUCTURE; DNA RECOMBINATION; DNA REPAIR; DNA REPLICATION; DNA TRANSCRIPTION; EPIGENETICS; GENE CONTROL; GENE SILENCING; HUMAN; MOLECULAR INTERACTION; NONHUMAN; NUCLEOSOME; PROTEIN STRUCTURE; REVIEW;

ANIMALS; CHROMATIN ASSEMBLY AND DISASSEMBLY; HISTONES; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEOSOMES; PROTEIN PROCESSING, POST-TRANSLATIONAL;

EID: 27144487352     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/14789450.2.5.719     Document Type: Review

References (71)

1. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389(6648), 251-260(1997). Contains high-resolution structures of the nucleosome that are key to understanding gene regulation and chromatin remodeling.
2. Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J. Mol. Biol. 319(5), 1097-1113 (2002). Contains high-resolution structures of the nucleosome that are key to understanding gene regulation and chromatin remodeling.
3. Dorigo B, Schalch T, Kulangara A et al. Nucleosome arrays reveal the two-start organization of the chromatin fiber. Science 306(5701), 1571-1573 (2004). Provides evidence for a two-start helical organization of the 30-nm chromatin fiber and has helped resolve a controversy over how individual nucleosomes are packed in the chromatin fiber.
4. van Holde KE. Chapter 7: Highter order structure. In: Chromatin. Springer-Verlag, London, UK, 317-354 (1988).
5. Francis NJ, Kingston RE, Woodcock CL. Chromatin compaction by a polycomb group protein complex. Science 306(5701), 1574-1577 (2004).
6. Arents G, Moudrianakis EN. The histone fold: a ubiquitous architectural motif utilized in DNA compaction and protein dimerization. Proc. Natl Acad. Sci. USA 92(24), 11170-11174 (1995). Describes the histone fold and its widespread presence in eukaryotic proteins present in the nucleus.
7. Peterson CL, Laniel MA. Histones and histone modifications. Curr. Biol. 14(14), R546-R551 (2004).
8. Rakyan VK, Hildmann T, Novik KL et al. DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project. PLoS Biol. 2(12), e405 (2004).
9. Roh TY, Cuddapah S, Zhao K. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev. 19(5), 542-552 (2005).
10. Roh TY, Ngau WC, Cui K, Landsman D, Zhao K. High-resolution genome-wide mapping of histone modifications. Nature Biotechnol. 22(8), 1013-1016 (2004).
11. Dion MF, Altschuler SJ, Wu LF, Rando OJ. Genomic characterization reveals a simple histone H4 acetylation code. Proc. Natl. Acad. Sci. USA (2005). Provides a systematic evaluation of histone H4 acetylation patterns and their effects on gene expression measured by microarray analysis.
12. Kurdistani SK, Tavazoie S, Grunstein M. Mapping global histone acetylation patterns to gene expression. Cell 117(6), 721-733 (2004).
13. Kornberg RD, Thomas JO. Chromatin structure; oligomers of the histones. Science 184(139), 865-868 (1974).
14. Kornberg RD. Chromatin structure: a repeating unit of histones and DNA. Science 184(139), 868-871 (1974).
15. Kelley RI. Isolation of a histone IIb1-IIb2 complex. Biochem. Biophys. Res. Commun. 54(4), 1588-1594 (1973).
16. Olins AL, Olins DE. Spheroid chromatin units (v bodies). Science 183(122), 330-332 (1974).
17. Woodcock CL. Ultrastructure of inactive chromatin. J. Cell Biol. 59(2), 368a (1973).
18. Richmond TJ, Finch JT, Rushton B, Rhodes D, Klug A. Structure of the nucleosome core particle at 7 Å resolution. Nature 311(5986), 532-537 (1984).
19. Baxevanis AD, Arents G, Moudrianakis EN, Landsman D. A variety of DNA-binding and multimeric proteins contain the histone fold motif. Nucleic Acids Res. 23(14), 2685-2691 (1995).
20. Kokubo T, Gong DW, Wootton JC et al. Molecular cloning of Drosophila TFIID subunits. Nature 367(6462), 484-487 (1994).
21. Jenuwein T, Allis CD. Translating the histone code. Science 293(5532), 1074-1080 (2001).
22. Brower-Toland B, Wacker DA, Fulbright RM et al. Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes. J. Mol. Biol. 346(1), 135-146 (2005).
23. Zheng C, Hayes JJ. Structures and interactions of the core histone tail domains. Biopolymers 68(4), 539-546 (2003).
24. Dorigo B, Schalch T, Bystricky K, Richmond TJ. Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J. Mol. Biol. 327(1), 85-96 (2003).
25. Chakravarthy S, Park YJ, Chodaparambil J, Edayathumangalam RS, Luger K. Structure and dynamic properties of nucleosome core particles. FEBS Lett. 579(4), 895-898 (2005).
26. Luger K. Structure and dynamic behavior of nucleosomes. Curr. Opin. Genet. Dev. 13(2), 127-135 (2003).
27. Sullivan SA, Landsman D. Characterization of sequence variability in nucleosome core histone folds. Proteins 52(3), 454-465 (2003).
28. Klug A, Rhodes D, Smith J, Finch JT, Thomas JO. A low resolution structure for the histone core of the nucleosome. Nature 287(5782), 509-516 (1980).
29. Muthurajan UM, Bao Y, Forsberg LJ et al. Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions. EMBO J. 23(2), 260-271 (2004).
30. Suto RK, Clarkson MJ, Tremethick DJ, Luger K. Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nature Struct. Biol. 7(12), 1121-1124 (2000).
31. Cosgrove MS, Boeke JD, Wolberger C. Regulated nucleosome mobility and the histone code. Nature Struct. Mol. Biol. 11(11), 1037-1043 (2004).
32. Korber P, Horz W. SWRred not shaken; mixing the histones. Cell 117(1), 5-7 (2004).
33. Malik HS, Henikoff S. Phylogenomics of the nucleosome. Nature Struct. Biol. 10(11), 882-891 (2003).
34. Kamakaka RT, Biggins S. Histone variants: deviants? Genes Dev. 19(3), 295-310 (2005).
35. Henikoff S, Furuyama T, Ahmad K. Histone variants, nucleosome assembly and epigenetic inheritance. Trends Genet. 20(7), 320-326 (2004).
36. Park YJ, Chodaparambil JV, Bao Y, McBryant SJ, Luger K. Nucleosome assembly protein 1 exchanges histone H2A-H2B dimers and assists nucleosome sliding. J. Biol. Chem. 280(3), 1817-1825 (2005).
37. Saeki H, Ohsumi K, Aihara H et al. Linker histone variants control chromatin dynamics during early embryogenesis. Proc. Natl Acad. Sci. USA 102(16), 5697-5702 (2005).
38. Meneghini MD, Wu M, Madhani HD. Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell 112(5), 725-736 (2003).
39. Chadwick BP, Willard HF. A novel chromatin protein, distantly related to histone H2A, is largely excluded from the inactive X chromosome. J. Cell Biol. 152(2), 375-384 (2001).
40. Bao Y, Konesky K, Park YJ et al. Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA. EMBO J. 23(16), 3314-3324 (2004).
41. Gautier T, Abbott DW, Molla A et al. Histone variant H2ABbd confers lower stability to the nucleosome. EMBO J. 5(7), 715-720 (2004).
42. Costanzi C, Stein P, Worrad DM, Schultz RM, Pehrson JR. Histone macroH2A1 is concentrated in the inactive X chromosome of female preimplantation mouse embryos. Development 127(11), 2283-2289 (2000).
43. Ladurner AG. Inactivating chromosomes: a macro domain that minimizes transcription. Mol. Cell 12(1), 1-3 (2003).
44. Angelov D, Molla A, Perche PY et al. The histone variant macroH2A interferes with transcription factor binding and SWI/SNF nucleosome remodeling. Mol. Cell 11(4), 1033-1041 (2003).
45. Rogakou EP, Pilch DR, Orr AH, Ivanova VS, Bonner WM. DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139. J. Biol. Chem. 273(10), 5858-5868 (1998).
46. Celeste A, Fernandez-Capetillo O, Kruhlak MJ et al. Histone H2AX phosphorylation is dispensable for the initial recognition of DNA breaks. Nature Cell Biol. 5(7), 675-679 (2003).
47. Thiriet C, Hayes JJ. Chromatin in need of a fix: phosphorylation of H2AX connects chromatin to DNA repair. Mol. Cell 18(6), 617-622 (2005).
48. Strickland M, Strickland WN, Brandt WF, Von Holt C. The complete amino-acid sequence of histone H2B(1) from sperm of the sea urchin Parechinus angulosus. Eur. J. Biochem. 77(2), 263-275 (1977).
49. Lieber T, Weisser K, Childs G. Analysis of histone gene expression in adult tissues of the sea urchins Strongylocentrotus purpuratus and Lytechinus pictus: tissue-specific expression of sperm histone genes. Mol. Cell Biol. 6(7), 2602-2612 (1986).
50. Ueda K, Kinoshita Y, Xu ZJ et al. Unusual core histones specifically expressed in male gametic cells of Lilium longiflorum. Chromosoma 108(8), 491-500 (2000).
51. Aul RB, Oko RJ. The major subacrosomal occupant of bull spermatozoa is a novel histone H2B. Dev. Biol. 242(2), 376-387 (2002).
52. Zalensky AO, Siino JS, Gineitis AA et al. Human testis/sperm-specific histone H2B (hTSH2B). Molecular cloning and characterization. J. Biol. Chem. 277(45), 43474-43480 (2002).
53. Ahmad K, Henikoff S. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell 9(6), 1191-1200 (2002).
54. Witt O, Albig W, Doenecke D. Testis-specific expression of a novel human H3 histone gene. Exp. Cell Res. 229(2), 301-306 (1996).
55. Albig W, Ebentheuer J, Klobeck G, Kunz J, Doenecke D. A solitary human H3 histone gene on chromosome 1. Hum. Genet. 97(4), 486-491 (1996).
56. Akhmanova A, Miedema K, Hennig W. Identification and characterization of the Drosophila histone H4 replacement gene. FEBS Lett. 388(2-3), 219-222 (1996).
57. Freitas MA, Sklenar AR, Parthun MR. Application of mass spectrometry to the identification and quantification of histone post-translational modifications. J. Cell Biochem. 92(4), 691-700 (2004).
58. Turner BM. Decoding the nucleosome. Cell 75(1), 5-8 (1993).
59. Henikoff S. Histone modifications: combinatorial complexity or cumulative simplicity? Proc. Natl Acad. Sci. USA 102(15), 5308-5309 (2005).
60. Xu F, Zhang K, Grunstein M. Acetylation in histone H3 globular domain regulates gene expression in yeast. Cell 121(3), 375-385 (2005).
61. Oliva R, Bazett-Jones DP, Locklear L, Dixon GH. Histone hyperacetylation can induce unfolding of the nucleosome core particle. Nucleic Acids Res. 18(9), 2739-2747 (1990).
62. Dunker AK, Lawson JD, Brown CJ et al. Intrinsically disordered protein. J. Mol. Graph Model 19(1), 26-59 (2001).
63. Ptitsyn OB. Molten globule and protein folding. Adv. Protein Chem. 47, 83-229 (1995).
64. Meador WE, Means AR, Quiocho FA. Modulation of calmodulin plasticity in molecular recognition on the basis of x-ray structures. Science 262(5140), 1718-1721 (1993).
65. Tuma R, Coward LU, Kirk MC, Barnes S, Prevelige PE Jr. Hydrogen-deuterium exchange as a probe of folding and assembly in viral capsids. J. Mol. Biol. 306(3), 389-396 (2001).
66. Wright PE, Dyson HJ. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 293(2), 321-331 (1999).
67. Iakoucheva LM, Radivojac P, Brown CJ et al. The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res. 32(3), 1037-1049 (2004).
68. Schalch T, Duda S, Sargent DF, Richmond TJ. X ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature 436(7047), 138-141 (2005). First low-resolution structure of a compacted tetranucleosome provides additional evidence for the two-start model organization of the chromatin fiber first confirmed by [3].
69. Nicholls A, Sharp KA, Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11(4), 281-296 (1991).
70. Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18(15), 2714-2723 (1997).
71. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 14(6), 1188-1190 (2004).