Structure and dynamic behavior of nucleosomes

Current Opinion in Genetics and Development

Volumn 13, Issue 2, 2003, Pages 127-135

  Luger, Karolin ^a  

^a Immunology and Pathology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HISTONE; TRANSCRIPTION FACTOR;

CHROMATIN CONDENSATION; CHROMATIN STRUCTURE; GENETIC ANALYSIS; HETEROCHROMATIN; MOLECULAR BIOLOGY; MUTATION; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; REVIEW; TRANSCRIPTION REGULATION; XENOPUS LAEVIS;

XENOPUS LAEVIS;

EID: 0037381213     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(03)00026-1     Document Type: Review

References (55)

1. Hansen J.C. Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functions. Annu. Rev. Biophys. Biomol. Struct. 31:2002;361-392.
2. Horn P.J., Peterson C.L. Chromatin higher order folding - wrapping up transcription. Science. 297:2002;1824-1827.
3. Pennings S., Meersseman G., Bradbury E.M. Mobility of positioned nucleosomes on 5 S rDNA. J. Mol. Biol. 220:1991;101-110.
4. Becker P.B., Horz W. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71:2002;247-273.
5. Becker P.B. Nucleosome sliding: facts and fiction. EMBO J. 21:2002;4749-4753.
6. Gasser S.M. Visualizing chromatin dynamics in interphase nuclei. Science. 296:2002;1412-1416.
7. Jenuwein T., Allis C.D. Translating the histone code. Science. 293:2001;1074-1080.
8. Berger S.L. Histone modifications in transcriptional regulation. Curr. Opin. Genet. Dev. 12:2002;142-148.
9. Urnov F.D. Methylation and the genome: the power of a small amendment. J. Nutr. 132:2002;2450S-2456S.
10. Volpe T.A., Kidner C., Hall I.M., Teng G., Grewal S.I., Martienssen R.A. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science. 297:2002;1833-1837. • Deletion of some genes that are part of the machinery responsible for RNAi results in the aberrant accumulation of complementary transcripts from centromeric heterochromatic repeats. This suggests a functional link between RNAi and the establishment and maintenance of heterochromatin.
11. van Leeuwen F., Gottschling D.E. Genome-wide histone modifications: gaining specificity by preventing promiscuity. Curr. Opin. Cell. Biol. 14:2002;756-762.
12. Harp J.M., Hanson B.L., Timm D.E., Bunick G.J. Asymmetries in the nucleosome core particle at 2.5 A resolution. Acta Crystallogr. D Biol. Crystallogr. 56:2000;1513-1534.
13. White C.L., Suto R.K., Luger K. Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. EMBO J. 20:2001;5207-5218. • Sequence differences in a region that is ubiquitinated by Rad6 [31] lead to changes in crystal packing, suggesting that there are several ways to pack nucleosomes in a thermodynamically favorable way.
14. Davey C.A., Sargent D.F., Luger K., Maeder A.W., Richmond T.J. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J. Mol. Biol. 319:2002;1097-1113. • The highest-resolution structure of any protein-DNA complex of this size. The manuscript focuses on the role of structured water at the protein-DNA interface. Water molecules not only contribute significantly to the stability of DNA-binding but also take part in adapting the histone surface to conformational variation in the DNA. It is suggested that bridging water molecules may play a principal role in facilitating nucleosome mobility.
15. Davey C.A., Richmond T.J. DNA-dependent divalent cation binding in the nucleosome core particle. Proc. Natl. Acad. Sci. USA. 99:2002;11169-11174.
16. Suto R.K., Clarkson M.J., Tremethick D.J., Luger K. Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nat. Struct. Biol. 7:2000;1121-1124.
17. Suto R.K., Edayathumangalam R.S., White C.L., Melander C., Gottesfeld J.M., Dervan P.B., Luger K. Crystal structures of nucleosome core particles in complex with minor groove binding ligands. J. Mol. Biol. 326:2003;371-380. • Three NCP-polyamide co-crystal structures show that ligand binding leads to local and global changes in DNA conformation, while maintaining a full complement of histone-DNA interactions. Experimental evidence is provided to support the hypothesis that twist defects can jump into nucleosomal DNA and diffuse along the DNA length, because it shows that twist defects are actively stabilized at multiple nucleosomal locations.
18. 2+-dependent, intramolecular folding of the nucleosomal arrays, suggesting that Sin-versions of histones may alleviate the need for SWI/SNF in vivo by disrupting higher-order chromatin folding.
19. Fan J.Y., Gordon F., Luger K., Hansen J.C., Tremethick D.J. The essential histone variant H2A.Z regulates the equilibrium between different chromatin conformational states. Nat. Struct. Biol. 19:2002;172-176. • Surface changes in the H2A.Z histone variant NCP structure [16] facilitate the intramolecular folding of nucleosomal arrays while simultaneously inhibiting the formation of highly condensed structures that result from intermolecular association.
20. Park J.H., Cosgrove M.S., Youngman E., Wolberger C., Boeke J.D. A core nucleosome surface crucial for transcriptional silencing. Nat. Genet. 32:2002;273-279. • The residues identified by a genetic screen cluster around (and include) H3 K79. Some are the structural and functional equivalents of the SIN mutants [37]. The surface may interact with specific silencing proteins, or it may be directly involved in fostering nucleosome-nucleosome contacts.
21. Dlakic M. Chromatin silencing protein and pachytene checkpoint regulator Dot1p has a methyltransferase fold. Trends Biochem. Sci. 26:2001;405-407.
22. van Leeuwen F., Gafken P.R., Gottschling D.E. Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell. 109:2002;745-756.
23. Ng H.H., Xu R.M., Zhang Y., Struhl K. Ubiquitination of histone H2B by Rad6 is required for efficient Dot1- mediated methylation of histone H3-lysine 79. J. Biol. Chem. 277:2002;34655-34657. • Rad6-mediated ubiquitination of H2B lysine 123 [31] is important for efficient methylation of lysine 79 of histone H3, suggesting that Rad6 affects telomeric silencing, at least in part, by influencing methylation of histone H3.
24. Feng Q., Wang H., Ng H.H., Erdjument-Bromage H., Tempst P., Struhl K., Zhang Y. Methylation of H3-Lysine 79 is mediated by a new family of HMTases without a SET domain. Curr. Biol. 12:2002;1052-1058.
25. Luger K., Maeder A.W., Richmond R.K., Sargent D.F., Richmond T.J. X-ray structure of the nucleosome core particle at 2.8 Å resolution. Nature. 389:1997;251-259.
26. Luger K., Maeder A.W., Sargent D.F., Richmond T.J. The atomic structure of the nucleosome core particle. J. Biomol. Struct. Dyn. 11:2000;185-189.
27. Luger K., Rechsteiner T.J., Richmond T.J. Preparation of nucleosome core particle from recombinant histones. Methods Enzymol. 304:1999;3-19.
28. Sullivan S., Sink D.W., Trout K.L., Makalowska I., Taylor P.M., Baxevanis A.D., Landsman D. The histone database. Nucleic Acids Res. 30:2002;341-342. • Annotated alignments of full-length non-redundant sets of sequences are now available on the web in both HTML and PDF formats. The database also provides summaries of information on solved histone-fold structures, post-translational modifications of histones, and the human histone gene complement.
29. Widom J. Role of DNA sequence in nucleosome stability and dynamics. Q Rev. Biophys. 34:2001;269-324.
30. Ahmad K., Henikoff S. The histone variant H3.3 marks active chromatin by replication- independent nucleosome assembly. Mol. Cell. 9:2002;1191-1200. • The histone variant H3.3 is the exclusive substrate for 'replication-independent' deposition. Residues on 'major', replication-dependent H3 that are responsible for excluding it from this pathway have been identified (see also Figure 1).
31. Robzyk K., Recht J., Osley M.A. Rad6-dependent ubiquitination of histone H2B in yeast. Science. 287:2000;501-504.
32. Simpson R.T., Thoma F., Brubaker J.M. Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones: a model system for study of higher order structure. Cell. 42:1985;799-808.
33. Hansen J.C., Ausio J., Stanik V.H., van Holde K.E. Homogeneous reconstituted oligonucleosomes, evidence for salt-dependent folding in the absence of histone H1. Biochemistry. 28:1989;9129-9136.
34. Redon C., Pilch D., Rogakou E., Sedelnikova O., Newrock K., Bonner W. Histone H2A variants H2AX and H2AZ. Curr. Opin. Genet. Dev. 12:2002;162-169.
35. Wolffe A.P., Pruss D. Deviant nucleosomes: the functional specialization of chromatin. Trends Genet. 12:1996;58-62.
36. Clarkson M.J., Wells J.R., Gibson F., Saint R., Tremethick D.J. Regions of variant histone His2AvD required for Drosophila development. Nature. 399:1999;694-697.
37. Kruger W., Peterson C.L., Sil A., Coburn C., Arents G., Moudrianakis E.N., Herskowitz I. Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription. Genes Dev. 9:1995;2770-2779.
38. Fleming A.B., Pennings S. Antagonistic remodelling by Swi-Snf and Tup1-Ssn6 of an extensive chromatin region forms the background for FLO1 gene regulation. EMBO J. 20:2001;5219-5231. • Differences occur between the relative effect of the mutants at different genes, implying a role for DNA sequence or local chromatin environment.
39. Luger K., Richmond T.J. DNA binding within the nucleosome core. Curr. Opin. Struct. Biol. 8:1998;33-40.
40. Wechser M.A., Kladde M.P., Alfieri J.A., Peterson C.L. Effects of Sin- versions of histone H4 on yeast chromatin structure and function. EMBO J. 16:1997;2086-2095.
41. Kurumizaka H., Wolffe A.P. Sin mutations of histone H3: influence on nucleosome core structure and function. Mol. Cell. Biol. 17:1997;6953-6969.
42. Recht J., Osley M.A. Mutations in both the structured domain and N-terminus of histone H2B bypass the requirement for Swi-Snf in yeast. EMBO J. 18:1999;229-240.
43. Ng H.H., Feng Q., Wang H., Erdjument-Bromage H., Tempst P., Zhang Y., Struhl K. Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. Genes Dev. 16:2002;1518-1527.
44. Lacoste N., Utley R.T., Hunter J.M., Poirier G.G., Cote J. Disruptor of telomeric silencing-1 is a chromatin-specific histone H3 methyltransferase. J. Biol. Chem. 277:2002;30421-30424.
45. Varga-Weisz P.D., Dalgaard J.Z. A mark in the core: silence no more! Mol. Cell. 9:2002;1154-1156.
46. Chafin D.R., Vitolo J.M., Henricksen L.A., Bambara R.A., Hayes J.J. Human DNA ligase I efficiently seals nicks in nucleosomes. EMBO J. 19:2000;5492-5501.
47. Angelov D., Charra M., Seve M., Cote J., Khochbin S., Dimitrov S. Differential remodeling of the HIV-1 nucleosome upon transcription activators and SWI/SNF complex binding. J. Mol. Biol. 302:2000;315-326.
48. Cirillo L.A., Lin F.R., Cuesta I., Friedman D., Jarnik M., Zaret K.S. Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. Mol. Cell. 9:2002;279-289.
49. Zhu Z., Thiele D.J. A specialized nucleosome modulates transcription factor access to a C. glabrata metal responsive promoter. Cell. 87:1996;459-470.
50. Dervan P.B. Molecular recognition of DNA by small molecules. Bioorg. Med. Chem. 9:2001;2215-2235.
51. Gottesfeld J.M., Melander C., Suto R.K., Raviol H., Luger K., Dervan P.B. Sequence-specific recognition of DNA in the nucleosome by pyrrole- imidazole polyamides. J. Mol. Biol. 309:2001;625-639.
52. Nilsen H., Lindahl T., Verreault A. DNA base excision repair of uracil residues in reconstituted nucleosome core particles. EMBO J. 21:2002;5943-5952.
53. Kosmoski J.V., Ackerman E.J., Smerdon M.J. DNA repair of a single UV photoproduct in a designed nucleosome. Proc. Natl. Acad. Sci. USA. 98:2001;10113-10118.
54. Hara R., Sancar A. The SWI/SNF chromatin-remodeling factor stimulates repair by human excision nuclease in the mononucleosome core particle. Mol. Cell. Biol. 22:2002;6779-6787.
55. Arents G., Burlingame R.W., Wang B.C., Love W.E., Moudrianakis E.N. The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix. Proc. Natl. Acad. Sci. USA. 88:1991;10148-10152.