Analysis of Saccharomyces cerevisiae histone H3 mutants reveals the role of the αN helix in nucleosome function

Biochemical and Biophysical Research Communications

Volumn 374, Issue 3, 2008, Pages 543-548

  Seol, Ja Hwan ^a   Kim, Hye Jin ^a   Yoo, Ja Kyung ^a   Park, Hyun Ju ^a   Cho, Eun Jung ^a  

^a Sungkyunkwan University   (South Korea)

Author keywords

DNA damage sensitive; Histone chaperone; Histone mutant; Nucleosome structure

Indexed keywords

ALANINE; CHAPERONE; CHROMATIN ASSEMBLY FACTOR 1; HISTONE H3;

ALPHA HELIX; AMINO ACID SUBSTITUTION; ARTICLE; CELL FUNCTION; DNA DAMAGE; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN FUNCTION; SACCHAROMYCES CEREVISIAE;

ALANINE; ALKYLATING AGENTS; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; CELL CYCLE PROTEINS; DNA MUTATIONAL ANALYSIS; HISTONES; HYDROXYUREA; METHYL METHANESULFONATE; MOLECULAR CHAPERONES; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEAR PROTEINS; NUCLEOSOMES; PROTEIN STRUCTURE, SECONDARY; RIBONUCLEOTIDE REDUCTASES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TANDEM REPEAT SEQUENCES;

SACCHAROMYCES CEREVISIAE;

EID: 48849099962     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2008.07.084     Document Type: Article

References (44)

1. Luger K., Mader A.W., Richmond R.K., Sargent D.F., and Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389 (1997) 251-260
2. White C.L., Suto R.K., and Luger C. Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. EMBO J. 20 (2001) 5207-5218
3. Luger K., Rechsteiner T.J., Flaus A.J., Waye M.M., and Richmond T.J. Characterization of nucleosome core particles containing histone proteins made in bacteria. J. Mol. Biol. 272 (1997) 301-311
4. Luger K., and Richmond T.J. The histone tails of the nucleosome. Curr. Opin. Genet. Dev. 8 (1998) 140-146
5. Cho E.J. RNA polymerase II carboxy-terminal domain with multiple connections. Exp. Mol. Med. 30 (2007) 247-254
6. Groth A., Rocha W., Verreault A., and Almouzni G. Chromatin challenges during DNA replication and repair. Cell 128 (2007) 721-733
7. Kouzarides T. Chromatin modifications and their function. Cell 128 (2007) 683-705
8. Peterson C.L., and Laniel M.A. Histones and histone modifications. Curr. Biol. 14 (2004) R546-R551
9. Hyland E.M., Cosgrove M.S., Molina H., Wang D., Pandey A., Cottee R.J., and Boeke J.D. Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae. Mol. Cell. Biol. 25 (2005) 10060-10070
10. Matsubara K., Sano N., Umehara T., and Horikoshi M. Global analysis of functional surfaces of core histones with comprehensive point mutants. Genes Cells 12 (2007) 13-33
11. van Leeuwen F., Gafken P.R., and Gottschling D.E. Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell 109 (2002) 745-756
12. Ng H.H., Feng Q., Wang H., Erdjument-Bromage H., Tempst P., Zhang Y., and 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
13. Recht J., Tsubota T., Tanny J.C., Diaz R.L., Berger J.M., Zhang X., Garcia B.A., Shabanowitz J., Burlingame A.L., Hunt D.F., Kaufman P.D., and Allis C.D. Histone chaperone Asf1 is required for histone H3 lysine 56 acetylation, a modification associated with S phase in mitosis and meiosis. Proc. Natl. Acad. Sci. USA 103 (2006) 6988-6993
14. Wysocki R., Javaheri A., Allard S., Sha F., Cote J., and Kron S.J. Role of Dot1-dependent histone H3 methylation in G1 and S phase DNA damage checkpoint functions of Rad9. Mol. Cell. Biol. 25 (2005) 8430-8443
15. Carrozza M.J., Li B., Florens L., Suganuma T., Swanson S.K., Lee K.K., Shia W.J., Anderson S., Yates J., Washburn M.P., and Workman J.L. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123 (2005) 581-592
16. Crampton A., Chang F., Pappas Jr. D.L., Frisch R.L., and Weinreich M. An ARS element inhibits DNA replication through a SIR2-dependent mechanism. Mol. Cell 30 (2008) 156-166
17. Fischle W., Tseng B.S., Dormann H.L., Ueberheide B.M., Garcia B.A., Shabanowitz J., Hunt D.F., Funabiki H., and Allis C.D. Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 438 (2005) 1116-1122
18. Santos-Rosa H., Schneider R., Bannister A.J., Sherriff J., Bernstein B.E., Emre N.C., Schreiber S.L., Mellor J., and Kouzarides T. Active genes are tri-methylated at K4 of histone H3. Nature 419 (2002) 407-411
19. Verreault A. De novo nucleosome assembly: new pieces in an old puzzle. Genes Dev. 14 (2000) 1430-1438
20. Loyola A., and Almouzni G. Histone chaperones, a supporting role in the limelight. Biochim. Biophys. Acta 1677 (2004) 3-11
21. Glowczewski L., Waterborg J.H., and Berman J.G. Yeast chromatin assembly complex 1 protein excludes nonacetylatable forms of histone H4 from chromatin and the nucleus. Mol. Cell. Biol. 24 (2004) 10180-10192
22. Henikoff S., and Ahmad K. Assembly of variant histones into chromatin. Annu. Rev. Cell Dev. Biol. 21 (2005) 133-153
23. Green E.M., Antczak A.J., Bailey A.O., Franco A.A., Wu K.J., Yates III J.R., and Kaufman P.D. Replication-independent histone deposition by the HIR complex and Asf1. Curr. Biol. 15 (2005) 2044-2049
24. Spector M.S., Raff A., DeSilva H., Lee K., and Osley M.A. Hir1p and Hir2p function as transcriptional corepressors to regulate histone gene transcription in the Saccharomyces cerevisiae cell cycle. Mol. Cell. Biol. 17 (1997) 545-552
25. Krawitz D.C., Kama T., and Kaufman P.D. Chromatin assembly factor I mutants defective for PCNA binding require Asf1/Hir proteins for silencing. Mol. Cell. Biol. 22 (2002) 614-625
26. Kim H.J., Seol J.H., Han J.W., Youn H.D., and Cho E.J. Histone chaperones regulate histone exchange during transcription. EMBO J. 26 (2007) 4467-4474
27. Zhang W., Bone J.R., Edmondson D.G., Turner B.M., and Roth S.Y. Essential and redundant functions of histone acetylation revealed by mutation of target lysines and loss of the Gcn5p acetyltransferase. EMBO J. 17 (1998) 3155-3167
28. Park J.H., Cosgrove M.S., Youngman E., Wolberger C., and Boeke J.D. A core nucleosome surface crucial for transcriptional silencing. Nat. Genet. 32 (2002) 273-279
29. Branzei D., and Foiani M. The Rad53 signal transduction pathway: replication fork stabilization, DNA repair, and adaptation. Exp. Cell Res. 312 (2006) 2654-2659
30. Sedgwick B. Repairing DNA-methylation damage. Nat. Rev. Mol. Cell Biol. 5 (2004) 148-157
31. Wyman C., and Kanaar R. DNA double-strand break repair: all's well that ends well. Annu. Rev. Genet. 40 (2006) 363-383
32. Strahl B.D., Grant P.A., Briggs S.D., Sun Z.W., Bone J.R., Caldwell J.A., Mollah S., Cook R.G., Shabanowitz J., Hunt D.F., and Allis C.D. Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol. Cell. Biol. 22 (2002) 1298-1306
33. Game J.C., Williamson M.S., Spicakova T., and Brown J.M. The RAD6/BRE1 histone modification pathway in Saccharomyces confers radiation resistance through a RAD51-dependent process that is independent of RAD18. Genetics 173 (2006) 1951-1968
34. Biswas D., Takahata S., Xin H., Dutta-Biswas R., Yu Y., Formosa T., and Stillman D.J. A role for Chd1 and Set2 in negatively regulating DNA replication in Saccharomyces cerevisiae. Genetics 178 (2008) 649-659
35. English C.M., Adkins M.W., Carson J.J., Churchill M.E., and Tyler J.K. Structural basis for the histone chaperone activity of Asf1. Cell 127 (2006) 495-508
36. Driscoll R., Hudson A., and Jackson S.P. Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56. Science 315 (2007) 649-652
37. Han J., Zhou H., Horazdovsky B., Zhang K., Xu R.M., and Zhang Z. Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication. Science 315 (2007) 653-655
38. Tsubota T., Berndsen C.E., Erkmann J.A., Smith C.L., Yang L., Freitas M.A., Denu J.M., and Kaufman P.D. Histone H3-K56 acetylation is catalyzed by histone chaperone-dependent complexes. Mol. Cell 25 (2007) 703-712
39. Kireeva M.L., Walter W., Tchernajenko V., Bondarenko V., Kashlev M., and Studitsky V.M. Nucleosome remodeling induced by RNA polymerase II: loss of the H2A/H2B dimer during transcription. Mol. Cell 9 (2002) 541-552
40. Kristjuhan A., and Svejstrup J.Q. Evidence for distinct mechanisms facilitating transcript elongation through chromatin in vivo. EMBO J. 23 (2004) 4243-4252
41. Lee C.K., Shibata Y., Rao B., Strahl B.D., and Lieb J.D. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet. 36 (2004) 900-905
42. Schwabish M.A., and Struhl K. Asf1 mediates histone eviction and deposition during elongation by RNA polymerase II. Mol. Cell 22 (2006) 415-422
43. Tyler J.K., Adams C.R., Chen S.R., Kobayashi R., Kamakaka R.T., and Kadonaga J.T. The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature 402 (1999) 555-560
44. Masumoto H., Hawke D., Kobayashi R., and Verreault A. Nature 436 (2005) 294-298