Deciphering the roles of the histone H2B N-terminal domain in genome-wide transcription

Molecular and Cellular Biology

Volumn 26, Issue 10, 2006, Pages 3842-3852

  Parra, Michael A ^a   Kerr, David ^a   Fahy, Deirdre ^a   Pouchnik, Derek J ^a   Wyrick, John J ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; COMPLEMENTARY DNA; COMPLEMENTARY RNA; DNA; HISTONE H2B; LYSINE; MESSENGER RNA; NICOTINAMIDE ADENINE DINUCLEOTIDE;

ARTICLE; BIOSYNTHESIS; CARBOHYDRATE METABOLISM; DNA DAMAGE; GENE EXPRESSION REGULATION; GENE MUTATION; GENETIC TRANSCRIPTION; GENOME; GENOTYPE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PRIORITY JOURNAL; PROTEIN DOMAIN; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SACCHAROMYCES CEREVISIAE; TELOMERE; TRANSCRIPTION REGULATION; ULTRAVIOLET IRRADIATION; VITAMIN METABOLISM; YEAST;

ACETYLATION; AMINO ACID SEQUENCE; CONSERVED SEQUENCE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENOME, FUNGAL; HISTONES; LYSINE; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PLASMIDS; PROTEIN ARRAY ANALYSIS; PROTEIN STRUCTURE, TERTIARY; REPRESSOR PROTEINS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SACCHAROMYCES CEREVISIAE; SEQUENCE DELETION; SPECIES SPECIFICITY; TELOMERE; TRANSCRIPTION, GENETIC; ULTRAVIOLET RAYS;

EID: 33646580356     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.26.10.3842-3852.2006     Document Type: Article

References (34)

1. Baudin, A., O. Ozier-Kalogeropoulos, A. Denouel, F. Lacroute, and C. Cullin. 1993. A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res. 21:3329-3330.
2. Berger, S. L. 2002. Histone modifications in transcriptional regulation. Curr. Opin. Genet. Dev. 12:142-148.
3. Davey, C. A., D. F. Sargent, K. Luger, A. W. Maeder, and T. J. Richmond. 2002. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J. Mol. Biol. 319:1097-1113.
4. Dion, M. F., S. J. Altschuler, L. F. Wu, and O. J. Rando. 2005. Genomic characterization reveals a simple histone H4 acetylation code. Proc. Natl. Acad. Sci. USA 102:5501-5506.
5. Felsenfeld, G., and M. Groudine. 2003. Controlling the double helix. Nature 421:448-453.
6. Fischle, W., Y. Wang, and C. D. Allis. 2003. Binary switches and modification cassettes in histone biology and beyond. Nature 425:475-479.
7. Gong, F., Y. Kwon, and M. J. Smerdon. 2005. Nucleotide excision repair in chromatin and the right of entry. DNA Repair (Amsterdam) 4:884-896.
8. Hansen, J. C., and A. P. Wolffe. 1994. A role for histones H2A/H2B in chromatin folding and transcriptional repression. Proc. Natl. Acad. Sci. USA 91:2339-2343.
9. Iizuka, M., and M. M. Smith. 2003. Functional consequences of histone modifications. Curr. Opin. Genet. Dev. 13:154-160.
10. Jenuwein, T., and C. D. Allis. 2001. Translating the histone code. Science 293:1074-1080.
11. Lenfant, F., R. K. Mann, B. Thomsen, X. Ling, and M. Grunstein. 1996. All four core histone N-termini contain sequences required for the repression of basal transcription in yeast. EMBO J. 15:3974-3985.
12. Martens, J. A., and F. Winston. 2003. Recent advances in understanding chromatin remodeling by Swi/Snf complexes. Curr. Opin. Genet. Dev. 13: 136-142.
13. Martin, A. M., D. J. Pouchnik, J. L. Walker, and J. J. Wyrick. 2004. Redundant roles for histone H3 N-terminal lysine residues in subtelomeric gene repression in Saccharomyces cerevisiae. Genetics 167:1123-1132.
14. Meneghini, M. D., M. Wu, and H. D. Madhani. 2003. Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell 112:725-736.
15. Peterson, C. L., and M. A. Laniel. 2004. Histones and histone modifications. Curr. Biol. 14:R546-R551.
16. Placek, B. J., and L. M. Gloss. 2002. The N-terminal tails of the H2A-H2B histones affect dimer structure and stability. Biochemistry 41:14960-14968.
17. Puerta, C., F. Hernandez, L. Lopez-Alarcon, and E. Palacian. 1995. Acetylation of histone H2A. H2B dimers facilitates transcription. Biochem. Biophys. Res. Commun. 210:409-416.
18. Recht, J., B. Dunn, A. Raff, and M. A. Osley. 1996. Functional analysis of histones H2A and H2B in transcriptional repression in Saccharomyces cerevisiae. Mol. Cell. Biol. 16:2545-2553.
19. Recht, J., and M. A. Osley. 1999. Mutations in both the structured domain and N-terminus of histone H2B bypass the requirement for Swi-Snf in yeast. EMBO J. 18:229-240.
20. Ren, B., F. Robert, J. J. Wyrick, O. Aparicio, E. G. Jennings, I. Simon, J. Zeitlinger, J. Schreiber, N. Hannett, E. Kanin, T. L. Volkert, C. J. Wilson, S. P. Bell, and R. A. Young. 2000. Genome-wide location and function of DNA binding proteins. Science 290:2306-2309.
21. Richmond, T. J., and C. A. Davey. 2003. The structure of DNA in the nucleosome core. Nature 423:145-150.
22. Roberts, C. J., B. Nelson, M. J. Marton, R. Stoughton, M. R. Meyer, H. A. Bennett, Y. D. He, H. Dai, W. L. Walker, T. R. Hughes, M. Tyers, C. Boone, and S. H. Friend. 2000. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287:873-880.
23. Robyr, D., Y. Suka, I. Xenarios, S. K. Kurdistani, A. Wang, N. Suka, and M. Grunstein. 2002. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell 109:437-446.
24. Roth, S. Y., J. M. Denu, and C. D. Allis. 2001. Histone acetyltransferases. Annu. Rev. Biochem. 70:81-120.
25. Sabet, N., F. Tong, J. P. Madigan, S. Volo, M. M. Smith, and R. H. Morse. 2003. Global and specific transcriptional repression by the histone H3 amino terminus in yeast. Proc. Natl. Acad. Sci. USA 100:4084-4089.
26. Sabet, N., S. Volo, C. Yu, J. P. Madigan, and R. H. Morse. 2004. Genomewide analysis of the relationship between transcriptional regulation by Rpd3p and the histone H3 and H4 amino termini in budding yeast. Mol. Cell. Biol. 24:8823-8833.
27. Sikorski, R. S., and P. Hieter. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19-27.
28. Suka, N., Y. Suka, A. A. Carmen, J. Wu, and M. Grunstein. 2001. Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin. Mol. Cell 8:473-479.
29. Thompson, J. S., X. Ling, and M. Grunstein. 1994. Histone H3 amino terminus is required for telomeric and silent mating locus repression in yeast. Nature 369:245-247.
30. Turner, B. M. 2002. Cellular memory and the histone code. Cell 111:285-291.
31. Vidanes, G. M., C. Y. Bonilla, and D. P. Toczyski. 2005. Complicated tails: histone modifications and the DNA damage response. Cell 121:973-976.
32. Wyatt, H. R., H. Liaw, G. R. Green, and A. J. Lustig. 2003. Multiple roles for Saccharomyces cerevisiae histone H2A in telomere position effect, Spt phenotypes and double-strand-break repair. Genetics 164:47-64.
33. Wyrick, J. J., F. C. Holstege, E. G. Jennings, H. C. Causton, D. Shore, M. Grunstein, E. S. Lander, and R. A. Young. 1999. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402: 418-421.
34. Zhang, L., E. E. Eugeni, M. R. Parthun, and M. A. Freitas. 2003. Identification of novel histone post-translational modifications by peptide mass fingerprinting. Chromosoma 112:77-86.