High-resolution genome-wide mapping of histone modifications

Nature Biotechnology

Volumn 22, Issue 8, 2004, Pages 1013-1016

  Roh, Tae Young ^a   Ngau, Wing Chi ^b   Cui, Kairong ^a   Landsman, David ^b   Zhao, Keji ^a  

^a NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLATION; DNA; PROTEINS;

CHROMATIN STRUCTURES; HISTONE MODIFICATION;

GENES;

HISTONE; HISTONE ACETYLTRANSFERASE; PROTEIN GCN5P; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; CHROMATIN STRUCTURE; GENE EXPRESSION; GENE MAPPING; GENETIC CODE; IMMUNOPRECIPITATION; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MODIFICATION; SACCHAROMYCES CEREVISIAE; SERIAL ANALYSIS OF GENE EXPRESSION;

CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME MAPPING; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENOME, FUNGAL; HISTONE CODE; HISTONES; PROMOTER REGIONS (GENETICS); SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA;

EUKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 3543008920     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt990     Document Type: Article

References (22)

1. Kornberg, R.D. & Lorch, Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98, 285-294 (1999).
2. Felsenfeld, G. & Groudine, M. Controlling the double helix. Nature 421, 448-453 (2003).
3. Velculescu, V.E., Zhang, L., Vogelstein, B. & Kinzler, K.W. Serial analysis of gene expression. Science 270, 484-487 (1995).
4. Velculescu, V.E. et al. Characterization of the yeast transcriptome. Cell 88, 243-251 (1997).
5. Saha, S. et al. Using the transcriptome to annotate the genome. Nat. Biotechnol. 20, 508-512 (2002).
6. Braunstein, M., Rose, A.B., Holmes, S.G., Allis, C.D. & Broach, J.R. Transcriptional silencing in yeast is associated with reduced nucleosome acetylation. Genes Dev. 7, 592-604 (1993).
7. Rundlett, S.E., Carmen, A.A., Suka, N., Turner, B.M. & Grunstein, M. Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature 392, 831-835 (1998).
8. Davie, J.R., Saunders, C.A. Walsh, J.M. & Weber, S.C. Histone modifications in the yeast S. cerevisiae. Nucleic Acids Res. 9, 3205-3216 (1981).
9. Vogelauer, M., Wu, J., Suka, N. & Grunstein, M. Global histone "acetylation and deacetytation in yeast. Nature 408, 495-498 (2000).
10. Grunstein, M. Yeast heterochromatin: regulation of its assembly and inheritance by histones. Cell 93, 325-328 (1998).
11. DuBois, M.L., Diede, S.J., Stellwagen, A.E. & Gottschling, D.E. All things must end: telomere dynamics in yeast. Cold Spring Harb. Symp. Quant. Biol. 65, 281-296 (2000)
12. Chan, C.S. & Tye, B.K. Organization of DNA sequences and replication origins at yeast telomeres. Cell 33, 563-573 (1983).
13. Pryde, F.E. & Louis, E.J. Limitations of silencing at native yeast telomeres. EMBO J. 18, 2538-2550 (1999).
14. Boeger, H., Griesenbeck, J., Strattan, J.S. & Kornberg, R.D. Nucleosomes unfold completely at a transcriptionally active promoter. Mol. Cell 11, 1587-1598 (2003).
15. Reinke, H. & Horz, W. Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol. Cell 11, 1599-1607 (2003).
16. Brownell, J.E. et al. Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84, 843-851 (1996).
17. Grant, P.A. et al. Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 11, 1640-1650 (1997).
18. Kuo, M.H. et al. Transcription-linked acetylation by Gcn5p of histones H3 and H4 at specific lysines. Nature 383, 269-272 (1996).
19. Horak, C.E. & Snyder, M. ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods Enzymol. 350, 469-483 (2002).
20. Wan, M., Zhao, K., Lee, S.S. & Francke, U. MECP2 truncating mutations cause histone H4 hyperacetylation in Rett syndrome. Hum. Mol. Genet. 10, 1085-1092 (2001).
21. Suka, N., Suka, Y., Carmen, A.A., Wu, J. & Grunstein, M. Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin. Mol. Cell 8, 473-479 (2001).
22. Mueller, P.R. & Wold, B. In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. Science 246, 780-786 (1989).