Evidence for nucleosome depletion at active regulatory regions genome-wide

Nature Genetics

Volumn 36, Issue 8, 2004, Pages 900-905

  Lee, Cheol Koo ^a   Shibata, Yoichiro ^b   Rao, Bhargavi ^a   Strahl, Brian D ^a,b   Lieb, Jason D ^a  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEAT SHOCK PROTEIN; HISTONE H3; HISTONE H4; NUCLEASE;

ACTIVE REGULATORY ELEMENT; ARTICLE; CHROMATIN; DROSOPHILA; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE LOCUS; GENOME; GLOBIN GENE; IMMUNOPRECIPITATION; IN VIVO STUDY; MIOSIS; NONHUMAN; NUCLEOSOME; NUCLEOTIDE REPEAT; PRIORITY JOURNAL; PROMOTER REGION; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; YEAST;

GENES, FUNGAL; HISTONES; NUCLEOSOMES; REGULATORY SEQUENCES, NUCLEIC ACID; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION, GENETIC;

DROSOPHILA MELANOGASTER; EUKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 3543023310     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/ng1400     Document Type: Article

References (29)

1. Weintraub, H. & Groudine, M. Chromosomal subunits in active genes have an altered conformation. Science 193, 848-856 (1976).
2. Wu, C., Wong, Y.C. & Elgin, S.C. The chromatin structure of specific genes: II. Disruption of chromatin structure during gene activity. Cell 16, 807-814 (1979).
3. Elgin, S.C. DNAase I-hypersensitive sites of chromatin. Cell 27, 413-415 (1981).
4. Reinke, H. & Horz, W. Histones are first hyperacetylated and then lose contact with the activated PH05 promoter. Mol. Cell 11, 1599-1607 (2003).
5. Boeger, H., Griesenbeck, J., Strattan, J.S. & Kornberg, R.D. Nucleosomes unfold completely at a transcriptionally active promoter. Mol. Cell 11, 1587-1598 (2003).
6. Svaren, J. & Horz, W. Transcription factors vs nucleosomes: regulation of the PH05 promoter in yeast. Trends Biochem. Sci. 22, 93-97 (1997).
7. Boeger, H., Griesenbeck, J., Strattan, J.S. & Kornberg, R.D. Removal of promoter nucleosomes by disassembly rather than sliding in vivo. Mol. Cell 14, 667-673 (2004).
8. Fedor, M.J. & Kornberg, R.D. Upstream activation sequence-dependent alteration of chromatin structure and transcription activation of the yeast GAL1-GAL10 genes. Mol. Cell. Biol. 9, 1721-1732 (1989).
9. Lohr, D. Nucleosome transactions on the promoters of the yeast GAL and PHO genes. J. Biol. Chem. 272, 26795-26798 (1997).
10. Dammann, R., Lucchini, R., Koller, T. & Sogo, J.M. Chromatin structures and transcription of rDNA in yeast Saccharomyces cerevisiae. Nucleic Acids Res. 21, 2331-2338 (1993).
11. Holstege, F.C. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717-728 (1998).
12. Belotserkovskaya, R. et al. FACT facilitates transcription-dependent nucleosome alteration. Science 301, 1090-1093 (2003).
13. Cavalli, G. & Thoma, F. Chromatin transitions during activation and repression of galactose-regulated genes in yeast. EMBO J. 12, 4603-4613 (1993).
14. Li, B., Nierras, C.R. & Warner, J.R. Transcriptional elements involved in the repression of ribosomal protein synthesis. Mol. Cell. Biol. 19, 5393-5404 (1999).
15. Gasch, A.P. et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241-4257 (2000).
16. Causton, H.C. et al. Remodeling of yeast genome expression in response to environmental changes. Mol. Biol. Cell 12, 323-337 (2001).
17. Lieb, J.D., Liu, X., Botstein, D. & Brown, P.O. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28, 327-334. (2001).
18. Yu, L. & Morse, R.H. Chromatin opening and transactivator potentiation by RAP1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 19, 5279-5288 (1999).
19. Kuo, M.H., Zhou, J., Jambeck, P., Churchill, M.E. & Allis, C.D. Histone acetyltransferase activity of yeast Gcn5p is required for the activation of target genes in vivo. Genes Dev. 12, 627-639 (1998).
20. Schnitzler, G., Sif, S. & Kingston, R.E. Human SWI/SNF interconverts a nucleosome between its base state and a stable remodeled state. Cell 94, 17-27 (1998).
21. Lusser, A. & Kadonaga, J.T. Chromatin remodeling by ATP-dependent molecular machines. Bioessays 25, 1192-1200 (2003).
22. Adkins, M.W., Howar, S.R. & Tyler, J.K. Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PH05 and PH08 genes. Mol. Cell 14, 657-666 (2004).
23. Nagy, P.L., Cleary, M.L., Brown, P.O. & Lieb, J.D. Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin. Proc. Natl. Acad. Sci. USA 100, 6364-6369 (2003).
24. Li, S. & Smerdon, M.J. Nucleosome structure and repair of N-methylpurines in the GAL1-10 genes of Saccharomyces cerevisiae. J. Biol. Chem. 277, 44651-44659 (2002).
25. Jackson, V. Formaldehyde cross-linking for studying nucleosomal dynamics. Methods 17, 125-139 (1999).
26. Kuo, M.H. & Allis, C.D. In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment. Methods 19, 425-433 (1999).
27. Ng, H.H., Ciccone, D.N., Morshead, K.B., Oettinger, M.A. & Struhl, K. Lysine-79 of histone H3 is hypomethylated at silenced loci in yeast and mammalian cells: A potential mechanism for position-effect variegation. Proc. Natl. Acad. Sci. USA 100, 1820-1825 (2003).
28. Liu, C.L., Schreiber, S.L. & Bernstein, B.E. Development and validation of a T7 based linear amplification for genomic DNA. BMC Genomics 4, 19 (2003).
29. Yang, Y.H. et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30, e15 (2002).