Evidence for nucleosome depletion at active regulatory regions genome-wide (original) (raw)

• Weintraub, H. & Groudine, M. Chromosomal subunits in active genes have an altered conformation. Science 193, 848–856 (1976).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Elgin, S.C. DNAase I-hypersensitive sites of chromatin. Cell 27, 413–415 (1981).
  Article CAS Google Scholar
• Reinke, H. & Horz, W. Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol. Cell 11, 1599–1607 (2003).
  Article CAS Google Scholar
• Boeger, H., Griesenbeck, J., Strattan, J.S. & Kornberg, R.D. Nucleosomes unfold completely at a transcriptionally active promoter. Mol. Cell 11, 1587–1598 (2003).
  Article CAS Google Scholar
• Svaren, J. & Horz, W. Transcription factors vs nucleosomes: regulation of the PHO5 promoter in yeast. Trends Biochem. Sci. 22, 93–97 (1997).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Lohr, D. Nucleosome transactions on the promoters of the yeast GAL and PHO genes. J. Biol. Chem. 272, 26795–26798 (1997).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Holstege, F.C. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717–728 (1998).
  Article CAS Google Scholar
• Belotserkovskaya, R. et al. FACT facilitates transcription-dependent nucleosome alteration. Science 301, 1090–1093 (2003).
  Article CAS Google Scholar
• Cavalli, G. & Thoma, F. Chromatin transitions during activation and repression of galactose-regulated genes in yeast. EMBO J. 12, 4603–4613 (1993).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Gasch, A.P. et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241–4257 (2000).
  Article CAS Google Scholar
• Causton, H.C. et al. Remodeling of yeast genome expression in response to environmental changes. Mol. Biol. Cell 12, 323–337 (2001).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Yu, L. & Morse, R.H. Chromatin opening and transactivator potentiation by RAP1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 19, 5279–5288 (1999).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Lusser, A. & Kadonaga, J.T. Chromatin remodeling by ATP-dependent molecular machines. Bioessays 25, 1192–1200 (2003).
  Article CAS Google Scholar
• 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 PHO5 and PHO8 genes. Mol. Cell 14, 657–666 (2004).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• Jackson, V. Formaldehyde cross-linking for studying nucleosomal dynamics. Methods 17, 125–139 (1999).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• 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).
  Article Google Scholar