Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation

March 21, 2008
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Peer-Reviewed Paper, View Original
Description:
The eukaryotic genome is packaged as chromatin with nucleosomes comprising its basic structural unit, but the detailed structure of chromatin and... » More
Citation:
PLoS Biol. 2008 Mar 18; 6(3):e65
Authors:
Sushma Shivaswamy, Akshay Bhinge, Yongjun Zhao, Steven Jones, Martin Hirst, Vishwanath r Iyer

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  1. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389: 251-260.
  2. Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF (2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309: 626-630.
  3. Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS (2007) Nucleosome positioning signals in genomic DNA. Genome Res 17: 1170-1177.
  4. Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y (2006) A genomic code for nucleosome positioning. Nature 442: 772-778.
  5. Wang JP, Widom J (2005) Improved alignment of nucleosome DNA sequences using a mixture model. Nucleic Acids Res 33: 6743-6755.
  6. Ioshikhes IP, Albert I, Zanton SJ, Pugh BF (2006) Nucleosome positions predicted through comparative genomics. Nat Genet 38: 1210-1215.
  7. Rando OJ, Ahmad K (2007) Rules and regulation in the primary structure of chromatin. Curr Opin Cell Biol 19: 250-256.
  8. Whitehouse I, Tsukiyama T (2006) Antagonistic forces that position nucleosomes in vivo. Nat Struct Mol Biol 13: 633-640.
  9. Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ (2007) Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446: 572-576.
  10. Li B, Carey M, Workman JL (2007) The role of chromatin during transcription. Cell 128: 707-719.
  11. Whitehouse I, Rando OJ, Delrow J, Tsukiyama T (2007) Chromatin remodelling at promoters suppresses antisense transcription. Nature 450: 1031-1035.
  12. Fascher KD, Schmitz J, Horz W (1993) Structural and functional requirements for the chromatin transition at the PHO5 promoter in Saccharomyces cerevisiae upon PHO5 activation. J Mol Biol 231: 658-667.
  13. Lee W, Tillo D, Bray N, Morse RH, Davis RW (2007) A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 39: 1235-1244.
  14. Bernstein BE, Liu CL, Humphrey EL, Perlstein EO, Schreiber SL (2004) Global nucleosome occupancy in yeast. Genome Biol 5: R62.
  15. Lee CK, Shibata Y, Rao B, Strahl BD, Lieb JD (2004) Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat Genet 36: 900-905.
  16. Garcia-Martinez J, Aranda A, Perez-Ortin JE (2004) Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol Cell 15: 303-313.
  17. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104.
  18. Hahn JS, Hu Z, Thiele DJ, Iyer VR (2004) Genome-wide analysis of the biology of stress responses through heat shock transcription factor. Mol Cell Biol 24: 5249-5256.
  19. Gorner W, Durchschlag E, Martinez-Pastor MT, Estruch F, Ammerer G (1998) Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity. Genes Dev 12: 586-597.
  20. Hu Z, Killion PJ, Iyer VR (2007) Genetic reconstruction of a functional transcriptional regulatory network. Nat Genet 39: 683-687.
  21. Robert F, Pokholok DK, Hannett NM, Rinaldi NJ, Chandy M (2004) Global position and recruitment of HATs and HDACs in the yeast genome. Mol Cell 16: 199-209.
  22. Lieb JD, Liu X, Botstein D, Brown PO (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28: 327-334.
  23. Marion RM, Regev A, Segal E, Barash Y, Koller D (2004) Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression. Proc Natl Acad Sci U S A 101: 14315-14322.
  24. Reid JL, Iyer VR, Brown PO, Struhl K (2000) Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase. Mol Cell 6: 1297-1307.
  25. Rudra D, Zhao Y, Warner JR (2005) Central role of Ifh1p-Fhl1p interaction in the synthesis of yeast ribosomal proteins. EMBO J 24: 533-542.
  26. Anderson JD, Widom J (2000) Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. J Mol Biol 296: 979-987.
  27. Kent NA, Eibert SM, Mellor J (2004) Cbf1p is required for chromatin remodeling at promoter-proximal CACGTG motifs in yeast. J Biol Chem 279: 27116-27123.
  28. Miyake T, Loch CM, Li R (2002) Identification of a multifunctional domain in autonomously replicating sequence-binding factor 1 required for transcriptional activation, DNA replication, and gene silencing. Mol Cell Biol 22: 505-516.
  29. Schawalder SB, Kabani M, Howald I, Choudhury U, Werner M (2004) Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1. Nature 432: 1058-1061.
  30. Wade JT, Hall DB, Struhl K (2004) The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes. Nature 432: 1054-1058.
  31. Zanton SJ, Pugh BF (2006) Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock. Genes Dev 20: 2250-2265.
  32. Guillemette B, Bataille AR, Gevry N, Adam M, Blanchette M (2005) Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol 3doi:10.1371/journal.pbio.0030384.
  33. Kim J, Iyer VR (2004) Global role of TATA box-binding protein recruitment to promoters in mediating gene expression profiles. Mol Cell Biol 24: 8104-8112.
  34. Basehoar AD, Zanton SJ, Pugh BF (2004) Identification and distinct regulation of yeast TATA box-containing genes. Cell 116: 699-709.
  35. Hertz GZ, Stormo GD (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15: 563-577.
  36. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
Copyright 2014 © Sushma Shivaswamy, Akshay Bhinge, Yongjun Zhao, Steven Jones, Martin Hirst, Vishwanath r Iyer. This pubcast is licensed under the terms of the Creative Commons Attribution License 3.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.