Searching journal content for articles similar to Zhong et al. 9 (11): 1040.

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  1. Research: Genome-wide cooperation by HAT Gcn5, remodeler SWI/SNF, and chaperone Ydj1 in promoter nucleosome eviction and transcriptional activation
    • Hongfang Qiu,
    • Răzvan V. Chereji,
    • Cuihua Hu,
    • Hope A. Cole,
    • Yashpal Rawal,
    • David J. Clark,
    • and Alan G. Hinnebusch
    Genome Res. February 2016 26: 211-225; Published in Advance November 24, 2015, doi:10.1101/gr.196337.115
    ...implicated Gcn5, Snf2, and Ydj1 in H3 eviction at most, but not all, Gcn4 target promoters, with Gcn5 generally playing the greatest role and Ydj1 the least. Remarkably, these three cofactors cooperate similarly in H3 eviction at virtually all yeast promoters. Defective H3 eviction in cofactor mutants...
  2. Methods: Refinement and expansion of signaling pathways: The osmotic response network in yeast
    • Irit Gat-Viks and
    • Ron Shamir
    Genome Res. March 2007 17: 358-367; Published in Advance January 31, 2007, doi:10.1101/gr.5750507
    ...Refinement and expansion of signaling pathways: The osmotic response network in yeast Irit Gat-Viks 1 and Ron Shamir School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel Abstract The analysis of large-scale genome...
  3. LETTER: Identification of functional transcription factor binding sites using closely related Saccharomyces species
    • Scott W. Doniger,
    • Juyoung Huh,
    • and Justin C. Fay
    Genome Res. May 2005 15: 701-709; Published in Advance April 18, 2005, doi:10.1101/gr.3578205
    ...substitution rate across the three yeast species is 0.57, which implies that 43% of intergenic sequences are functionally constrained. The extent to which conserved TFBSs can account for this constraint is discussed below. Identification of functionally constrained Ndt80 and Ume6 binding sites using a neutral...
    OPEN ACCESS ARTICLE
  4. LETTER: Genome-wide Co-occurrence of Promoter Elements Reveals a cis-Regulatory Cassette of rRNA Transcription Motifs in Saccharomyces cerevisiae
    • Priya Sudarsanam,
    • Yitzhak Pilpel,
    • and George M. Church
    Genome Res. November 1, 2002 12: 1723-1731; doi:10.1101/gr.301202
    ....O. ( 2000 ) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11 : 4241 – 4257 . ↵ GuhaThakurta D. , Stormo G.D. ( 2001 ) Identifying target sites for cooperatively binding factors. Bioinformatics 17 : 608 – 621 . ↵ Halfon M.S. , Grad Y. , Church G...
  5. LETTER: From Gene Networks to Gene Function
    • Thomas Schlitt,
    • Kimmo Palin,
    • Johan Rung,
    • Sabine Dietmann,
    • Michael Lappe,
    • Esko Ukkonen,
    • and Alvis Brazma
    Genome Res. December 2003 13: 2568-2576; doi:10.1101/gr.1111403
    ...to SGD ( http://www.yeast.org/ ). This would imply that Kin3p may be involved in cell growth, budding, or related processes. View larger version: In this window In a new window Figure 4 Visualization of the source gene pairs with highly similar target sets as a graph. Genes involved in the same...
  6. Methods: Discovering regulatory binding-site modules using rule-based learning
    • Torgeir R. Hvidsten,
    • Bartosz Wilczyński,
    • Andriy Kryshtafovych,
    • Jerzy Tiuryn,
    • Jan Komorowski,
    • and Krzysztof Fidelis
    Genome Res. June 2005 15: 856-866; doi:10.1101/gr.3760605
    ...suggests that one way for RAP1 to specifically target ribosomal proteins in growing yeast cells is to require the presence of MCM1 and SWI5. This is also supported by the Gene Ontology annotations in Table 1 , which suggests that the genes associated with the binding sites RAP1, MCM1′, and SWI5...
  7. Method: Linking the signaling cascades and dynamic regulatory networks controlling stress responses
    • Anthony Gitter,
    • Miri Carmi,
    • Naama Barkai,
    • and Ziv Bar-Joseph
    Genome Res. February 2013 23: 365-376; Published in Advance October 11, 2012, doi:10.1101/gr.138628.112
    ..., and the affected genes. The signaling and regulatory components of our networks are linked via a set of common transcription factors that serve as targets in the signaling network and as regulators of the transcriptional response network. Detailed case studies of stress responses in budding yeast demonstrate...
  8. Letter: The functional importance of telomere clustering: Global changes in gene expression result from SIR factor dispersion
    • Angela Taddei,
    • Griet Van Houwe,
    • Shigeki Nagai,
    • Ionas Erb,
    • Erik van Nimwegen,
    • and Susan M. Gasser
    Genome Res. April 2009 19: 611-625; Published in Advance January 29, 2009, doi:10.1101/gr.083881.108
    ...2007 ). This clustering phenomenon occurs for telomeric repeats (in yeast) or centromeric heterochromatin (e.g., in fission yeast, Drosophila , and mammals). Given that these repetitive sequences generally nucleate patterns of histone modification that are recognized by histone-binding repressors...
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