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Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

Author

Listed:
  • Vishwanath R. Iyer

    (Stanford University Medical Center
    University of Texas at Austin)

  • Christine E. Horak

    (Cellular and Developmental Biology, Yale University
    University of Texas at Austin)

  • Charles S. Scafe

    (Stanford University Medical Center
    Applied Biosystems)

  • David Botstein

    (Stanford University Medical Center)

  • Michael Snyder

    (Cellular and Developmental Biology, Yale University)

  • Patrick O. Brown

    (Stanford University Medical Center
    Howard Hughes Medical Institute, Stanford University Medical Center)

Abstract

Proteins interact with genomic DNA to bring the genome to life; and these interactions also define many functional features of the genome. SBF and MBF are sequence-specific transcription factors that activate gene expression during the G1/S transition of the cell cycle in yeast1,2. SBF is a heterodimer of Swi4 and Swi6, and MBF is a heterodimer of Mbp1 and Swi6 (refs 1, 3). The related Swi4 and Mbp1 proteins are the DNA-binding components of the respective factors, and Swi6 may have a regulatory function4,5. A small number of SBF and MBF target genes have been identified3,6,7,8,9,10. Here we define the genomic binding sites of the SBF and MBF transcription factors in vivo, by using DNA microarrays. In addition to the previously characterized targets, we have identified about 200 new putative targets. Our results support the hypothesis that SBF activated genes are predominantly involved in budding, and in membrane and cell-wall biosynthesis, whereas DNA replication and repair are the dominant functions among MBF activated genes6,11. The functional specialization of these factors may provide a mechanism for independent regulation of distinct molecular processes that normally occur in synchrony during the mitotic cell cycle.

Suggested Citation

  • Vishwanath R. Iyer & Christine E. Horak & Charles S. Scafe & David Botstein & Michael Snyder & Patrick O. Brown, 2001. "Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF," Nature, Nature, vol. 409(6819), pages 533-538, January.
    • Handle: RePEc:nat:nature:v:409:y:2001:i:6819:d:10.1038_35054095
    DOI: 10.1038/35054095
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    Citations

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    Cited by:

    1. Emily N Manderson & Mohan Malleshaiah & Stephen W Michnick, 2008. "A Novel Genetic Screen Implicates Elm1 in the Inactivation of the Yeast Transcription Factor SBF," PLOS ONE, Public Library of Science, vol. 3(1), pages 1-9, January.
    2. Zhengdong D Zhang & Joel Rozowsky & Michael Snyder & Joseph Chang & Mark Gerstein, 2008. "Modeling ChIP Sequencing In Silico with Applications," PLOS Computational Biology, Public Library of Science, vol. 4(8), pages 1-10, August.
    3. Cheemeng Tan & Robert Phillip Smith & Ming-Chi Tsai & Russell Schwartz & Lingchong You, 2014. "Phenotypic Signatures Arising from Unbalanced Bacterial Growth," PLOS Computational Biology, Public Library of Science, vol. 10(8), pages 1-10, August.
    4. Xinyi Liu & Bin Liu & Zhimin Huang & Ting Shi & Yingyi Chen & Jian Zhang, 2012. "SPPS: A Sequence-Based Method for Predicting Probability of Protein-Protein Interaction Partners," PLOS ONE, Public Library of Science, vol. 7(1), pages 1-6, January.
    5. G. Saharidis & I. Androulakis & M. Ierapetritou, 2011. "Model building using bi-level optimization," Journal of Global Optimization, Springer, vol. 49(1), pages 49-67, January.
    6. Eilon Sharon & Shai Lubliner & Eran Segal, 2008. "A Feature-Based Approach to Modeling Protein–DNA Interactions," PLOS Computational Biology, Public Library of Science, vol. 4(8), pages 1-17, August.
    7. Xun Lan & Christopher Adams & Mark Landers & Miroslav Dudas & Daniel Krissinger & George Marnellos & Russell Bonneville & Maoxiong Xu & Junbai Wang & Tim H-M Huang & Gavin Meredith & Victor X Jin, 2011. "High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology," PLOS ONE, Public Library of Science, vol. 6(7), pages 1-11, July.
    8. John E Reid & Lorenz Wernisch, 2014. "STEME: A Robust, Accurate Motif Finder for Large Data Sets," PLOS ONE, Public Library of Science, vol. 9(3), pages 1-11, March.
    9. Kyoung-Jae Won & Saurabh Agarwal & Li Shen & Robert Shoemaker & Bing Ren & Wei Wang, 2009. "An Integrated Approach to Identifying Cis-Regulatory Modules in the Human Genome," PLOS ONE, Public Library of Science, vol. 4(5), pages 1-8, May.

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