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Deconvolution of Chromatin Immunoprecipitation-Microarray (ChIP-chip) Analysis of MBF Occupancies Reveals the Temporal Recruitment of Rep2 at the MBF Target Genes

Majid Eshaghi, Lei Zhu, Zhaoqing Chu, Juntao Li, Chee Seng Chan, Atif Shahab, R. Krishna M. Karuturi, Jianhua Liu
Majid Eshaghi
1Laboratory of Systems Biology, Genome Institute of Singapore, Singapore 138672
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Lei Zhu
1Laboratory of Systems Biology, Genome Institute of Singapore, Singapore 138672
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Zhaoqing Chu
1Laboratory of Systems Biology, Genome Institute of Singapore, Singapore 138672
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Juntao Li
2Laboratory of Computational and Mathematical Biology, Genome Institute of Singapore, Singapore 138672
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Chee Seng Chan
3Laboratory of Research Computing, Genome Institute of Singapore, Singapore 138672
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Atif Shahab
3Laboratory of Research Computing, Genome Institute of Singapore, Singapore 138672
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R. Krishna M. Karuturi
2Laboratory of Computational and Mathematical Biology, Genome Institute of Singapore, Singapore 138672
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Jianhua Liu
1Laboratory of Systems Biology, Genome Institute of Singapore, Singapore 138672
4Department of Biochemistry, National University of Singapore, Singapore 117597, Republic of Singapore
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  • For correspondence: liujh@gis.a-star.edu.sg
DOI: 10.1128/EC.00218-10
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ABSTRACT

MBF (or DSC1) is known to regulate transcription of a set of G1/S-phase genes encoding proteins involved in regulation of DNA replication. Previous studies have shown that MBF binds not only the promoter of G1/S-phase genes, but also the constitutive genes; however, it was unclear if the MBF bindings at the G1/S-phase and constitutive genes were mechanistically distinguishable. Here, we report a chromatin immunoprecipitation-microarray (ChIP-chip) analysis of MBF binding in the Schizosaccharomyces pombe genome using high-resolution genome tiling microarrays. ChIP-chip analysis indicates that the majority of the MBF occupancies are located at the intragenic regions. Deconvolution analysis using Rpb1 ChIP-chip results distinguishes the Cdc10 bindings at the Rpb1-poor loci (promoters) from those at the Rpb1-rich loci (intragenic sequences). Importantly, Res1 binding at the Rpb1-poor loci, but not at the Rpb1-rich loci, is dependent on the Cdc10 function, suggesting a distinct binding mechanism. Most Cdc10 promoter bindings at the Rpb1-poor loci are associated with the G1/S-phase genes. While Res1 or Res2 is found at both the Cdc10 promoter and intragenic binding sites, Rep2 appears to be absent at the Cdc10 promoter binding sites but present at the intragenic sites. Time course ChIP-chip analysis demonstrates that Rep2 is temporally accumulated at the coding region of the MBF target genes, resembling the RNAP-II occupancies. Taken together, our results show that deconvolution analysis of Cdc10 occupancies refines the functional subset of genomic binding sites. We propose that the MBF activator Rep2 plays a role in mediating the cell cycle-specific transcription through the recruitment of RNAP-II to the MBF-bound G1/S-phase genes.

FOOTNOTES

    • Received 8 September 2010.
    • Accepted 4 November 2010.
    • Accepted manuscript posted online 12 November 2010.
  • ↵§ Supplemental material for this article may be found at http://dx.doi.org/10.1128/EC.00218-10.

  • Copyright © 2011, American Society for Microbiology
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Deconvolution of Chromatin Immunoprecipitation-Microarray (ChIP-chip) Analysis of MBF Occupancies Reveals the Temporal Recruitment of Rep2 at the MBF Target Genes
Majid Eshaghi, Lei Zhu, Zhaoqing Chu, Juntao Li, Chee Seng Chan, Atif Shahab, R. Krishna M. Karuturi, Jianhua Liu
Eukaryotic Cell Jan 2011, 10 (1) 130-141; DOI: 10.1128/EC.00218-10

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Deconvolution of Chromatin Immunoprecipitation-Microarray (ChIP-chip) Analysis of MBF Occupancies Reveals the Temporal Recruitment of Rep2 at the MBF Target Genes
Majid Eshaghi, Lei Zhu, Zhaoqing Chu, Juntao Li, Chee Seng Chan, Atif Shahab, R. Krishna M. Karuturi, Jianhua Liu
Eukaryotic Cell Jan 2011, 10 (1) 130-141; DOI: 10.1128/EC.00218-10
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