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Promoter-specific binding of Rap1 revealed by genome-wide maps of protein–DNA association

Nature Genetics volume 28, pages 327–334 (2001)Cite this article

An Erratum to this article was published on 01 September 2001

Abstract

We determined the distribution of repressor-activator protein 1 (Rap1) and the accessory silencing proteins Sir2, Sir3 and Sir4 in vivo on the entire yeast genome, at a resolution of 2 kb. Rap1 is central to the cellular economy during rapid growth, targeting 294 loci, about 5% of yeast genes, and participating in the activation of 37% of all RNA polymerase II initiation events in exponentially growing cells. Although the DNA sequence recognized by Rap1 is found in both coding and intergenic sequences, the binding of Rap1 to the genome was highly specific to intergenic regions with the potential to act as promoters. This global phenomenon, which may be a general characteristic of sequence-specific transcriptional factors, indicates the existence of a genome-wide molecular mechanism for marking promoter regions.

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Figure 1: Determination of Rap1 targets.
Figure 2: Map of the interaction between Rap1 and the S. cerevisiae genome.
Figure 3: Rap1 binds preferentially to potential promoters
Figure 4: Rap1 binds to the promoters of heavily transcribed genes.

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References

  1. Moretti, P., Freeman, K., Coodly, L. & Shore, D. Evidence that a complex of Sir proteins interacts with the silencer and telomere-binding protein Rap1. Genes Dev. 8, 2257–2269 (1994).

    Article  CAS  Google Scholar 

  2. Shore, D. Telomerase and telomere-binding proteins: controlling the endgame. Trends Biochem. Sci. 22, 233–235 (1997).

    Article  CAS  Google Scholar 

  3. Aparicio, O.M., Billington, B.L. & Gottschling, D.E. Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae. Cell 66, 1279–1287 (1991).

    Article  CAS  Google Scholar 

  4. Konig, P., Giraldo, R., Chapman, L. & Rhodes, D. The crystal structure of the DNA-binding domain of yeast Rap1 in complex with telomeric DNA. Cell 85, 125–136 (1996).

    Article  CAS  Google Scholar 

  5. Cockell, M. et al. The carboxy termini of Sir4 and Rap1 affect Sir3 localization: evidence for a multicomponent complex required for yeast telomeric silencing. J. Cell Biol. 129, 909–924 (1995).

    Article  CAS  Google Scholar 

  6. Hecht, A., Laroche, T., Strahl-Bolsinger, S., Gasser, S.M. & Grunstein, M. Histone H3 and H4 N-termini interact with Sir3 and Sir4 proteins: a molecular model for the formation of heterochromatin in yeast. Cell 80, 583–592 (1995).

    Article  CAS  Google Scholar 

  7. Guarente, L. Sir2 links chromatin silencing, metabolism, and aging. Genes Dev. 14, 1021–1026 (2000).

    Article  CAS  Google Scholar 

  8. Warner, J.R. The economics of ribosome biosynthesis in yeast. Trends Biochem. Sci. 24, 437–440 (1999).

    Article  CAS  Google Scholar 

  9. Morse, R.H. Rap, Rap, open up! New wrinkles for Rap1 in yeast. Trends Genet. 16, 51–53 (2000).

    Article  CAS  Google Scholar 

  10. Li, B., Oestreich, S. & de Lange, T. Identification of human Rap1: implications for telomere evolution. Cell 101, 471–483 (2000).

    Article  CAS  Google Scholar 

  11. Graham, I.R., Haw, R.A., Spink, K.G., Halden, K.A. & Chambers, A. In vivo analysis of functional regions within yeast Rap1p. Mol. Cell. Biol. 19, 7481–7490 (1999).

    Article  CAS  Google Scholar 

  12. Freeman, K., Gwadz, M. & Shore, D. Molecular and genetic analysis of the toxic effect of Rap1 overexpression in yeast. Genetics 141, 1253–1262 (1995).

    Article  CAS  Google Scholar 

  13. Wyrick, J.J. et al. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402, 418–421 (1999).

    Article  CAS  Google Scholar 

  14. Reid, J.L., Iyer, V.R., Brown, P.O. & Struhl, K. Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase. Mol. Cell 6, 1297–1307 (2000).

    Article  CAS  Google Scholar 

  15. Iyer, V.A. et al. Genomic binding distribution of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533–538 (2001).

    Article  CAS  Google Scholar 

  16. Conrad, M.N., Wright, J.H., Wolf, A.J. & Zakian, V.A. Rap1 protein interacts with yeast telomeres in vivo: overproduction alters telomere structure and decreases chromosome stability. Cell 63, 739–750 (1990).

    Article  CAS  Google Scholar 

  17. Gotta, M. et al. The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae. J. Cell Biol. 134, 1349–1363 (1996).

    Article  CAS  Google Scholar 

  18. Strahl-Bolsinger, S., Hecht, A., Luo, K. & Grunstein, M. Sir2 and Sir4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev. 11, 83–93 (1997).

    Article  CAS  Google Scholar 

  19. Hecht, A., Strahl-Bolsinger, S. & Grunstein, M. Spreading of transcriptional repressor Sir3 from telomeric heterochromatin. Nature 383, 92–96 (1996).

    Article  CAS  Google Scholar 

  20. Pryde, F.E. & Louis, E.J. Limitations of silencing at native yeast telomeres. EMBO J. 18, 2538–2550 (1999).

    Article  CAS  Google Scholar 

  21. Donze, D., Adams, C.R., Rine, J. & Kamakaka, R.T. The boundaries of the silenced HMR domain in Saccharomyces cerevisiae. Genes Dev. 13, 698–708 (1999).

    Article  CAS  Google Scholar 

  22. Lascaris, R.F., Mager, W.H. & Planta, R.J. DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences. Bioinformatics 15, 267–277 (1999).

    Article  CAS  Google Scholar 

  23. Costanzo, M.C. et al. The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res. 28, 73–76 (2000).

    Article  CAS  Google Scholar 

  24. Remacle, J.E. & Holmberg, S. A REB1-binding site is required for GCN4-independent ILV1 basal level transcription and can be functionally replaced by an ABF1-binding site. Mol. Cell. Biol. 12, 5516–5526 (1992).

    CAS  Google Scholar 

  25. Gonçalves, P.M. et al. C-terminal domains of general regulatory factors Abf1p and Rap1p in Saccharomyces cerevisiae display functional similarity. Mol. Microbiol. 19, 535–543 (1996).

    Article  Google Scholar 

  26. Cherry, J.M. et al. Saccharomyces Genome Database. 12/01/1999 edn Vol. 1999 (2000).

  27. Mewes, H.W. et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 27, 44–48 (1999).

    Article  CAS  Google Scholar 

  28. Lopez, N., Halladay, J., Walter, W. & Craig, E.A. SSB, encoding a ribosome-associated chaperone, is coordinately regulated with ribosomal protein genes. J. Bacteriol. 181, 3136–3143 (1999).

    Article  CAS  Google Scholar 

  29. Holstege, F.C. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717–728 (1998).

    Article  CAS  Google Scholar 

  30. Liu, X., Brutlag, D.L. & Liu, J.S. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput. 127–138 (2001).

  31. Graham, I.R. & Chambers, A. Use of a selection technique to identify the diversity of binding sites for the yeast Rap1 transcription factor. Nucleic Acids Res 22, 124–130 (1994).

    Article  CAS  Google Scholar 

  32. Buchman, A.R., Kimmerly, W.J., Rine, J. & Kornberg, R.D. Two DNA-binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae. Mol. Cell. Biol. 8, 210–225 (1988).

    CAS  Google Scholar 

  33. Idrissi, F.Z. & Piña, B. Functional divergence between the half-sites of the DNA-binding sequence for the yeast transcriptional regulator Rap1p. Biochem. J. 341, 477–482 (1999).

    Article  CAS  Google Scholar 

  34. Tjian, R. & Maniatis, T. Transcriptional activation: a complex puzzle with few easy pieces. Cell 77, 5–8 (1994).

    Article  CAS  Google Scholar 

  35. Leblanc, B.P., Benham, C.J. & Clark, D.J. An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled. Proc. Natl. Acad. Sci. USA 97, 10745–10750 (2000).

    Article  CAS  Google Scholar 

  36. Peterson, C.L. & Workman, J.L. Promoter targeting and chromatin remodeling by the SWI/SNF complex. Curr. Opin. Genet. Dev. 10, 187–192 (2000).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank V. Iyer for initiating work on the intergenic yeast array, and other members of the Brown and Botstein labs for advice and technical support. We thank D. Brutlag and J. Liu for advice in developing BioProspector, J. Derisi for software that maps the IP data, and J. Rine for yeast strains. This work was supported by a grant from the National Human Genome Research Institute and by the Howard Hughes Medical Institute. P.O.B. is an associate investigator of the Howard Hughes Medical Institute, and the Helen Hay Whitney Foundation supports J.D.L.

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Authors and Affiliations

  1. Department of Biochemistry, Stanford University, Stanford, 94305-5428, California, USA

    Jason D. Lieb & Patrick O. Brown

  2. Stanford Medical Informatics, Stanford University, Stanford, 94305-5428, California, USA

    Xiaole Liu

  3. Department of Genetics, Stanford University, Stanford, 94305-5428, California, USA

    David Botstein

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  1. Jason D. Lieb
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  2. Xiaole Liu
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  4. Patrick O. Brown
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Correspondence to Patrick O. Brown.

Supplementary information

Web Figure A

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Web Figure H:

Download the .cdt, .gtr, and .pcl files corresponding to the cluster of gene expression profiles for the genes downstream of intergenic fragments selected by the Rap1p IP. These files must be loaded into Treeview to view the clusters. Instructions for using Treeview (http://rana.lbl.gov/EisenSoftware.htm) can be found in the Treview Manual.

Web Figure H: .cdt, .gtr, and .pcl files (ZIP 702 KB)

Web Figure H: Treeview Manual (PDF 291 KB)

Web Figure I

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Web Table I

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Lieb, J., Liu, X., Botstein, D. et al. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein–DNA association. Nat Genet 28, 327–334 (2001). https://doi.org/10.1038/ng569

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