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Gene Review

RAP1  -  Rap1p

Saccharomyces cerevisiae S288c

Synonyms: DNA-binding protein RAP1, GRF1, N1310, Repressor/activator site-binding protein, SBF-E, ...
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Disease relevance of RAP1

  • In addition, gel electrophoretic mobility shift and DNase I protection studies, involving yeast gene products expressed in E. coli, suggest that this trans-acting DNA-binding protein is encoding by the RAP1 gene [1].
  • SKO1/ACR1, which encodes a CREB-like repressor protein in yeast, was isolated as a high copy suppressor of the toxicity caused by RAP1 overexpression [2].
  • Saccharomyces cerevisiae multifunctional protein RAP1 binds to a conserved sequence in the Polyoma virus enhancer and is responsible for its transcriptional activity in yeast cells [3].
  • Here, we show that the breast cancer susceptibility gene product, breast cancer susceptibility gene 1, and the human homologue of yeast Rap1, hRap1, are also associated with APBs specifically during late S-G(2) phase of the cell cycle [4].
  • The Rap1p binding domain distorted DNA molecules encompassing the UASrpg sequence or the telomeric-like sequence, as revealed by both KMnO4 hypersensitivity and by hydroxyl radical foot-printing analysis [5].

High impact information on RAP1

  • Computational analysis predicts that proteins capable of recruiting the chromatin regulator Tup1 act to restrict the binding distribution of Rap1 in the presence of glucose [6].
  • We show that repressor-activator protein 1 (Rap1), a master regulator of yeast metabolism, binds to an expanded target set after glucose depletion despite decreasing protein levels and no evidence of posttranslational modification [6].
  • Using PBMs, we identified the DNA binding-site sequence specificities of the yeast transcription factors Abf1, Rap1 and Mig1 [7].
  • We find that most nucleoporins and karyopherins preferentially associate with a subset of highly transcribed genes and with genes that possess Rap1 binding sites whereas the RanGEF preferentially associates with transcriptionally inactive genes [8].
  • 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 [9].

Biological context of RAP1

  • In strains deficient for either SIR3 or SIR4, telomeres lose their perinuclear localization, as monitored by RAP1 immunofluorescence [10].
  • The yeast ARS binding factor 1 (ABF1)--where ARS is an autonomously replicating sequence--and repressor/activator protein 1 (RAP1) have been implicated in DNA replication, transcriptional activation, and transcriptional silencing [11].
  • The RAP1 protein provides the specificity for the localization of heterochromatin through its recognition of telomeric DNA sequences [12].
  • Previous studies have indicated that the regulatory function of RAP1 is determined by the context of its binding site and, presumably, its interactions with other factors [13].
  • We propose that RAP1 acts in the initiation of transcriptional silencing by recruiting a complex of SIR proteins to the chromosome via protein-protein interactions [14].

Anatomical context of RAP1


Associations of RAP1 with chemical compounds

  • UAS elements which bound the RAP1 protein or the ABFI protein modulated glucose-dependent induction of ENO1 and ENO2 expression [19].
  • Although expression of the ribosomal protein genes was reduced in response to histidine limitation, the level of RAP1 DNA-binding activity in cell extracts was unaffected [20].
  • The sequence of a 13.5 kb DNA segment from the left arm of yeast chromosome XIV reveals MER1; RAP1; a new putative member of the DNA replication complex and a new putative serine/threonine phosphatase gene [21].
  • The complex character of URS(1) includes the presence of two different cis-acting sequences: (i) a RAP1 (repressor activator protein 1)-binding site that is capable of binding the RAP1 protein in vitro and (ii) two putative ethanol-repression sequences, the modification of which derepresses the AAC3 gene [22].
  • We have found that RAP1, in addition to its known binding activity for double-stranded DNA, interacts with the G-rich strand containing guanine base (G)-tetrads [23].

Physical interactions of RAP1

  • Previous experiments suggested that SIR1 might be localized to the silencers by binding to ORC and/or RAP1 [24].
  • RAP1 binding at the core region is unaffected by SIR3 overproduction and RAP1 shows no evidence of spreading [25].
  • Here, we show that a small carboxy-terminal domain of RAP1 is sufficient to establish repression when fused to the GAL4 DNA-binding domain (GBD) and targeted to mutated HMR silencers containing GAL4 DNA-binding sites [26].
  • In Saccharomyces cerevisiae, efficient expression of glycolytic and translational component genes requires two DNA binding proteins, RAP1 (which binds to UASRPG) and GCR1 (which binds to the CT box) [27].
  • The properties of SIR4 dosage suppression suggest that SIR4 protein may interact directly with RAP1 at silencers [28].

Regulatory relationships of RAP1

  • Surprisingly, the UAS fragment composed of the 22-mer sequence containing exclusively a RAP1 binding sequence showed full activation, suggesting that the RAP1-dependent transcriptional activation is a primary positive control in the TDH3 gene expression [29].
  • This suggests that RAP1 may be involved in transcriptional control of many other glycolytic genes in addition to the PGK gene [30].
  • Overexpression of Sir3p completely suppressed the reduction in TPE observed with expression of Rap1 delta BBp, but did not restore high levels of TPE to cells with extra telomeres [31].
  • (Capieaux, E., Vignais, M.-L., Sentenac, A. and Goffeau, A. (1989). J. Biol. Chem. 264, 7437-7446), who show that the transcriptional factor TUF/RAP1 binds to upstream activating sequences in the PMA1 gene [32].
  • The function of repressor activator protein 1 (Rap1p) at glycolytic enzyme gene upstream activating sequence (UAS) elements in Saccharomyces cerevisiae is to facilitate binding of glycolysis regulatory protein 1 (Gcr1p) at adjacent sites [33].

Other interactions of RAP1

  • This balance is regulated by telomere length and by interactions between the RAP1 carboxyl terminus and both RIF1 and SIR4 proteins [26].
  • However, GBD/RAP1-mediated silencing is independent of SIR1, whose product is normally required for the establishment of repression at HMR [26].
  • Silencing by GBD/RAP1 hybrids, like normal silencing at HMR, requires the trans-acting factors SIR2, SIR3, and SIR4 [26].
  • In addition, overexpression of either RIF1 or RIF2 decreases telomere length, and co-overexpression of these proteins can reverse the telomere elongation effect of overexpression of the Rap1p carboxyl terminus [34].
  • In vivo, cac1/rlf2 mutants are defective in telomeric silencing and mislocalize Rap1p, a telomere-binding protein [35].

Analytical, diagnostic and therapeutic context of RAP1

  • Dissection of a carboxy-terminal region of the yeast regulatory protein RAP1 with effects on both transcriptional activation and silencing [36].
  • Despite the altered distribution of Rap1p in rlf2 mutant cells, fluorescence in situ hybridization to subtelomeric repeats shows that the distribution of telomeric DNA is similar in wild-type and mutant cells [37].
  • Mobility shift and Western immunoblot analyses indicate that each allele produces a truncated RAP1 protein, lacking the C-terminal 144 to 165 amino acids but capable of efficient DNA binding [38].
  • We suggest the existence of multiple binding to the ENO1 UAS by at least two factors: one is the factor which we purified with a molecular mass of 32 kDa on SDS/PAGE and the other is the factor like RAP1 protein which generally recognizes the RPG-box-like sequence [39].
  • This difference may be explained by the ability of the Rap1p carboxyl terminus to interact independently with Sir4p, which we demonstrate by in vitro binding and two-hybrid assays [40].


  1. The DNA-binding protein RAP1 is required for efficient transcriptional activation of the yeast PYK glycolytic gene. McNeil, J.B., Dykshoorn, P., Huy, J.N., Small, S. Curr. Genet. (1990) [Pubmed]
  2. Molecular and genetic analysis of the toxic effect of RAP1 overexpression in yeast. Freeman, K., Gwadz, M., Shore, D. Genetics (1995) [Pubmed]
  3. Saccharomyces cerevisiae multifunctional protein RAP1 binds to a conserved sequence in the Polyoma virus enhancer and is responsible for its transcriptional activity in yeast cells. Pollice, A., Ciaramella, M., Pulitzer, J.F. FEBS Lett. (1993) [Pubmed]
  4. Assembly of functional ALT-associated promyelocytic leukemia bodies requires Nijmegen Breakage Syndrome 1. Wu, G., Jiang, X., Lee, W.H., Chen, P.L. Cancer Res. (2003) [Pubmed]
  5. Structural and functional heterogeneity of Rap1p complexes with telomeric and UASrpg-like DNA sequences. Idrissi, F.Z., Fernández-Larrea, J.B., Piña, B. J. Mol. Biol. (1998) [Pubmed]
  6. A chromatin-mediated mechanism for specification of conditional transcription factor targets. Buck, M.J., Lieb, J.D. Nat. Genet. (2006) [Pubmed]
  7. Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Mukherjee, S., Berger, M.F., Jona, G., Wang, X.S., Muzzey, D., Snyder, M., Young, R.A., Bulyk, M.L. Nat. Genet. (2004) [Pubmed]
  8. Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Casolari, J.M., Brown, C.R., Komili, S., West, J., Hieronymus, H., Silver, P.A. Cell (2004) [Pubmed]
  9. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Lieb, J.D., Liu, X., Botstein, D., Brown, P.O. Nat. Genet. (2001) [Pubmed]
  10. SIR3 and SIR4 proteins are required for the positioning and integrity of yeast telomeres. Palladino, F., Laroche, T., Gilson, E., Axelrod, A., Pillus, L., Gasser, S.M. Cell (1993) [Pubmed]
  11. Similarity between the transcriptional silencer binding proteins ABF1 and RAP1. Diffley, J.F., Stillman, B. Science (1989) [Pubmed]
  12. Molecular model for telomeric heterochromatin in yeast. Grunstein, M. Curr. Opin. Cell Biol. (1997) [Pubmed]
  13. A RAP1-interacting protein involved in transcriptional silencing and telomere length regulation. Hardy, C.F., Sussel, L., Shore, D. Genes Dev. (1992) [Pubmed]
  14. Evidence that a complex of SIR proteins interacts with the silencer and telomere-binding protein RAP1. Moretti, P., Freeman, K., Coodly, L., Shore, D. Genes Dev. (1994) [Pubmed]
  15. Localization of RAP1 and topoisomerase II in nuclei and meiotic chromosomes of yeast. Klein, F., Laroche, T., Cardenas, M.E., Hofmann, J.F., Schweizer, D., Gasser, S.M. J. Cell Biol. (1992) [Pubmed]
  16. Activation of gastrin gene transcription in islet cells by a RAP1-like cis-acting promoter element. Simon, B., Tillotson, L., Brand, S.J. FEBS Lett. (1994) [Pubmed]
  17. RAP-1 factor is necessary for DNA loop formation in vitro at the silent mating type locus HML. Hofmann, J.F., Laroche, T., Brand, A.H., Gasser, S.M. Cell (1989) [Pubmed]
  18. UASrpg can function as a heterochromatin boundary element in yeast. Bi, X., Broach, J.R. Genes Dev. (1999) [Pubmed]
  19. Multiple factors bind the upstream activation sites of the yeast enolase genes ENO1 and ENO2: ABFI protein, like repressor activator protein RAP1, binds cis-acting sequences which modulate repression or activation of transcription. Brindle, P.K., Holland, J.P., Willett, C.E., Innis, M.A., Holland, M.J. Mol. Cell. Biol. (1990) [Pubmed]
  20. Association of RAP1 binding sites with stringent control of ribosomal protein gene transcription in Saccharomyces cerevisiae. Moehle, C.M., Hinnebusch, A.G. Mol. Cell. Biol. (1991) [Pubmed]
  21. The sequence of a 13.5 kb DNA segment from the left arm of yeast chromosome XIV reveals MER1; RAP1; a new putative member of the DNA replication complex and a new putative serine/threonine phosphatase gene. Coster, F., Van Dyck, L., Jonniaux, J.L., Purnelle, B., Goffeau, A. Yeast (1995) [Pubmed]
  22. A carbon-source-responsive element is required for regulation of the hypoxic ADP/ATP carrier (AAC3) isoform in Saccharomyces cerevisiae. Sokolíková, B., Sabová, L., Kissová, I., Kolarov, J. Biochem. J. (2000) [Pubmed]
  23. Promotion of parallel DNA quadruplexes by a yeast telomere binding protein: a circular dichroism study. Giraldo, R., Suzuki, M., Chapman, L., Rhodes, D. Proc. Natl. Acad. Sci. U.S.A. (1994) [Pubmed]
  24. Role of interactions between the origin recognition complex and SIR1 in transcriptional silencing. Triolo, T., Sternglanz, R. Nature (1996) [Pubmed]
  25. SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Strahl-Bolsinger, S., Hecht, A., Luo, K., Grunstein, M. Genes Dev. (1997) [Pubmed]
  26. Action of a RAP1 carboxy-terminal silencing domain reveals an underlying competition between HMR and telomeres in yeast. Buck, S.W., Shore, D. Genes Dev. (1995) [Pubmed]
  27. GCR1, a transcriptional activator in Saccharomyces cerevisiae, complexes with RAP1 and can function without its DNA binding domain. Tornow, J., Zeng, X., Gao, W., Santangelo, G.M. EMBO J. (1993) [Pubmed]
  28. Separation of transcriptional activation and silencing functions of the RAP1-encoded repressor/activator protein 1: isolation of viable mutants affecting both silencing and telomere length. Sussel, L., Shore, D. Proc. Natl. Acad. Sci. U.S.A. (1991) [Pubmed]
  29. The UAS of the yeast GAPDH promoter consists of multiple general functional elements including RAP1 and GRF2 binding sites. Yagi, S., Yagi, K., Fukuoka, J., Suzuki, M. J. Vet. Med. Sci. (1994) [Pubmed]
  30. Transcriptional control of the Saccharomyces cerevisiae PGK gene by RAP1. Chambers, A., Tsang, J.S., Stanway, C., Kingsman, A.J., Kingsman, S.M. Mol. Cell. Biol. (1989) [Pubmed]
  31. Extra telomeres, but not internal tracts of telomeric DNA, reduce transcriptional repression at Saccharomyces telomeres. Wiley, E.A., Zakian, V.A. Genetics (1995) [Pubmed]
  32. Transcriptional regulation by glucose of the yeast PMA1 gene encoding the plasma membrane H(+)-ATPase. Rao, R., Drummond-Barbosa, D., Slayman, C.W. Yeast (1993) [Pubmed]
  33. Multiple domains of repressor activator protein 1 contribute to facilitated binding of glycolysis regulatory protein 1. López, M.C., Smerage, J.B., Baker, H.V. Proc. Natl. Acad. Sci. U.S.A. (1998) [Pubmed]
  34. A novel Rap1p-interacting factor, Rif2p, cooperates with Rif1p to regulate telomere length in Saccharomyces cerevisiae. Wotton, D., Shore, D. Genes Dev. (1997) [Pubmed]
  35. Chromatin assembly factor I contributes to the maintenance, but not the re-establishment, of silencing at the yeast silent mating loci. Enomoto, S., Berman, J. Genes Dev. (1998) [Pubmed]
  36. Dissection of a carboxy-terminal region of the yeast regulatory protein RAP1 with effects on both transcriptional activation and silencing. Hardy, C.F., Balderes, D., Shore, D. Mol. Cell. Biol. (1992) [Pubmed]
  37. RLF2, a subunit of yeast chromatin assembly factor-I, is required for telomeric chromatin function in vivo. Enomoto, S., McCune-Zierath, P.D., Gerami-Nejad, M., Sanders, M.A., Berman, J. Genes Dev. (1997) [Pubmed]
  38. C-terminal truncation of RAP1 results in the deregulation of telomere size, stability, and function in Saccharomyces cerevisiae. Kyrion, G., Boakye, K.A., Lustig, A.J. Mol. Cell. Biol. (1992) [Pubmed]
  39. Purification and characterization of a nuclear factor which binds specifically to the upstream activation sequence of Saccharomyces cerevisiae enolase 1 gene. Machida, M., Jigami, Y., Tanaka, H. Eur. J. Biochem. (1989) [Pubmed]
  40. Multiple interactions in Sir protein recruitment by Rap1p at silencers and telomeres in yeast. Moretti, P., Shore, D. Mol. Cell. Biol. (2001) [Pubmed]
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