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TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila

Abstract

Drosophila TATA-box-binding protein (TBP)-related factor 2 (TRF2) is a member of a family of TBP-related factors present in metazoan organisms. Recent evidence suggests that TRF2s are required for proper embryonic development and differentiation1,2,3,4,5. However, true target promoters and the mechanisms by which TRF2 operates to control transcription remain elusive. Here we report the antibody affinity purification of a Drosophila TRF2-containing complex that contains components of the nucleosome remodelling factor (NURF) chromatin remodelling complex as well as the DNA replication-related element (DRE)-binding factor DREF. This latter finding led us to potential target genes containing TRF2-responsive promoters. We have used a combination of in vitro and in vivo assays to show that the DREF-containing TRF2 complex directs core promoter recognition of the proliferating cell nuclear antigen (PCNA) gene. We also identified additional TRF2-responsive target genes involved in DNA replication and cell proliferation. These data suggest that TRF2 functions as a core promoter-selectivity factor responsible for coordinating transcription of a subset of genes in Drosophila.

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Figure 1: Purification of a Drosophila TRF2 complex by co-immunoprecipitation polyacrylamide gradient gel electrophoresis (PAGE) a, Co-immunoprecipitation using anti-TRF2 and anti-DREF monoclonal antibodies.
Figure 2: The PCNA tandem promoters use two distinct transcription start sites designated start site 1 (+1) and start site 2 (-63).
Figure 3: The PCNA tandem promoters are synergistically activated by TRF2, DREF and E2F in SL2 cells.
Figure 4: Microarray analysis of TRF2-responsive target genes.
Figure 5: Double-stranded RNA interference in SL2 cells and promoter occupancy of TRF2 and DREF.

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References

  1. Dantonel, J. C., Quintin, S., Lakatos, L., Labouesse, M. & Tora, L. TBP-like factor is required for embryonic RNA polymerase II transcription in C. elegans. Mol. Cell 6, 715–722 (2000)

    Article  CAS  Google Scholar 

  2. Kaltenbach, L., Horner, M. A., Rothman, J. H. & Mango, S. E. The TBP-like factor CeTLF is required to activate RNA polymerase II transcription during C. elegans embryogenesis. Mol. Cell 6, 705–713 (2000)

    Article  CAS  Google Scholar 

  3. Martianov, I. et al. Late arrest of spermiogenesis and germ cell apoptosis in mice lacking the TBP-like TLF/TRF2 gene. Mol. Cell 7, 509–515 (2001)

    Article  ADS  CAS  Google Scholar 

  4. Veenstra, G. J., Weeks, D. L. & Wolffe, A. P. Distinct roles for TBP and TBP-like factor in early embryonic gene transcription in Xenopus. Science 290, 2312–2315 (2000)

    Article  ADS  CAS  Google Scholar 

  5. Zhang, D., Penttila, T. L., Morris, P. L., Teichmann, M. & Roeder, R. G. Spermiogenesis deficiency in mice lacking the Trf2 gene. Science 292, 1153–1155 (2001)

    Article  ADS  CAS  Google Scholar 

  6. Freiman, R. N. et al. Requirement of tissue-selective TBP-associated factor TAFII105 in ovarian development. Science 293, 2084–2087 (2001)

    Article  ADS  CAS  Google Scholar 

  7. Hiller, M. A., Lin, T. Y., Wood, C. & Fuller, M. T. Developmental regulation of transcription by a tissue-specific TAF homolog. Genes Dev. 15, 1021–1030 (2001)

    Article  CAS  Google Scholar 

  8. Holmes, M. C. & Tjian, R. Promoter-selective properties of the TBP-related factor TRF1. Science 288, 867–870 (2000)

    Article  ADS  CAS  Google Scholar 

  9. Takada, S., Lis, J. T., Zhou, S. & Tjian, R. A TRF1: BRF complex directs Drosophila RNA polymerase III transcription. Cell 101, 459–469 (2000)

    Article  CAS  Google Scholar 

  10. Rabenstein, M. D., Zhou, S., Lis, J. T. & Tjian, R. TATA box-binding protein (TBP)-related factor 2 (TRF2), a third member of the TBP family. Proc. Natl Acad. Sci. USA 96, 4791–4796 (1999)

    Article  ADS  CAS  Google Scholar 

  11. Goodrich, J. A. & Tjian, R. TBP-TAF complexes: selectivity factors for eukaryotic transcription. Curr. Opin. Cell Biol. 6, 403–409 (1994)

    Article  CAS  Google Scholar 

  12. Hansen, S. K., Takada, S., Jacobson, R. H., Lis, J. T. & Tjian, R. Transcription properties of a cell type-specific TATA-binding protein, TRF. Cell 91, 71–83 (1997)

    Article  CAS  Google Scholar 

  13. Hirose, F. et al. Isolation and characterization of cDNA for DREF, a promoter-activating factor for Drosophila DNA replication-related genes. J. Biol. Chem. 271, 3930–3937 (1996)

    Article  CAS  Google Scholar 

  14. Hirose, F., Yamaguchi, M., Handa, H., Inomata, Y. & Matsukage, A. Novel 8-base pair sequence (Drosophila DNA replication-related element) and specific binding factor involved in the expression of Drosophila genes for DNA polymerase alpha and proliferating cell nuclear antigen. J. Biol. Chem. 268, 2092–2099 (1993)

    CAS  PubMed  Google Scholar 

  15. Tsukiyama, T., Daniel, C., Tamkun, J. & Wu, C. ISWI, a member of the SWI2/SNF2 ATPase family, encodes the 140 kDa subunit of the nucleosome remodeling factor. Cell 83, 1021–1026 (1995)

    Article  CAS  Google Scholar 

  16. Ito, T., Bulger, M., Pazin, M. J., Kobayashi, R. & Kadonaga, J. T. ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90, 145–155 (1997)

    Article  CAS  Google Scholar 

  17. VargaWeisz, P. D. et al. Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature 388, 598–602 (1997)

    Article  ADS  CAS  Google Scholar 

  18. Martínez-Balbás, M. A., Tsukiyama, T., Gdula, D. & Wu, C. Drosophila NURF-55, a WD repeat protein involved in histone metabolism. Proc. Natl Acad. Sci. USA 95, 132–137 (1998)

    Article  ADS  Google Scholar 

  19. Gdula, D. A., Sandaltzopoulos, R., Tsukiyama, T., Ossipow, V. & Wu, C. Inorganic pyrophosphatase is a component of the Drosophila nucleosome remodeling factor complex. Genes Dev. 12, 3206–3216 (1998)

    Article  CAS  Google Scholar 

  20. Xiao, H. et al. Dual functions of largest nurf subunit nurf301 in nucleosome sliding and transcription factor interactions. Mol. Cell 8, 531–543 (2001)

    Article  CAS  Google Scholar 

  21. Bell, A. C., West, A. G. & Felsenfeld, G. Insulators and boundaries: versatile regulatory elements in the eukaryotic genome. Science 291, 447–450 (2001)

    Article  ADS  CAS  Google Scholar 

  22. Lieb, B., Carl, M., Hock, R., Gebauer, D. & Scheer, U. Identification of a novel mRNA-associated protein in oocytes of Pleurodeles waltl and Xenopus laevis. Exp. Cell Res. 245, 272–281 (1998)

    Article  CAS  Google Scholar 

  23. Yamaguchi, M., Hirose, F. & Matsukage, A. Roles of multiple promoter elements of the proliferating cell nuclear antigen gene during Drosophila development. Genes Cells 1, 47–58 (1996)

    Article  CAS  Google Scholar 

  24. Dynlacht, B. D., Brook, A., Dembski, M., Yenush, L. & Dyson, N. DNA-binding and trans-activation properties of Drosophila E2F and DP proteins. Proc. Natl Acad. Sci. USA 91, 6359–6363 (1994)

    Article  ADS  CAS  Google Scholar 

  25. Clemens, J. C. et al. Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways. Proc. Natl Acad. Sci. USA 97, 6499–6503 (2000)

    Article  ADS  CAS  Google Scholar 

  26. Smale, S. T. Core promoters: active contributors to combinatorial gene regulation. Genes Dev. 15, 2503–2508 (2001)

    Article  CAS  Google Scholar 

  27. Coligan, J. E., Margulies, D. H., Shevach, E. M. & Strober, W. (eds) Current Protocols in Immunology (John Wiley & Sons, New York, 1991)

  28. Heberlein, U. & Tjian, R. Temporal pattern of alcohol dehydrogenase gene transcription reproduced by Drosophila stage-specific embryonic extracts. Nature 331, 410–415 (1988)

    Article  ADS  CAS  Google Scholar 

  29. Lockhart, D. J. et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnol. 14, 1675–1680 (1996)

    Article  CAS  Google Scholar 

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Acknowledgements

We thank M. Haggart and R. Bell for technical assistance; D. Fyodorov and J. Kadonaga for providing antibodies raised against Acf, ISWI and p55/NURF-55; F. Hirose for generously providing Hybridoma cell lines producing anti-DREF antibody; T. Orr-Weaver for generously providing antibody raised against E2F prior to publication; E. Morris and N. Dyson for providing E2F and DP plasmids; H. Xiao and C. Wu for analysing NURF-301 for peptide sequence matches before publication; and Y. Isogai for providing affinity purified antibodies for ChIPs. We also thank Y. Berghöfer-Hochheimer, R. Freiman, B. Glover, Y. Isogai, T. Kutzkey and B. Lemon for comments on the manuscript, and all members in our laboratory for discussions and technical advice. A.H. was in part supported by a research fellowship by the Deutsche Forschungsgemeinschaft (DFG).

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Correspondence to Robert Tjian.

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Hochheimer, A., Zhou, S., Zheng, S. et al. TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila. Nature 420, 439–445 (2002). https://doi.org/10.1038/nature01167

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