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General transcription factors bind promoters repressed by Polycomb group proteins

Abstract

To maintain cell identity during development and differentiation, mechanisms of cellular memory have evolved that preserve transcription patterns in an epigenetic manner. The proteins of the Polycomb group (PcG) are part of such a mechanism, maintaining gene silencing. They act as repressive multiprotein complexes that may render target genes inaccessible to the transcriptional machinery1,2, inhibit chromatin remodelling3,4, influence chromosome domain topology5 and recruit histone deacetylases (HDACs)6. PcG proteins have also been found to bind to core promoter regions7, but the mechanism by which they regulate transcription remains unknown. To address this, we used formaldehyde-crosslinked chromatin immunoprecipitation (X-ChIP) to map TATA-binding protein (TBP), transcription initiation factor IIB (TFIIB) and IIF (TFIIF), and dHDAC1 (RPD3) across several Drosophila promoter regions. Here we show that binding of PcG proteins to repressed promoters does not exclude general transcription factors (GTFs) and that depletion of PcG proteins by double-stranded RNA interference leads to de-repression of developmentally regulated genes. We further show that PcG proteins interact in vitro with GTFs. We suggest that PcG complexes maintain silencing by inhibiting GTF-mediated activation of transcription.

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Figure 1: Analysis of the gene expression and acetylation state of BX-C, engrailed, empty spiracles, RpII140 and brown genes.
Figure 2: PCR analysis of the protein distribution at BX-C, engrailed, empty spiracles, RpII140 and brown promoter regions.
Figure 3: Interaction of TBP with PcG proteins.
Figure 4: Post-transcriptional silencing of Pc and ph in SL-2 cells.

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References

  1. Pirrotta, V. PcG complexes and chromatin silencing. Curr. Opin. Genet. Dev. 7, 249–258 (1997).

    Article  CAS  PubMed  Google Scholar 

  2. Paro, R. & Harte, P. J. in Epigenetic Mechanisms of Gene Regulation (eds Russo, V. E. A., Martienssen, R. A. & Riggs, A. R.) 507–528 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1996).

    Google Scholar 

  3. Breiling, A., Bonte, E., Ferrari, S., Becker, P. B. & Paro, R. The Drosophila Polycomb protein interacts with nucleosomal core particles in vitro via its repression domain. Mol. Cell. Biol. 19, 8451–8460 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Shao, Z. et al. Stabilization of chromatin structure by PRC1, a Polycomb complex. Cell 98, 37–46 (1999).

    Article  CAS  PubMed  Google Scholar 

  5. Lupo, R., Breiling, A., Bianchi, M. E. & Orlando, V. Drosophila chromosome condensation proteins Topoisomerase II and Barren colocalize with Polycomb and maintain Fab-7 PRE silencing. Mol. Cell 7, 127–136 (2001).

    Article  CAS  PubMed  Google Scholar 

  6. van der Vlag, J. & Otte, A. P. Transcriptional repression mediated by the human polycomb-group protein EED involves histone deacetylation. Nature Genet. 23, 474–478 (1999).

    Article  CAS  PubMed  Google Scholar 

  7. Orlando, V., Jane, E. P., Chinwalla, V., Harte, P. J. & Paro, R. Binding of trithorax and Polycomb proteins to the bithorax complex: dynamic changes during early Drosophila embryogenesis. EMBO J. 17, 5141–5150 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Strutt, H., Cavalli, G. & Paro, R. Co-localization of Polycomb protein and GAGA factor on regulatory elements responsible for the maintenance of homeotic gene expression. EMBO J. 16, 3621–3632 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Strutt, H. & Paro, R. The Polycomb Group protein complex of Drosophila melanogaster has different compositions at different target genes. Mol. Cell. Biol. 17, 6773–6783 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Paro, R. & Zink, B. The Polycomb gene is differentially regulated during oogenesis and embryogenesis of Drosophila melanogaster. Mech. Dev. 40, 37–46 (1992).

    Article  Google Scholar 

  11. White, D. A., Belyaev, N. D. & Turner, B. M. Preparation of site-specific antibodies to acetylated histones. Methods 19, 417–424 (1999).

    Article  CAS  PubMed  Google Scholar 

  12. Gregory, R. I. et al. DNA methylation is linked to deacetylation of histone H3, but not H4, on the imprinted genes Snrpn and U2af1-rs1. Mol. Cell. Biol. (in the press).

  13. Cavalli, G. & Paro, R. Epigenetic inheritance of active chromatin after removal of the main transactivator. Science 286, 955–958 (1999).

    Article  CAS  PubMed  Google Scholar 

  14. Chinwalla, V., Jane, E. P. & Harte, P. J. The Drosophila trithorax protein binds to specific chromosomal sites and is co-localized with Polycomb at many sites. EMBO J. 14, 2056–2065 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Barlow, A. L. et al. dSIR2 and HDAC6; two novel, inhibitor-resistant deacetylases in Drosophila melanogaster. Exp. Cell Res. 265, 90–103 (2001).

    Article  CAS  PubMed  Google Scholar 

  16. Imhof, A. et al. Acetylation of general transcription factors by histone acetyltransferases. Curr. Biol. 7, 689–692 (1997).

    Article  MathSciNet  CAS  PubMed  Google Scholar 

  17. Waltzer, L. & Bienz, M. Drosophila CBP represses the transcription factor TCF to antagonize Wingless signalling. Nature 395, 521–525 (1998).

    Article  CAS  PubMed  Google Scholar 

  18. Tsai, S. C. et al. Histone deacetylase interacts directly with DNA topoisomerase II. Nature Genet. 26, 349–353 (2000).

    Article  CAS  PubMed  Google Scholar 

  19. Johnson, C. A., Padget, K., Austin, C. A. & Turner, B. M. Deacetylase activity associates with topoisomerase II and is necessary for etoposide-induced apoptosis. J. Biol. Chem. 276, 4539–4542 (2001).

    Article  CAS  PubMed  Google Scholar 

  20. Ptashne, M. & Gann, A. Transcriptional activation by recruitment. Nature 386, 569–577 (1997).

    Article  CAS  PubMed  Google Scholar 

  21. Kuras, L. & Struhl, K. Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme. Nature 399, 609–613 (1999).

    Article  CAS  PubMed  Google Scholar 

  22. 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  PubMed  Google Scholar 

  23. Weeks, J. R., Hardin, S. E., Shen, J., Lee, J. M. & Greenleaf, A. L. Locus-specific variation in phosphorylation state of RNA polymerase II in vivo: correlations with gene activity and transcript processing. Genes Dev. 7, 2329–2344 (1993).

    Article  CAS  PubMed  Google Scholar 

  24. Rougvie, A. E. & Lis, J. T. The RNA polymerase II molecule at 5′ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell 54, 795–804 (1988).

    Article  CAS  PubMed  Google Scholar 

  25. Kyba, M. & Brock, H. W. The Drosophila Polycomb Group protein Psc contacts Ph and Pc through specific conserved domains. Mol. Cell. Biol. 18, 2712–2720 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Hammond, S. M., Caudy, A. A. & Hannon, G. J. Post-transcriptional gene silencing by double-stranded RNA. Nature Rev. Genet. 2, 110–119 (2001).

    Article  CAS  PubMed  Google Scholar 

  27. Wei, Q., Marchler, G., Edington, K., Karsch-Mizrachi, I. & Paterson, B. M. RNA interference demonstrates a role for nautilus in the myogenic conversion of Schneider cells by daughterless. Dev. Biol. 228, 239–255 (2000).

    Article  CAS  PubMed  Google Scholar 

  28. Beuchle, D., Struhl, G. & Muller, J. Polycomb group proteins and heritable silencing of Drosophila Hox genes. Development 128, 993–1004 (2001).

    CAS  PubMed  Google Scholar 

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Acknowledgements

We thank B. M. Paterson for advice concerning the RNAi experiments and J. Kadonaga for discussions and comments on the manuscript. We are indebted to J. Butler, J. Kadonaga, A. Barlow and R. Paro for providing (respectively) dTBP, dTFIIB, dTFIIF, dHDAC1 and PC antibodies. We thank N. Collu for technical assistance. This work was supported by a postdoctoral fellowship to A.B. by EU-TMR, and by research grants from A.I.R.C. and TELETHON to V.O., from the Wellcome Trust and the Human Frontier Science Program to B.M.T. and from MURST to M.E.B.

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Correspondence to Valerio Orlando.

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Breiling, A., Turner, B., Bianchi, M. et al. General transcription factors bind promoters repressed by Polycomb group proteins. Nature 412, 651–655 (2001). https://doi.org/10.1038/35088090

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