Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

A conserved activation element in BMP signaling during Drosophila development

Nature Structural & Molecular Biology volume 17, pages 69–76 (2010)Cite this article

Abstract

The transforming growth factor β (TGF-β) family member Decapentaplegic (Dpp) is a key regulator of patterning and growth in Drosophila development. Previous studies have identified a short DNA motif called the silencer element (SE), which recruits a trimeric Smad complex and the repressor Schnurri to downregulate target enhancers upon Dpp signaling. We have now isolated the minimal enhancer of the dad gene and discovered a short motif we termed the activating element (AE). The AE is similar to the SE and recruits the Smad proteins via a conserved mechanism. However, the AE and SE differ at important nucleotide positions. As a consequence, the AE does not recruit Schnurri but rather integrates repressive input by the default repressor Brinker and activating input by the Smad signal transducers Mothers against Dpp (Mad) and Medea via competitive DNA binding. The AE allows the identification of hitherto unknown direct Dpp targets and is functionally conserved in vertebrates.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Identification of the highly conserved minimal dad enhancer.
Figure 2: Dad13 is directly regulated by Mad–Medea and Brk.
Figure 3: A small DNA element integrates activating Smad and repressive Brk input.
Figure 4: Functional AEs are present in other enhancers.
Figure 5: The function of the AE is evolutionary conserved.
Figure 6: Despite their high similarity, SE and AE exert opposite functions.

Similar content being viewed by others

References

  1. Derynck, R. & Miyazono, K. TGF-β and the TGF-β Family (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2007).

  2. Shi, Y. & Massague, J. Mechanisms of TGF-β signaling from cell membrane to the nucleus. Cell 113, 685–700 (2003).

    Article  CAS  Google Scholar 

  3. Schmierer, B. & Hill, C.S. TGFβ-SMAD signal transduction: molecular specificity and functional flexibility. Nat. Rev. Genet. 8, 970–982 (2007).

    Article  CAS  Google Scholar 

  4. Feng, X.H. & Derynck, R. Specificity and versatility in tgf-β signaling through Smads. Annu. Rev. Cell Dev. Biol. 21, 659–693 (2005).

    Article  CAS  Google Scholar 

  5. Campbell, G. & Tomlinson, A. Transducing the Dpp morphogen gradient in the wing of Drosophila: regulation of Dpp targets by brinker. Cell 96, 553–562 (1999).

    Article  CAS  Google Scholar 

  6. Jazwinska, A., Kirov, N., Wieschaus, E., Roth, S. & Rushlow, C. The Drosophila gene brinker reveals a novel mechanism of Dpp target gene regulation. Cell 96, 563–573 (1999).

    Article  CAS  Google Scholar 

  7. Jazwinska, A., Rushlow, C. & Roth, S. The role of brinker in mediating the graded response to Dpp in early Drosophila embryos. Development 126, 3323–3334 (1999).

    CAS  PubMed  Google Scholar 

  8. Minami, M., Kinoshita, N., Kamoshida, Y., Tanimoto, H. & Tabata, T. brinker is a target of Dpp in Drosophila that negatively regulates Dpp-dependent genes. Nature 398, 242–246 (1999).

    Article  CAS  Google Scholar 

  9. Pyrowolakis, G., Hartmann, B., Muller, B., Basler, K. & Affolter, M. A simple molecular complex mediates widespread BMP-induced repression during Drosophila development. Dev. Cell 7, 229–240 (2004).

    Article  CAS  Google Scholar 

  10. Gao, S., Steffen, J. & Laughon, A. Dpp-responsive silencers are bound by a trimeric Mad-Medea complex. J. Biol. Chem. 280, 36158–36164 (2005).

    Article  CAS  Google Scholar 

  11. Pyrowolakis, G., Hartmann, B. & Affolter, M. TGF-β family signaling in Drosophila. in The TGF-β Family (eds. Derynck, R. & Miyazono, K.) 493–526 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2007).

  12. Kim, J., Johnson, K., Chen, H.J., Carroll, S. & Laughon, A. Drosophila Mad binds to DNA and directly mediates activation of vestigial by decapentaplegic. Nature 388, 304–308 (1997).

    Article  CAS  Google Scholar 

  13. Shi, Y. et al. Crystal structure of a Smad MH1 domain bound to DNA: insights on DNA binding in TGF-β signaling. Cell 94, 585–594 (1998).

    Article  CAS  Google Scholar 

  14. Zawel, L. et al. Human Smad3 and Smad4 are sequence-specific transcription activators. Mol. Cell 1, 611–617 (1998).

    Article  CAS  Google Scholar 

  15. Marty, T., Muller, B., Basler, K. & Affolter, M. Schnurri mediates Dpp-dependent repression of brinker transcription. Nat. Cell Biol. 2, 745–749 (2000).

    Article  CAS  Google Scholar 

  16. Torres-Vazquez, J., Park, S., Warrior, R. & Arora, K. The transcription factor Schnurri plays a dual role in mediating Dpp signaling during embryogenesis. Development 128, 1657–1670 (2001).

    CAS  PubMed  Google Scholar 

  17. Tsuneizumi, K. et al. Daughters against dpp modulates dpp organizing activity in Drosophila wing development. Nature 389, 627–631 (1997).

    Article  CAS  Google Scholar 

  18. Sivasankaran, R., Vigano, M.A., Muller, B., Affolter, M. & Basler, K. Direct transcriptional control of the Dpp target omb by the DNA binding protein Brinker. EMBO J. 19, 6162–6172 (2000).

    Article  CAS  Google Scholar 

  19. Xu, M., Kirov, N. & Rushlow, C. Peak levels of BMP in the Drosophila embryo control target genes by a feed-forward mechanism. Development 132, 1637–1647 (2005).

    Article  CAS  Google Scholar 

  20. Barrio, R. & de Celis, J.F. Regulation of spalt expression in the Drosophila wing blade in response to the decapentaplegic signaling pathway. Proc. Natl. Acad. Sci. USA 101, 6021–6026 (2004).

    Article  CAS  Google Scholar 

  21. Rushlow, C., Colosimo, P.F., Lin, M.C., Xu, M. & Kirov, N. Transcriptional regulation of the Drosophila gene zen by competing Smad and Brinker inputs. Genes Dev. 15, 340–351 (2001).

    Article  CAS  Google Scholar 

  22. Zhang, H., Levine, M. & Ashe, H.L. Brinker is a sequence-specific transcriptional repressor in the Drosophila embryo. Genes Dev. 15, 261–266 (2001).

    Article  CAS  Google Scholar 

  23. Kirkpatrick, H., Johnson, K. & Laughon, A. Repression of dpp targets by binding of brinker to mad sites. J. Biol. Chem. 276, 18216–18222 (2001).

    Article  CAS  Google Scholar 

  24. Saller, E. & Bienz, M. Direct competition between Brinker and Drosophila Mad in Dpp target gene transcription. EMBO Rep. 2, 298–305 (2001).

    Article  CAS  Google Scholar 

  25. Grieder, N.C., Marty, T., Ryoo, H.D., Mann, R.S. & Affolter, M. Synergistic activation of a Drosophila enhancer by HOM/EXD and DPP signaling. EMBO J. 16, 7402–7410 (1997).

    Article  CAS  Google Scholar 

  26. Marty, T. et al. A HOX complex, a repressor element and a 50 bp sequence confer regional specificity to a DPP-responsive enhancer. Development 128, 2833–2845 (2001).

    CAS  PubMed  Google Scholar 

  27. Rothe, M., Nauber, U. & Jackle, H. Three hormone receptor-like Drosophila genes encode an identical DNA-binding finger. EMBO J. 8, 3087–3094 (1989).

    Article  CAS  Google Scholar 

  28. Chen, C.K. et al. The transcription factors KNIRPS and KNIRPS RELATED control cell migration and branch morphogenesis during Drosophila tracheal development. Development 125, 4959–4968 (1998).

    CAS  PubMed  Google Scholar 

  29. Pankratz, M.J., Busch, M., Hoch, M., Seifert, E. & Jackle, H. Spatial control of the gap gene knirps in the Drosophila embryo by posterior morphogen system. Science 255, 986–989 (1992).

    Article  CAS  Google Scholar 

  30. Karaulanov, E., Knochel, W. & Niehrs, C. Transcriptional regulation of BMP4 synexpression in transgenic Xenopus. EMBO J. 23, 844–856 (2004).

    Article  CAS  Google Scholar 

  31. Yao, L.C. et al. Schnurri transcription factors from Drosophila and vertebrates can mediate Bmp signaling through a phylogenetically conserved mechanism. Development 133, 4025–4034 (2006).

    Article  CAS  Google Scholar 

  32. Ross, S. & Hill, C.S. How the Smads regulate transcription. Int. J. Biochem. Cell Biol. 40, 383–408 (2008).

    Article  CAS  Google Scholar 

  33. Yu, P.B. et al. Dorsomorphin inhibits BMP signals required for embryogenesis and iron metabolism. Nat. Chem. Biol. 4, 33–41 (2008).

    Article  CAS  Google Scholar 

  34. Barolo, S. & Posakony, J.W. Three habits of highly effective signaling pathways: principles of transcriptional control by developmental cell signaling. Genes Dev. 16, 1167–1181 (2002).

    Article  CAS  Google Scholar 

  35. Dai, H. et al. The zinc finger protein schnurri acts as a Smad partner in mediating the transcriptional response to decapentaplegic. Dev. Biol. 227, 373–387 (2000).

    Article  CAS  Google Scholar 

  36. Gao, S. & Laughon, A. Flexible interaction of Drosophila Smad complexes with bipartite binding sites. Biochim. Biophys. Acta 1769, 484–496 (2007).

    Article  CAS  Google Scholar 

  37. Korchynskyi, O. & ten Dijke, P. Identification and functional characterization of distinct critically important bone morphogenetic protein–specific response elements in the Id1 promoter. J. Biol. Chem. 277, 4883–4891 (2002).

    Article  CAS  Google Scholar 

  38. Brodin, G., Ahgren, A., ten Dijke, P., Heldin, C.H. & Heuchel, R. Efficient TGF-β induction of the Smad7 gene requires cooperation between AP-1, Sp1 and Smad proteins on the mouse Smad7 promoter. J. Biol. Chem. 275, 29023–29030 (2000).

    Article  CAS  Google Scholar 

  39. Denissova, N.G., Pouponnot, C., Long, J., He, D. & Liu, F. Transforming growth factor β–inducible independent binding of SMAD to the Smad7 promoter. Proc. Natl. Acad. Sci. USA 97, 6397–6402 (2000).

    Article  CAS  Google Scholar 

  40. Nagarajan, R.P., Zhang, J., Li, W. & Chen, Y. Regulation of Smad7 promoter by direct association with Smad3 and Smad4. J. Biol. Chem. 274, 33412–33418 (1999).

    Article  CAS  Google Scholar 

  41. von Gersdorff, G. et al. Smad3 and Smad4 mediate transcriptional activation of the human Smad7 promoter by transforming growth factor β. J. Biol. Chem. 275, 11320–11326 (2000).

    Article  CAS  Google Scholar 

  42. Benchabane, H. & Wrana, J.L. GATA- and Smad1-dependent enhancers in the Smad7 gene differentially interpret bone morphogenetic protein concentrations. Mol. Cell. Biol. 23, 6646–6661 (2003).

    Article  CAS  Google Scholar 

  43. Nellen, D., Burke, R., Struhl, G. & Basler, K. Direct and long-range action of a DPP morphogen gradient. Cell 85, 357–368 (1996).

    Article  CAS  Google Scholar 

  44. Müller, B., Hartmann, B., Pyrowolakis, G., Affolter, M. & Basler, K. Conversion of an extracellular Dpp/BMP morphogen gradient into an inverse transcriptional gradient. Cell 113, 221–233 (2003).

    Article  Google Scholar 

  45. Chen, D. & McKearin, D.M. A discrete transcriptional silencer in the bam gene determines asymmetric division of the Drosophila germline stem cell. Development 130, 1159–1170 (2003).

    Article  CAS  Google Scholar 

  46. Kosman, D. et al. Multiplex detection of RNA expression in Drosophila embryos. Science 305, 846 (2004).

    Article  CAS  Google Scholar 

  47. Markstein, M., Markstein, P., Markstein, V. & Levine, M.S. Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc. Natl. Acad. Sci. USA 99, 763–768 (2002).

    Article  CAS  Google Scholar 

  48. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29 (2000).

    Article  CAS  Google Scholar 

  49. Kent, W.J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002).

    Article  CAS  Google Scholar 

  50. Segalat, L., Berger, G. & Lepesant, J.A. Dissection of the Drosophila pourquoi-pas? promoter: complex ovarian expression is driven by distinct follicle cell- and germ line–specific enhancers. Mech. Dev. 47, 241–251 (1994).

    Article  CAS  Google Scholar 

  51. Bischof, J., Maeda, R.K., Hediger, M., Karch, F. & Basler, K. An optimized transgenesis system for Drosophila using germ line–specific phiC31 integrases. Proc. Natl. Acad. Sci. USA 104, 3312–3317 (2007).

    Article  CAS  Google Scholar 

  52. Brand, A.H. & Perrimon, N. Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118, 401–415 (1993).

    CAS  Google Scholar 

  53. Cordier, F., Hartmann, B., Rogowski, M., Affolter, M. & Grzesiek, S. DNA recognition by the brinker repressor–an extreme case of coupling between binding and folding. J. Mol. Biol. 361, 659–672 (2006).

    Article  CAS  Google Scholar 

  54. Ohshiro, T. & Saigo, K. Transcriptional regulation of breathless FGF receptor gene by binding of TRACHEALESS/dARNT heterodimers to three central midline elements in Drosophila developing trachea. Development 124, 3975–3986 (1997).

    CAS  PubMed  Google Scholar 

  55. Nikaido, M., Tada, M., Takeda, H., Kuroiwa, A. & Ueno, N. In vivo analysis using variants of zebrafish BMPR-IA: range of action and involvement of BMP in ectoderm patterning. Development 126, 181–190 (1999).

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We are deeply thankful to B. Hartmann (University of Freiburg) for generously providing the flies transgenic for UAS-ShnVP16. Work in the lab of M.A. was supported by the Kantons Basel-Stadt and Basel-Land, by the Swiss National Science Foundation and by SystemsX.ch within the framework of the wingX RTD. Work in G.P.'s laboratory was supported by the German Research Foundation (SFB592) and the Excellence Initiative of the German Federal and State Governments (EXC294).

Author information

Author notes

  1. Christian Wolf

    Present address: Present address: Intervet Innovation GmbH, Drug Discovery, Schwabenheim, Germany.,

Authors and Affiliations

  1. Biozentrum der Universität Basel, Basel, Switzerland

    Alexander Weiss, Elín Ellertsdóttir & Markus Affolter

  2. Institut für Biologie I, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany

    Enrica Charbonnier & George Pyrowolakis

  3. Centre for Biological Signalling Studies (bioss), Albert-Ludwigs-Universität Freiburg, Freiburg, Germany

    Enrica Charbonnier & George Pyrowolakis

  4. Bioinformatics and Pattern Discovery Group, IBM T. J. Watson Research Center, Yorktown Heights, New York, USA

    Aristotelis Tsirigos

  5. Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany

    Christian Wolf & Reinhard Schuh

Authors
  1. Alexander Weiss
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Enrica Charbonnier
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Elín Ellertsdóttir
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Aristotelis Tsirigos
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Christian Wolf
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Reinhard Schuh
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. George Pyrowolakis
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Markus Affolter
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

A.W., E.C., E.E. and C.W. performed the experiments; A.T. and A.W. generated the bioinformatic data; A.W. and M.A. wrote the manuscript; M.A., G.P. and R.S. contributed to design and interpretation of the experiments and payed the bills.

Corresponding authors

Correspondence to George Pyrowolakis or Markus Affolter.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 and Supplementary Table 1 (PDF 1744 kb)

Supplementary Table 2

List of conserved AEs. (XLS 260 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Weiss, A., Charbonnier, E., Ellertsdóttir, E. et al. A conserved activation element in BMP signaling during Drosophila development. Nat Struct Mol Biol 17, 69–76 (2010). https://doi.org/10.1038/nsmb.1715

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.1715

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing