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.

  • Perspective
  • Published:

Combinatorial control of gene expression

Abstract

Revealing the molecular principles of eukaryotic transcription factor assembly on specific DNA sites is pivotal to understanding how genes are differentially expressed. By analyzing structures of transcription factor complexes bound to specific DNA elements we demonstrate how protein and DNA regulators manage gene expression in a combinatorial fashion.

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

Access options

Buy this article

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

Figure 1: Examples of transcription factor–DNA complexes involved in combinatorial control of gene expression.
Figure 2: Importance of DNA site architecture in POU factor–mediated gene expression regulation.
Figure 3: Interaction diagram of Oct-1 and Sox-2.

Similar content being viewed by others

References

  1. Glass, C.K. Differential recognition of target genes by nuclear receptor monomers, dimers, and heterodimers. Endocr. Rev. 15, 391–407 (1994).

    CAS  PubMed  Google Scholar 

  2. Shore, P. & Sharrocks, A.D. The MADS-box family of transcription factors. Eur. J. Biochem. 229, 1–13 (1995).

    Article  CAS  Google Scholar 

  3. Wegner, M. From head to toes: the multiple facets of Sox proteins. Nucleic Acids Res. 27, 1409–1420 (1999).

    Article  CAS  Google Scholar 

  4. Herr, W. & Cleary, M.A. The POU domain: versatility in transcriptional regulation by a flexible two-in-one DNA-binding domain. Genes Dev. 9, 1679–1693 (1995).

    Article  CAS  Google Scholar 

  5. Ptashne, M. & Gann, A. Genes & Signals (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2002).

    Google Scholar 

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

    Article  CAS  Google Scholar 

  7. Lefstin, J.A. & Yamamoto, K.R. Allosteric effects of DNA on transcriptional regulators. Nature 392, 885–888 (1998).

    Article  CAS  Google Scholar 

  8. Rastinejad, F., Perlmann, T., Evans, R.M. & Sigler, P.B. Structural determinants of nuclear receptor assembly on DNA direct repeats. Nature 375, 203–211 (1995).

    Article  CAS  Google Scholar 

  9. Mangelsdorf, D.J. & Evans, R.M. The RXR heterodimers and orphan receptors. Cell 83, 841–850 (1995).

    Article  CAS  Google Scholar 

  10. Pellegrini, L., Tan, S. & Richmond, T.J. Structure of serum response factor core bound to DNA. Nature 376, 490–498 (1995).

    Article  CAS  Google Scholar 

  11. Hassler, M. & Richmond, T.J. The B-box dominates SAP-1-SRF interactions in the structure of the ternary complex. EMBO J. 20, 3018–3028 (2001).

    Article  CAS  Google Scholar 

  12. Tan, S. & Richmond, T.J. Crystal structure of the yeast MATα2/MCM1/DNA ternary complex. Nature 391, 660–666 (1998).

    Article  CAS  Google Scholar 

  13. Ryan, A.K. & Rosenfeld, M.G. POU domain family values: flexibility, partnerships, and developmental codes. Genes Dev. 11, 1207–1225 (1997).

    Article  CAS  Google Scholar 

  14. Kamachi, Y., Uchikawa, M. & Kondoh, H. Pairing SOX off: with partners in the regulation of embryonic development. Trends Genet. 16, 182–187 (2000).

    Article  CAS  Google Scholar 

  15. Dailey, L. & Basilico, C. Coevolution of HMG domains and homeodomains and the generation of transcriptional regulation by Sox/POU complexes. J. Cell Physiol. 186, 315–328 (2001).

    Article  CAS  Google Scholar 

  16. Ambrosetti, D.C., Basilico, C. & Dailey, L. Synergistic activation of the fibroblast growth factor 4 enhancer by Sox2 and Oct-3 depends on protein-protein interactions facilitated by a specific spatial arrangement of factor binding sites. Mol. Cell. Biol. 17, 6321–6329 (1997).

    Article  CAS  Google Scholar 

  17. Avilion, A.A. et al. Multipotent cell lineages in early mouse development depend on SOX2 function. Genes Dev. 17, 126–140 (2003).

    Article  CAS  Google Scholar 

  18. Remenyi, A. et al. Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers. Genes Dev. 17, 2048–2059 (2003).

    Article  CAS  Google Scholar 

  19. Di Rocco, G. et al. The recruitment of SOX/OCT complexes and the differential activity of HOXA1 and HOXB1 modulate the Hoxb1 auto-regulatory enhancer function. J. Biol. Chem. 276, 20506–20515 (2001).

    Article  CAS  Google Scholar 

  20. Williams, D.C. Jr., Cai, M. & Clore, G.M. Molecular basis for synergistic transcriptional activation by Oct1 and Sox2 revealed from the solution structure of the 42-kDa Oct1.Sox2.Hoxb1-DNA ternary transcription factor complex. J. Biol. Chem. 279, 1449–1457 (2004).

    Article  CAS  Google Scholar 

  21. Kamachi, Y., Uchikawa, M., Tanouchi, A., Sekido, R. & Kondoh, H. Pax6 and SOX2 form a co-DNA-binding partner complex that regulates initiation of lens development. Genes Dev. 15, 1272–1286 (2001).

    Article  CAS  Google Scholar 

  22. Klemm, J.D., Rould, M.A., Aurora, R., Herr, W. & Pabo, C.O. Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. Cell 77, 21–32 (1994).

    Article  CAS  Google Scholar 

  23. Tomilin, A. et al. Synergism with the coactivator OBF-1 (OCA-B, BOB-1) is mediated by a specific POU dimer configuration. Cell 103, 853–864 (2000).

    Article  CAS  Google Scholar 

  24. Remenyi, A. et al. Differential dimer activities of the transcription factor Oct-1 by DNA-induced interface swapping. Mol. Cell 8, 569–580 (2001).

    Article  CAS  Google Scholar 

  25. Chasman, D., Cepek, K., Sharp, P.A. & Pabo, C.O. Crystal structure of an OCAB peptide bound to an Oct-1 POU domain/octamer DNA complex: specific recognition of a protein-DNA interface. Genes Dev. 13, 2650–2657 (1999).

    Article  CAS  Google Scholar 

  26. Magne, S., Caron, S., Charon, M., Rouyez, M.C. & Dusanter-Fourt, I. STAT5 and Oct-1 form a stable complex that modulates cyclin D1 expression. Mol. Cell. Biol. 23, 8934–8945 (2003).

    Article  CAS  Google Scholar 

  27. Scully, K.M. et al. Allosteric effects of Pit-1 DNA sites on long-term repression in cell type specification. Science 290, 1127–1131 (2000).

    Article  CAS  Google Scholar 

  28. Bulyk, M.L. Computational prediction of transcription-factor binding site locations. Genome Biol. 5, 201 (2003).

    Article  Google Scholar 

  29. Taverner, N.V., Smith, J.C. & Wardle, F.C. Identifying transcriptional targets. Genome Biol. 5, 210 (2004).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Attila Reményi.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Reményi, A., Schöler, H. & Wilmanns, M. Combinatorial control of gene expression. Nat Struct Mol Biol 11, 812–815 (2004). https://doi.org/10.1038/nsmb820

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb820

This article is cited by

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