Supplementary Materials

Supplementary Materials for:

The cis-Regulatory Logic of Hedgehog Gradient Responses: Key Roles for Gli Binding Affinity, Competition, and Cooperativity

David S. Parker, Michael A. White, Andrea I. Ramos, Barak A. Cohen, Scott Barolo*

*To whom correspondence should be addressed. E-mail: sbarolo{at}umich.edu

This PDF file includes:

  • Text 1. Modeling different biophysical mechanisms.
  • Text 2. Parameter sensitivity analysis of repressor cooperativity and differential affinity models.
  • Text 3. Testing model fits.
  • Methods
  • Fig. S1. Annotated sequences of enhancer constructs.
  • Fig. S2. Relative in vitro binding affinities of Ci binding sites regulating ptc and dpp.
  • Fig. S3. Twelve-species alignments of Ci binding sites.
  • Fig. S4. Improving the affinity of Ci sites in the dppD enhancer causes misinterpretation of Hh gradients and lethal developmental defects.
  • Fig. S5. Overgrowth and patterning defects in imaginal discs of dppD-Ciptc>dpp transgenic larvae.
  • Fig. S6. Best fits of four general classes of biophysical models to high-affinity (3xCiptc) and low-affinity (3xCiwt) data.
  • Fig. S7. Best-fit equal-affinity models of individual cooperative mechanisms.
  • Fig. S8. Prediction of single high-affinity site expression by repressor cooperativity and differential affinity models trained on new or old data.
  • Fig. S9. Repressor cooperativity and differential affinity model sensitivity to parameter changes.
  • Fig. S10. Repressor and activator occupancy of high- and low-affinity enhancers.
  • Table S1. Sequences of EMSA oligonucleotides.
  • Table S2. Parameters included in the model.
  • Table S3. Best-fit parameter values of four general models.
  • Table S4. Parameters for repressor cooperativity and differential affinity models.
  • References

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Citation: D. S. Parker, M. A. White, A. I. Ramos, B. A. Cohen, S. Barolo, The cis-Regulatory Logic of Hedgehog Gradient Responses: Key Roles for Gli Binding Affinity, Competition, and Cooperativity. Sci. Signal. 4, ra38 (2011).

© 2011 American Association for the Advancement of Science