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

Sci. Signal., 7 June 2011
Vol. 4, Issue 176, p. ra38
DOI: 10.1126/scisignal.2002077

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

  1. David S. Parker1,*,,
  2. Michael A. White2,*,
  3. Andrea I. Ramos1,
  4. Barak A. Cohen2, and
  5. Scott Barolo1,
  1. 1Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109–2200, USA.
  2. 2Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
  1. To whom correspondence should be addressed. E-mail: sbarolo{at}
  • * These authors contributed equally to this work.

  • Present address: Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.


Gradients of diffusible signaling proteins control precise spatial patterns of gene expression in the developing embryo. Here, we use quantitative expression measurements and thermodynamic modeling to uncover the cis-regulatory logic underlying spatially restricted gene expression in a Hedgehog (Hh) gradient in Drosophila. When Hh signaling is low, the Hh effector Gli, known as Cubitus interruptus (Ci) in Drosophila, acts as a transcriptional repressor; when Hh signaling is high, Gli acts as a transcriptional activator. Counterintuitively and in contrast to previous models of Gli-regulated gene expression, we found that low-affinity binding sites for Ci were required for proper spatial expression of the Hh target gene decapentaplegic (dpp) in regions of low Hh signal. Three low-affinity Ci sites enabled expression of dpp in response to low signal; increasing the affinity of these sites restricted dpp expression to regions of maximal signaling. A model incorporating cooperative repression by Ci correctly predicted the in vivo expression of a reporter gene controlled by a single Ci site. Our work clarifies how transcriptional activators and repressors, competing for common binding sites, can transmit positional information to the genome. It also provides an explanation for the widespread presence of conserved, nonconsensus Gli binding sites in Hh target genes.


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

Genome-wide identification of phospho-regulators of Wnt signaling in Drosophila
S. Swarup, T. Pradhan-Sundd, and E. M. Verheyen
Development 142, 1502-1515 (15 April 2015)

A theoretical framework for the regulation of Shh morphogen-controlled gene expression
M. Cohen, K. M. Page, R. Perez-Carrasco, C. P. Barnes, and J. Briscoe
Development 141, 3868-3878 (15 October 2014)

Modular Evolution of DNA-Binding Preference of a Tbrain Transcription Factor Provides a Mechanism for Modifying Gene Regulatory Networks
A. M. Cheatle Jarvela, L. Brubaker, A. Vedenko, A. Gupta, B. A. Armitage, M. L. Bulyk, and V. F. Hinman
Mol Biol Evol 31, 2672-2688 (1 October 2014)

A model of spatially restricted transcription in opposing gradients of activators and repressors
M. A. White, D. S. Parker, S. Barolo, and B. A. Cohen
Mol Syst Biol 8, 614-614 (23 July 2014)

A Gli silencer is required for robust repression of gremlin in the vertebrate limb bud
Q. Li, J. P. Lewandowski, M. B. Powell, J. L. Norrie, S. H. Cho, and S. A. Vokes
Development 141, 1906-1914 (1 May 2014)

Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants
I. Mogno, J. C. Kwasnieski, and B. A. Cohen
Genome Res 23, 1908-1915 (1 November 2013)

Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning
K. A. Peterson, Y. Nishi, W. Ma, A. Vedenko, L. Shokri, X. Zhang, M. McFarlane, J.-M. Baizabal, J. P. Junker, A. van Oudenaarden et al.
Genes Dev. 26, 2802-2816 (15 December 2012)

Differential regulation of mesodermal gene expression by Drosophila cell type-specific Forkhead transcription factors
X. Zhu, S. M. Ahmad, A. Aboukhalil, B. W. Busser, Y. Kim, T. R. Tansey, A. Haimovich, N. Jeffries, M. L. Bulyk, A. M. Michelson et al.
Development 139, 1457-1466 (15 April 2012)

Beyond the Balance of Activator and Repressor
T. Whitington, A. Jolma, and J. Taipale
Sci Signal 4, pe29-pe29 (7 June 2011)

Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882