Introduction
Binding site discovery:
-Computational -Experimental
Cis-regulatory evolution
Organisms
-Yeast
-Fly
-Mouse
-Human
Binding site degeneracy
Functional variants
Cis-regulatory code
Regulatory networks

Functional binding site variants
Functional variants are nucleotide variants at a particular position in a TF binding site motif that cause differential expression of target genes.

Primary literature
Chan, S. K., H. D. Ryoo, A. Gould, R. Krumlauf, and R. S. Mann. 1997. Switching the in vivo specificity of a minimal Hox-responsive element. Development 124:2007-2014.

Chen, W., and K. Struhl. 1988. Saturation mutagenesis of a yeast his3 "TATA element": genetic evidence for a specific TATA-binding protein. Proc Natl Acad Sci U S A 85:2691-2695.

Gage, P. J., H. Suh, and S. A. Camper. 1999. The bicoid-related Pitx gene family in development. Mamm Genome 10:197-200.

Gaudet, J., and S. E. Mango. 2002. Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4. Science 295:821-825.

Gaudet, J., S. Muttumu, M. Horner, and S. E. Mango. 2004. Whole-genome analysis of temporal gene expression during foregut development. PLoS Biol 2:e352.

Giordano, M., M. Godi, F. Giacopelli, M. Lessi, S. Mellone, R. Paracchini, A. Petri, J. Bellone, R. Ravazzolo, G. Bona, and P. Momigliano-Richiardi. 2006. A variation in a Pit-1 site in the growth hormone gene (GH1) promoter induces a differential transcriptional activity. Mol Cell Endocrinol 249:51-57.

Harbury, P. A., and K. Struhl. 1989. Functional distinctions between yeast TATA elements. Molecular and Cellular Biology 9:5298-5304.

Jacobson, E. M., P. Li, A. Leon-del-Rio, M. G. Rosenfeld, and A. K. Aggarwal. 1997. Structure of Pit-1 POU domain bound to DNA as a dimer: unexpected arrangement and flexibility. Genes Dev. %R 10.1101/gad.11.2.198 11:198-212.

Lanctot, C., B. Lamolet, and J. Drouin. 1997. The bicoid-related homeoprotein Ptx1 defines the most anterior domain of the embryo and differentiates posterior from anterior lateral mesoderm. Development 124:2807-2817.

Lee, T. I., N. J. Rinaldi, F. Robert, D. T. Odom, Z. Bar-Joseph, G. K. Gerber, N. M. Hannett, C. T. Harbison, C. M. Thompson, I. Simon, J. Zeitlinger, E. G. Jennings, H. L. Murray, D. B. Gordon, B. Ren, J. J. Wyrick, J. B. Tagne, T. L. Volkert, E. Fraenkel, D. K. Gifford, and R. A. Young. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799-804.

Lefstin, J. A., and K. R. Yamamoto. 1998. Allosteric effects of DNA on transcriptional regulators. Nature 392:885-888.

Merika, M., and D. Thanos. 2001. Enhanceosomes. Curr Opin Genet Dev 11:205-208.

Papatsenko, D., and M. Levine. 2005. Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo. Proc Natl Acad Sci U S A 102:4966-4971.

Scully, K. M., E. M. Jacobson, K. Jepsen, V. Lunyak, H. Viadiu, C. Carriere, D. W. Rose, F. Hooshmand, A. K. Aggarwal, and M. G. Rosenfeld. 2000. Allosteric Effects of Pit-1 DNA Sites on Long-Term Repression in Cell Type Specification. Science 290:1127-1131.

Struhl, K. 1986. Constitutive and inducible Saccharomyces cerevisiae promoters: evidence for two distinct molecular mechanisms. Molecular and Cellular Biology 6:3847-3853.

Tanay, A., I. Gat-Viks, and R. Shamir. 2004. A global view of the selection forces in the evolution of yeast cis-regulation. Genome Res 14:829-834.

Tremblay, J. J., C. G. Goodyer, and J. Drouin. 2000. Transcriptional properties of Ptx1 and Ptx2 isoforms. Neuroendocrinology 71:277-286.

Wefald, F. C., B. H. Devlin, and R. S. Williams. 1990. Functional heterogeneity of mammalian TATA-box sequences revealed by interaction with a cell-specific enhancer. Nature 344:260-262.

Databases and datasets
In progress...

Software and tools
In progress...

Labs
In progress...