Posted by Victor Hanson-Smith.
For the next ten weeks, our conversation will focus on the evolution of transcription factors and their corresponding DNA binding sites. A growing body of EvoDevo research shows that cis-regulatory mutations play a significant role in the evolution of morphological, physiological and behavioral phenotypes. In a 2007 Nature Reviews Genetics article, Greg Wray highlighted twenty such cis-regulatory mutations with interesting phenotypic consequences. A lot of new research has been published since then, and we want to know: what is the current knowledge on the evolution of transcriptional regulation?
Below is a reading list of (a few) relevant publications. Over the next ten weeks, we’ll read and discuss the articles on this list. Do you think we overlooked any papers? Feel free to post your comments down below.
- “Evolution of alternative transcriptional circuits with identical logic.” Tsong et al., Nature 2006. (From the Johnson lab)
- “Gene duplication and the adaptive evolution of a classic genetic switch.” Hittinger and Carroll, Nature 2007. (See the Hittinger lab and the Carroll lab)
- “Functional specificity of a Hox protein mediated by the recognition of minor groove structure.” Joshi et al., Cell 2007. (from the Honig lab)
- “Evolution of eukaryotic transcription circuits.” Tuch, et al., Science 2008. (From the Johnson lab)
- “The evolution of combinatorial gene regulation in fungi.” Tuch, et al., PLoS Biology 2008. (From the Johnson lab)
- “Evolutionary Tinkering with Conserved Components of a Transcriptional Regulatory Network.” Lavoie, et al., PLoS Biology 2008.
- “Conservation of enhancer location in divergent insects.” Cande et al., PNAS 2009. (From the Levine lab)
- “The role of DNA shape in protein-DNA recognition.” Rohs et al., Nature 2009. (From the Honig lab)
- “A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors.” Grove et al., Cell 2009. (from the Bulyk Lab)
- “Diversity and Complexity in DNA Recognition by Transcription Factors” Badis et al., Science 2009. (From the Bulyk Lab)
- “Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.” Li et al., 2009. (From the Eisen Lab)
- “Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species.” Bradley et al, PLoS Biology 2010. (From the Eisen Lab)