Evolution of cis-regulatory elements
From Shiu Lab
When the expression patterns of gene family members are examined, one major finding is that expression divergence seems to occur rather quickly. This is why we are interested in the expression divergence of gene family members as stated earlier. For a thorough understanding of the contribution of expression divergence to duplicate gene evolution, we have to have a very good knowledge about the regulatory networks in the genome of interests. One area we are interested in is the prediction of cis-regulatory elements in Arabidopsis thaliana. Cis-regulatory elements are short stretches of DNA sequences that control the expression of nearby genes. Change in these elements is thought to be fast and significantly contribute to the initial functional divergence between duplicate genes. Together with trans-acting factors such as transcription factors and the genes they control, cis-regulatory elements form an integral part of the transcriptional regulatory network. How many cis-elements are there? Each gene usually has multiple cis-elements. How do they work together to specify a particular expression pattern? We are interested in first finding potential cis-elements from the Arabidopsis genome and then using machine-learning methods to dissect their interactions.
