An ambitious EC-funded research initiative on epigenetics advancing towards systems biology

Computational Biology Unit, Uni Computing, Uni Research, Bergen, Norway

Computational analysis of cis-regulatory elements in epigenetics and development

Web Page

Our research focuses on understanding development, gene regulation, and epigenetics on a genome-wide scale, in the context of evolution. We have developed a method for genome-wide single-species prediction of cis-regulatory elements. Applying this method to fly Polycomb/Trithorax Response Elements (PREs) on the basis of binding sites for recruiting factors, we were able to significantly expand the set of known Polycomb targets in Drosophila beyond the Hox genes (Ringrose et al., Dev Cell 2003). We generalised the method into a versatile program, jPREdictor, for the fast prediction of any kind of cis-regulatory elements on a genome-wide scale (Fiedler and Rehmsmeier, Nucl Acids Res 2006). To evaluate cis-regulatory evolution, we developed an alignment-independent comparative method that is not restricted to sequence conserved elements. Applying this method to several Drosophila species showed that PRE evolution is extraordinarily dynamic (Hauenschild et al., PLoS Biol 2008).