Relevant Group Publications: Genome Res 2009

While vertebrates share a large set of conserved candidate regulatory elements, it is reported that these elements have not been conserved in ascidians or the cephalochordate amphioxus. In the recent genome sequence analysis paper of amphioxus a very small number of vertebrate CNEs were published, further fuelling speculation that their evolution into a large set of highly conserved non-coding sequences is a key characteristic of the ancestral vertebrate body plan.

Our approach for identifying conserved non-coding elements (CNEs) between evolutionary distant genomes which relies on sensitive local similarity searches in the genomic regions surrounding phylogenetically defined gene families (Hufton et al 2009) uncovered more than a thousand CNEs conserved between amphioxus and vertebrates. In vivo testing of 42 of our CNEs in transgenic zebrafish assays - including examples from vertebrates and amphioxusÑrevealed that the majority are functional enhancers [1].

To understand how regulatory elements involve we study the regulatory motif evolution within the Sonic hedgehog (Shh) gene across multiple teleosts.