Board Thread:Fossil Fuels/@comment-3213993-20150831073147

Enhancers are important to gene regulation. They are regulatory sequences, and changes in enhancers are often responsible for major phenotypic changes. Finding enhancers in archosaur genomes will be important to creating dinosaur facismiles. However, as they are often found thousands or even millions of base pairs away from the genes that they regulate, they cannot be found using bioinformatic methods.

How are enhancers found? I ask because there are three major genes of interest that are involved in making archosaurian traits. Sonic hedgehog and fibroblast growth factor 8 are expressed in different regions in non-avian reptiles than in birds, and by blocking their expression using chemicals, researchers were able to make chicken embryos with vaguely dinosaur-like skulls. However, they did not find the genetic change responsible for this. If enhancers are responsible for this (the most likely explanation), how would researchers find those enhancers?

Another tricky gene is C2CD3. This is the affected gene in the fatal embryonic mutation talpid2, which causes fatal defects but also triggers rudimentary tooth development in chick embryos. Because the protein sequence, while conserved in many regions, is not as conserved in others, and due to the gene's pleiotropic nature, we cannot reconstruct the ancestral archosaur version of the gene, and insertion of that or the alligator/lizard version of the protein-coding sequence will likely have either no effect or additional undesirable effects on phenotype. Therefore, if the tooth development in the chick embryos is following the same pathway as in other animals (a big assumption), the key to triggering tooth development may lie in an enhancer region of the gene in the alligator or lizard genome.

So, again, how would researchers find these enhancers? 