I am working with a colleague in London who has run ChIP-seq on a certain tissue from chickens for the purpose of identifying conserved enhancer regions. A collaborator of her's in the USA has concurrently managed to run whole genome sequencing on the same tissues in human. As this particular tissue is very difficult to obtain, we are resorted to trying to align the chicken enhancers to the key genetic variants identified in human.
So far, an approach using 'synteny' and LASTZ_NET alignments (EPO alignments are not available for Chicken-to-human, apparently? - conservation genetics is not quite my area) has not really 'worked': >75% of the chicken regions are not found in human, but my colleague believes that we are quite related [evolutionarily] to chickens and that most of these conserved enhancers should be found in human.
We also tried an approach whereby we examine the chicken enhancer regions for regulatory elements, e.g., key TFBS, and then search for these motifs in human. This worked better than the synteny-based approach, but my colleague still believes there should be more concordance between the chicken enhancers and the human genome.
Any other ideas will be appreciated.