The goal of these projects is to gain some understanding of how genomic DNA in general, and regulatory DNA in specific, has diverged between closely related species (such as mouse, human, and rat) and between more distantly related species (such as mouse and chick).
One effective way of finding regulatory regions in the genome is to use comparative sequence analysis to identify conserved non-coding regions near the gene or genes of interest. A computational toolset that can be used to do this is FamilyRelations/Cartwheel, a project under development here at Caltech.
There is a tutorial to help you learn how to use FamilyRelations and Cartwheel.
Using FR/Cartwheel, do one or both of the projects below. The Myf5 project is relatively easy; the Sox2 project involves more work. Note that your TA, Tracy, is away for the week of April 12th, and that Titus Brown (firstname.lastname@example.org) should be contacted regarding this project as well as any problems with FamilyRelations/Cartwheel.
Myf5 is one of the earliest known myogenic regulators. Quite a bit is known about its transcriptional regulation; see e.g. this paper (PubMed ID: 11311165).
We have downloaded 200kb regions containing the myf5 gene from each of the human (Homo sapiens), rat (Rattus norvegicus), mouse (Mus musculus), and chick (Gallus gallus) genomes. Upload the regions to Cartwheel, find any match(es) to the mouse Myf5 protein, and use the pair view and triple view in FRII to answer some or all of the following questions:
Sox2 is an important early regulator of chick midline development. In this paper (PubMed ID: 12689590) on sox2 transcriptional regulation in chick, Kondoh's lab does an excellent job of first finding the regulatory regions that control sox2 expression, and then verifying that they are conserved.
In addition to the questions raised above for the myf5 project, answer some or all of the following questions: