A semester-long genetics lab exploring gene families through comparative genomics and CRISPR-based gene editing
Author: Jennifer Kennell
Affiliation: Vassar College
Keywords: f. classroom undergraduate research experience (CURE)
Course-based undergraduate research experiences (CUREs) offer students opportunities to gain the benefits of conducting independent research in the context of a course laboratory. Recently my research lab has become interested in studying members of the Haloacid Dehalogenase (HAD) family of non-protein phosphatases. In particular, we began by characterizing in Drosophila possible orthologs of Phosphoglycolate Phosphatase (PGP), an enzyme that was recently identified as playing an evolutionarily conserved role in dephosphorylating toxic side products of glycolysis. Using the tools I have learned through participation in the Genomics Education Partnership (GEP) Pathways Project, I have developed a CURE for my intermediate-level Molecular Genetics class that involves annotation of possible orthologs of these phosphatases in various Drosophila species. Each semester students annotate a different family member and perform evolutionary analyses of the predicted gene and protein sequences. In addition, they also generate a mutation in the D. melanogaster ortholog using transgene based CRISPR-Cas9 gene editing; these mutant lines can then be used in future studies by independent research students in my laboratory. Through the gene annotation portion of the project students get hands on experience with comparative genomics approaches while reinforcing their understanding of eukaryotic gene structure and evolution. And through the mutagenesis portion of the project they gain experience in setting up fly crosses, analyzing progeny, and conducting molecular analyses to identify possible mutations in the new fly lines they generate. The guide RNA transgenic lines necessary for the project are readily available through various stock centers or are fairly straightforward to generate and make excellent independent projects for undergraduates. This CURE is very flexible and can easily accommodate any gene or gene family of interest. The mutagenesis portion of the project can also easily be incorporated into the existing GEP Pathways Project studying the Insulin pathway.