Hafen Lab: Master thesis/semester project on CRISPR/Cas9-mediated SNP changes to elucidate cause of size variations
How genetic variation (e.g. SNP) leads to different traits/phenotypes in natural populations is a fundamental and challenging problem in both the life and medical sciences. This project will involve several objectives to tackle this problem by first establishing an efficient in vivo CRISPR/Cas9 method and then using this method to change phenotype-associated SNPs in inbred Drosophila lines derived from a natural population.
Genetic variation – genetic differences within and between populations of the same species (e.g. SNP) – is relevant to the outcome of various traits/phenotypes such as shape, behavior, and fitness. How genetic variation could produce phenotypes is a fundamental and challenging problem in both the life and medical sciences. Our group has worked on this problem using a naturally derived population of inbred lines of the model organism, Drosophila melanogaster (fruit fly). Our recent genome- and proteome-wide association studies for wing size have led to the identification of many SNPs [1] and proteins [2], respectively, of which occurrence/abundance statistically correlate with the variations in size. These raise the question if these SNPs and specific abundance of the proteins are the cause of the variations in size. The project consists of three objectives: (1) evaluation of the functionality of the proteins controlling wing size using transgenic RNAi, (2) establishment of an efficient fly CRISPR/Cas9 method for SNP changes, and (3) validation of the SNPs by SNP changes in naturally derived inbred line(s) using the CRISPR/Cas9 method. Through this project, we will obtain insights into how genetic variation produces the variation in size through affecting abundance of proteins.
Methods: CRISPR/Cas9, microinjection, microscopy, fly genetics, and image/data analysis.
Contact: Dr. Ryohei Yagi
[1] Vonesch SC, Lamparter D, Mackay TF, Bergmann S, Hafen E. Genome-Wide Analysis Reveals Novel Regulators of Growth in Drosophila melanogaster. PLoS Genet. 2016, 12(1):e1005616. doi: 10.1371/journal.pgen.1005616.
[2] Okada H, Ebhardt HA, Vonesch SC, Aebersold R, Hafen E. Proteome-wide association studies identify biochemical modules associated with a wing-size phenotype in Drosophila melanogaster. Nat Commun. 2016, 7:12649. doi: 10.1038/ncomms12649.