Bachelor Thesis Project
Background
High-throughput loss-of-function screening allows a systematic and large-scale quantitative analysis and functional annotation of all genes in the genome. With homogeneous and pathway-specific reporter assays only giving very limited information about cellular phenotypes, high-content microscopy combined with image analysis provides a multi-dimensional and quantitative single-cell readout of loss-of-function phenotypes.
Summary
For my Bachelor thesis project I focused on functionally analyzing a set of previously unknown genes that clustered into a functional module that was highly enriched in genes involved in regulation of genomic integrity and DNA damage response. Based on phenotype similarity we hypothesized that those genes might be involved in similar functions than known genes. I confirmed this hypothesis by using high-throughput in situ cytometry after knockdown of candidate genes. To compare putative conserved functions of those candidate genes I performed similar experiments using Drosophila cultured cells after depletion of homologous genes. Furthermore, because of their predicted function in DNA damage response I also checked for ectopic activation of DDR following knockdown in combination with DNA damage inducing agents.
In summary, we could show that quantitative automated analysis of perturbation phenotypes on a genome-wide scale provides an effective way of annotating unknown genes by categorizing them into known functional modules based on their phenotypic profile.
Part of the work I performed during my Bachelor thesis was later published as part of a paper by Fuchs et al. 2010 entitled "Clustering phenotype populations by genome-wide RNAi and multiparametric imaging". I have also made my thesis available via figshare.