Microarray Analysis of mRNA Decay Assays and Prediction of Drug Target Conservation

Licentiate thesis, 2008

This thesis contains two papers concerning (I) the evolutionary conservation of drug targets and its potential use in environmental risk assessments and (II) mRNA degradation as a control mechanism during osmotic stress in the yeast S. cerevisiae. Environmental risk assessments are needed for the approval of new pharmaceutical compounds. To date, the risk assessments are mainly focused on organisms like algae and Daphnia. The conservation of drug targets in species relevant for ecotoxicity testing is a key aspect in developing more targeted test strategies on higher organisms like fish or amphibians. With information on predicted proteomes for a wide range of species it is possible to extract and compile data on evolutionary conservation for drug targets. In paper I, orthology data is compiled and analyzed for a set of drug targets in several species, and the result evaluated based on an extensive literature search. mRNA degradation can be investigated on a genome-wide scale with the use of a transcriptional inhibitor and subsequent hybridization of RNA pools, isolated at a set of timepoints, to microarrays. Due to the complexity of the microarray methodology in this context, the data are in need of processing and transformation to deduce relevant information on changes in degradation rates. In paper II, mRNA degradation is investigated as a posttranscriptional control effect in connection to hyperosmotic stress. We conclude that mRNA degradation mechanisms are important regulatory keys in the stress response.