Yeast translational profiling: rcm1 knockout vs. wild-type with oxidative stress

Rcm1 methylates ribosomal RNA at C2278 and a knockout of this gene induces structural alterations of rRNA and decreased translational fidelity. To test the influence of rcm1 knockout on the specific translation of mRNAs, we analysed the mRNA recruitment pattern into polysomes versus total cellular mRNAs under different oxidative stress conditions by microarrays. In order to estimate the efficiency of translation of individual mRNAs, we calculated the translational efficiency (TE) as ratio between signal intensity in the polysome fraction (‘translatome’) versus signal intensity in the total yeast cell lysate (‘transcriptome’) for each probeset on the array. Genes with at least 2-fold up- or downregulation at p < 0.05 were defined to be significantly translationally up- or downregulated. 2 genotypes (wild-type and rcm1 knockout), 3 oxidative stress treatments (0, 30 and 90 min H2O2), 2 biological replicates, common reference design with common reference pool = RNA pool of all 24 samples