Global transcriptome changes after nitrogen replenishment in S288c yeast strain

The study on the effect of nitrogen replenishment on the gene expression showed that 390 genes were significantly upregulated (with a logFC ranging from 4.5 to 0.8), among which those related to RNA binding, ribosome binding, structural constituent of ribosome, transferase activity and transcription. 833 genes were significantly down-regulated (with a logFC ranging from -0.8 to -5.2) including those related to stress response, amino-acid catabolism process, protein catabolic process (ubiquitin-dependent and vacuolar protein degradation). But the most interesting and unexpected changes were those related to the down-regulation of the glycolytic transcripts. In fact, we observed a rapid down-regulation of many glycolytic mRNA (25/34) 30 min after nitrogen repletion. These data were surprising as expression of the glycolytic genes are generally considered as stable and sometimes they are even used as housekeeping control genes. In addition, the decoupling of the glycolytic gene expression from the expression of RP genes, ribosomal genes or those related to protein synthesis is unique to the present dataset as in most other data expression of these groups are tightly correlated when nutrients are available. This prompts us to examine in some details the factors which led to the control of the glycolytic mRNA instability in conditions of nitrogen replenishment. Analysis used RNA collected at 30 min of the beginning of the alcoholic fermentation of S288C with NH4 addition and S288C with H2O addition (control). Experiments made in duplicates - dye-swap design