RNAseq and ribosome profiling of yeast cells grown under methionine restriction condition.

We characterize the translational and transcriptional programs induced by MetR and investigate the potential mechanisms through which methionine regulates gene expression, using the budding yeast S. cerevisiae as the model organism. Using ribosomal profiling and RNA-seq, we systematically compared the translational and transcriptional profiles of cells growing in the normal and methionine restricted media. We observed a broad spectrum of gene expression changes in response to MetR, including hundreds of genes whose transcript level and/or translational efficiency changed significantly. These genes fall into specific functional classes that are informative of the physiological state of the cell under MetR. Analysis of ribosome loading patterns of genes with increased translational efficiency suggested mechanisms both similar and different from the canonical model of translational regulation by general amino acid starvation. Analysis of the genes with decreased translational efficiency added support to the thiolation model of translational regulation by methionine. Since MetR extends the lifespan of many species, the list of genes we identified in this study can be good candidates for studying the downstream effectors of lifespan extension. Overall design: The initial cell culture was incubated in 300 ml SD medium overnight to an OD600 0.8~1.0, then diluted by five fold using fresh SD media and incubated for another 4 hours under 30oC to an OD600 0.8~1.0. The sample was then divided equally into two aliquots. Cells were separated from the media by spin-down at 3000 g for 5 minutes and re-suspended in SD and MetR media respectively. All samples were incubated for another hour before harvesting. All the steps were carried out at 30°C. Raw sequences were obtained from Illumina Hiseq 2000.

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Zou K, Ouyang Q, Li H, Zheng J