Saccharomyces Cerevisiae Modulates Cell Growth via Alternative Polyadenylation
Dynamic 3' UTRs variation mediated by APA is one of the major determinants of post-transcriptional regulation. Though some progress has been made in understanding its function in mammalian cells, the role of APA in the model organism S. cerevisiae, which lack of miRNAs, is a matter of debate. Unlike mammalian cells, most of S. cerevisiae genes tend to express mRNAs with longer 3' UTRs in proliferating cells. Further analysis demonstrated that 3' UTRs length and mRNA expression were negatively correlated in different growth conditions. By combining APA sequencing and polysome profiling, we observed that mRNA isoforms with shorter 3' UTRs with a higher translational efficiency in proliferating cells but not quiescent. Further analysis demonstrated that different function genes translational efficiency control by APA are differential modulated and closely related with growth conditions. Furthermore, we observed the correlation between asRNAs and translational efficiency of different length 3' UTR transcripts, suggests asRNAs may involve in the regulation of translational efficiency mediated by APA. Thus, this study indicates conservation of molecular function of APA in different Eukaryotes, highlighting the importance of APA in regulating gene function. Overall design: S. cerevisiae S288C cells (ATCC, 204508) were cultured at 30°C in rich YPD media (1% Yeast Extract, 2% Peptone, 2% Dextrose) with shaking at 220 rpm. The exponential phase cells were harvested at mid-log phase with the OD600 values being 0.6-0.8. For stationary cells, the same cells were then grown to an OD600 of 2.1–2.3. Then exponential and stationary phase cells were sequenced to identify dynamic 3'UTR change by IVT-SAPAS as previous (Fu et al., 2015). Furthermore, exponential and stationary phase cells were performed polysome profiling to analysis relationship of 3'UTR length and translational efficiency according to DAVID Bartel lab's protocol (http://bartellab.wi.mit.edu/protocols.html.) with some modification. To identify the genes with significant poly(A) sites switching, we performed the test of linear trend alternative to independence (Agresti, 2003). Briefly, a 2XC table was constructed with the number of reads of APA sites for each gene, with APA sites as columns (from the site with shortest 3' UTR to that with longest) and the two compared samples as rows; then, Pearson correlation r and statistic   were calculated to obtain a p values. A threshold of FDR<=0.01 & | r |>0.1 was used to identify significant poly(A) sites switching.