David Gresham | bioRxiv Science

bioRxiv2016

Growth Rate-Dependent Global Amplification of Gene Expression

Regulation of cell growth rate is essential for maintaining cellular homeostasis and survival in diverse conditions. Changes in cell growth rate result in changes in rRNA and tRNA content, but the effect of cell growth rate on mRNA abundance is not known. We developed a new method for measuring absolute transcript abundances using RNA-seq, SPike in-based Absolute RNA Quantification (SPARQ), that does not assume a constant transcriptome size and applied it to the model eukaryote, Saccharomyces cerevisiae (budding yeast), grown at different rates. We find that increases in cell growth rate result in increased absolute abundance of almost every transcript, with significant coordinated changes in abundances among functionally related transcripts. mRNA degradation and synthesis rates increase with increased growth rate, but to differing extents, resulting in the observed net increases in absolute abundance. We propose that regulation of ribosome abundance links environmental conditions to transcriptome amplification via nutrient-sensing pathways.

Cell Biology↗

bioRxiv2015

Global determinants of mRNA degradation rates in Saccharomyces cerevisiae

Degradation of mRNA contributes to variation in transcript abundance. Studies of individual mRNAs show that cis and trans factors control mRNA degradation rates. However, transcriptome-wide studies have failed to identify global relationships between transcript properties and mRNA degradation. We investigated the contribution of cis and trans factors to transcriptome-wide degradation rate variation in the budding yeast, Saccharomyces cerevisiae, using multiple regression analysis. We find that multiple transcript properties are associated with mRNA degradation rates and that a model incorporating these factors explains [~]50% of the genome-wide variance. Predictors of mRNA degradation rates include transcript length, abundance, ribosome density, codon adaptation index (CAI) and GC content of the third position in codons. To validate these factors we studied individual transcripts expressed from identical promoters. We find that decreasing ribosome density by mutating the translational start site of the GAP1 transcript increases its degradation rate. Using variants of GFP that differ at synonymous sites, we show that increased GC content of the third position of codons results in decreased mRNA degradation rate. Thus, in steady-state conditions, a large fraction of genome-wide variation in mRNA degradation rates is determined by inherent properties of transcripts related to protein translation rather than specific regulatory mechanisms.

Genomics↗