Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

Data on absolute molecule numbers will empower the modeling, understanding, and comparison of cellular functions and biological systems. We quantified transcriptomes and proteomes in fission yeast during cellular proliferation and quiescence. This rich resource provides the first comprehensive reference for all RNA and most protein concentrations in a eukaryote under two key physiological conditions. The integrated data set supports quantitative biology and affords unique insights into cell regulation. Although mRNAs are typically expressed in a narrow range above 1 copy/cell, most long, noncoding RNAs, except for a distinct subset, are tightly repressed below 1 copy/cell. Cell-cycle-regulated transcription tunes mRNA numbers to phase-specific requirements but can also bring about more switch-like expression. Proteins greatly exceed mRNAs in abundance and dynamic range, and concentrations are regulated to functional demands. Upon transition to quiescence, the proteome changes substantially, but, in stark contrast to mRNAs, proteins do not uniformly decrease but scale with cell volume. [Display omitted] ▸ Cellular numbers for all RNAs and most proteins during proliferation and quiescence ▸ Cells contain 1-10 copies of most mRNAs and ∼100–1 million copies of most proteins ▸ Distinct subset of long noncoding RNAs is expressed above 1 copy/cell ▸ Quiescent cells show ∼4-fold lower RNA concentrations and highly remodeled proteome Quantitative RNA-seq and mass spectrometry in two cellular states are used to show that proteins greatly exceed mRNAs in abundance and dynamic range in yeast, and concentrations are regulated to functional demands. Upon transition to quiescence, the proteome changes substantially, but in contrast to mRNAs, proteins do not uniformly decrease but scale with cell volume.