Regulation of transcription elongation anticipates alternative gene expression strategies across the cell cycle

Increasing evidence supports that the activity of RNA polymerase II (RNA pol II) during transcription elongation can be regulated to control transcription rates. Using genomic run-on (GRO) and RNA pol II chromatin immunoprecipitation (RPCC), we have respectively measured active and total RNA pol II present in the body of genes at 3 different stages of the mitotic cell cycle of Saccharomyces cerevisiae : G1, S and G2/M. Comparison of active and total RNA pol II values at these three points defined different patterns of transcription elongation control across the cell cycle. Previously characterized cycling genes were found associated to some of these elongation patterns. A cluster of genes with very divergent GRO and RPCC patterns was significantly enriched in genes functionally related to ribosome biogenesis (RiBi) and the structural components of the ribosome. We confirmed that RiBi mRNA expression upregulates after START but decreases after mitosis. Finally, we analysed the contribution of mRNA stability to each cluster and found that concerted control of RNA pol II activity and mRNA decay is needed to fully understand alternative strategies of gene expression across the cell cycle.