Abstract

Transcriptome analysis by total mRNA profiling provides a measurement of the degree of variation for the amount of each single mRNA species after a physiological or pathological transition of cell state. It has become a general notion that variations in protein levels do not necessarily correlate with variations in total mRNA levels, for the presence of post-transcriptional controls which influence the fate of cytoplasmic mRNAs and affect their translational fitness. Nevertheless, the extent of this phenomenon and the rules, if any, governing it are still generally unknown. To address this issue we took advantage of a number of studies performed using polysomal mRNA profiling in combination with classical total mRNA profiling in different mammalian and yeast systems. A normalization of the raw data coming from these datasets and a statistical meta-analysis aimed at maximizing uniformity in data processing have been performed. From the comparison of the results an extensive uncoupling between transcriptome and translatome variations of mRNA levels emerges, measured by a significant difference between steady state and polysomal fold changes induced by a cellular physiological or pathological transition. It seems clear that virtually the majority of significant changes in cytoplasmic mRNA steady-state levels are subjected to a further elaboration by a post-transcriptional decision program, leading either to a widespread buffering of the cytoplasmic changes which transfers only a small fraction of them to translation, either to the creation of new changes which cannot be detected at the transcriptional level, yet capable of heavily influencing protein synthesis rates. An explanatory model characterized by a cytoplasmic mRNA storage compartments is proposed and the involvement of P-bodies and the miRNA pathway in post-transcriptional reprogramming of gene expression has been experimentally tested in the biological model of EGF induction, in order to explain how a change in translational fitness can counteract or magnify a parallel change in citoplasmic mRNA availability. To investigate the role of specific cellular mechanism in generating uncoupling between transcriptome and translatome changes, the experimental model has been altered through silencing of three key genes involved in post-transcriptional regulation pathways: 4E-T, Xrn1 and Dicer.