The role of RNA Polymerase II-dependent transcription elongation in the cross-talk between mRNA synthesis and decay.

Abstract

The main molecule in gene expression is messenger RNA (mRNA) which transfers the information contained in genes in the nucleus to the cytoplasm where it is translated into proteins that carry out cellular functions. mRNA levels are determined through its synthesis, by the RNA polymerase II, and degradation, which involves the Ccr4-Not complex and Xrn1. It has become increasingly apparent that the mRNA concentration in a cell is maintained at a particular level even through stressful situations. The way the cell is able to do this is by a cross-talk between the machinery responsible for its transcription and that responsible for its degradation. In this work we have attempted to unravel the mechanisms by which this cross-talk occurs. For this complex task, we first studied how transcription and degradation was affected after deleting a single gene known to be involved in either one of these mechanisms. This study confirmed the existence of a strong feedback between mRNA synthesis and decay, and also helped us uncover some of the elements important for this cross-talk. The most interesting finding was the correlation between transcription elongation and mRNA degradation, suggesting that it is directly relevant for cross-talk. Second, we mathematically modelled and computationally simulated this coupling between transcription and mRNA decay. Thanks to in silico experimentation, we found that two proteins involved in degradation (Ccr4-Not and Xrn1) were most likely also involved in transcription, and therefore the feedback mechanism. This result complements that of the first study and places both Ccr4-Not and Xrn1 as important proteins for cross-talk. Finally, we analysed the exonuclease Xrn1 in depth through genome-wide experiments. This study allowed us to conclude that Xrn1 is directly involved in transcription and influence both early and late RNA polymerase II-dependent transcription elongation. The results of this thesis have enabled us to come up with a model for how the cross-talk could work in yeast cells and allowed us to envision new hypotheses to explain the novel results.