טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentHaimovich Gal
SubjectA Novel Role for mRNA Decay Factors in mRNA Synthesis
DepartmentDepartment of Medicine
Supervisor Professor Mordechai Choder
Full Thesis textFull thesis text - English Version


Abstract

Maintaining the proper level of mRNA is a key aspect in the regulation of gene expression, since achieving appropriate expression (temporally, spatially and in quantity) is vital for the cells to function, adapt and survive. The balance between mRNA synthesis (in the nucleus) and decay (in the cytoplasm) determines these levels.  Recently, we showed that RNA polymerase II controls cytoplasmic mRNA decay via two of its subunits. Here, we ask whether the cytoplasmic 5'-3' mRNA decay machinery (decaysome) can, conversely, affect mRNA synthesis.

It has been previously shown that some mRNAs accumulate in the cell when they are stabilized due to a defect in the decay process. We show that, counter intuitively, the steady state levels of most mRNAs do not increase following their stabilization by deletion of decaysome factors (DFs), indicating that the mRNA level in yeast is highly robust to perturbations in the decaysome. Furthermore, both inducible and on-going transcription is impaired in cells expressing enzymatically inactive forms of DFs. The possible indirect effect of DFs on transcription due to global slow decay is ruled out.

Consistently, we found that all examined DFs shuttle between the cytoplasm and the nucleus, in a manner dependent on proper degradation of mRNA. Importantly, a positive correlation is found between the capacities of DFs to shuttle with transcription efficiency. In the nucleus, the DFs associate with active chromatin, and when tethered to promoters, can stimulate transcription in a non-trivial manner. Whole-genome analysis, combined with biochemical and imaging data, suggests a direct coupling between the two roles.

Our findings demonstrate that the decaysome has a dual role in maintaining mRNA levels, which constitute a conceptual leap in our understanding of gene expression. Hence, gene expression is a circular process in which the hitherto first and last stages are interconnected. Cyclic processes are inherently robust, because defects in one stage affect the overall pace of the entire process, thereby maintaining the essential balance between the stages. The maintenance of mRNA levels is one manifestation of this principle.

This work was done in collaboration with the research groups of Xavier Darzacq (Ecole Normale Superiure, Paris, France) and Jose Perez-Ortin (U. Valencia, Spain).