Developing a screen to discover novel mRNA 3’-UTR-mediated scaffolding of protein- protein interactors

Messenger RNAs (mRNAs) fulfill the vital responsibility of conveying the genetic information encoded in DNA within the nucleus to the ribosomes in the cytoplasm of the cell. In other words, it is the connection between the genetic information coding for a protein and the protein itself. However, recent data suggests that mRNAs may play other roles besides serving only as protein synthesis templates. One such function that may be of particular importance is the ability of the mRNA to act as a scaffold for protein-protein interactions (PPIs) to occur. More specifically, the 3’untranslated region (3’-UTR) of the mRNA of one of the protein interactors is bound to by the other protein interactor as the scaffolding mRNA is nascently synthesizing the first protein interactor. Then, through proximity-based interactions, the two proteins interact and form a complex. This model proposes a new method by which proteins find each other in the cell and form protein complexes, yet it is not known how prevalent this scaffolding strategy is, what protein complexes primarily use it, what features of the 3’-UTR allow such interactions to occur, etc. Therefore, a high-throughput screen that would reveal all possible cases of 3’-UTR-mediated PPI scaffolding occurring within the transcriptome of the model organism Saccharomyces cerevisiae (S. cerevisiae or Baker’s yeast) needed to be developed in order to answer these questions. The purpose of this thesis is to expand on the research done already to develop this screen as well as the future steps required to complete it