Date of Award

Spring 1-1-2018

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

First Advisor

Roy Parker

Second Advisor

Chris Link

Third Advisor

Tom Cech

Fourth Advisor

Sabrina Spencer

Fifth Advisor

John Rinn

Abstract

Ribonucleoprotein (RNP) granules, which are composed of numerous RNAs and proteins, are ubiquitous features of eukaryotic cells. This thesis investigates the assembly mechanisms of P-bodies and stress granules, two cytoplasmic granules that rely on RNAs unengaged in translation to form. Previous studies in the field have focused on the roles of proteins, and specifically their intrinsically disordered regions (IDRs), in targeting components and driving granule assembly. However, domain analysis of four proteins illustrates that having an IDR is neither sufficient nor necessary for targeting to P-bodies. Although IDRs have been shown to be important in some contexts, these results suggest that IDRs are not solely responsible for RNP granule formation. With this in mind, the assembly roles of RNA were considered. RNAs self-assemble robustly in vitro, aided by crowders and salt. Remarkably, when total yeast RNA is allowed to assemble in vitro, the RNAs that are enriched in these assemblies are the same RNAs that are enriched in stress granules in vivo. This, in addition to observations compiled from the literature, suggests that RNA-RNA interactions may play an important role in the assembly of many RNP granules. Preliminary interrogation into RNA sequences important for RNA localization to stress granules has revealed that the addition of certain sequences can significantly alter RNA localization under stress despite total length being held constant. This argues for the presence of stress granule targeting elements within RNA, although further mechanistic investigation is required. Taken together, this thesis works towards understanding RNP assembly and the mechanisms that target their components.

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