Date of Award

Spring 1-1-2018

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

First Advisor

Roy Parker

Second Advisor

Dylan Taatjes

Third Advisor

Karolin Luger

Fourth Advisor

Robin Dowell

Fifth Advisor

John Rinn

Abstract

Stress granules are non-membranous assemblies of RNA and protein that form during conditions in which translation initiation is limited. Stress granules are of interest due to their potential role in the regulation of gene expression and their relation to other cytoplasmic RNP granules, such as p-bodies, germ granules, and neuronal granules. Additionally, stress granules are related to pathological aggregates observed in neurodegenerative diseases since (1) they share many protein components with these aggregates and (2) mutations that promote stress granule assembly or inhibit their clearance are causative in neurodegenerative disease.

The goals of this thesis are (1) to understand the dynamics of stress granule assembly and disassembly, (2) to elucidate the RNA composition of stress granules, and (3) to understand how RNAs are targeted to stress granules. Herein we make several important observations about the composition and dynamics of stress granules. i) Stress granules assemble through a multistep process in which stable substructures, termed cores, form first and coalesce into larger stress granules. ii) Stress granules are a composite of many mRNAs and lncRNAs, and transcripts vary in their degree of recruitment from <1% to >95% enriched in stress granules. iii) RNAs partition to stress granules on the basis of their length and translation status, with long poorly translated transcripts showing enhanced partitioning to stress granules. iv) The RNA composition of stress granules is largely conserved from yeast to humans, between different stresses, and between different protein cores. v) RNA can partition to stress granules independently of individual RBPs, suggesting that RNA partitioning to stress granules is either based on RNA-RNA interactions, or through the summation of the effects of many different RBPs.

Our findings also pave the way for testing stress granule function by providing a list of stress granule enriched RNAs which will presumably be most affected by stress granules. Finally, our results also have implications outside of stress granule biology and provide insights into how RNAs might partition into other RNP granules.

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