Date of Award

Spring 1-1-2018

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

First Advisor

Roy Parker

Second Advisor

Thomas Cech

Third Advisor

Natalie Ahn

Fourth Advisor

John Rinn

Fifth Advisor

Bradley Olwin

Abstract

RNA and proteins (RNPs) can form highly ordered aggregates in living organisms with functional or toxic properties. Clumps of toxic, cytoplasmic RNP aggregates are steeped in an association with neuronal (e.g. amyotrophic lateral sclerosis) and skeletal muscle (e.g. inclusion body myositis) degenerative diseases. The role of these aggregates in disease pathology is unknown; however, these aggregates may arise from molecularly similar RNP aggregates, called stress granules, which form naturally in all cells. Stress granules are conserved higher order RNP assemblies that form during physiologic stress when RNA translation is decreased. Clarifying the properties of higher order RNP assemblies in healthy tissue will likely beget a new understanding into their role in health and disease. Here, I explore the properties and regulation of stress granules and how aberrant RNP granules that accumulate in degenerative disease are formed.

I provide new insight into the structure, regulation, and formation of stress granules with the following key observations: i) Stress granules are highly structured, stable macromolecular assemblies, which form and disassemble in an energy dependent multistep process. ii) Stress granules have a unique RNP composition, which is capable of forming a dense web of RNP interactions iii) Stress granule formation, dynamics and clearance are regulated by an armada of conserved ATP-requiring chaperones. These observations suggest higher order RNP assemblies are capable of forming highly stable structures that must be actively regulated by the cell likely to ensure functionality and to prevent the aberrant accumulation of RNP aggregates.

Higher order, amyloid-like aggregates of the RNA-binding protein, TDP-43, may be the causative agent in several neuronal and skeletal muscle diseases. By examining normal skeletal muscle regeneration, I discovered TDP-43 forms an amyloid-like oligomeric assembly, termed myo-granule, capable of binding and likely trafficking RNA to regulate skeletal muscle formation. These results demonstrate cytoplasmic amyloid-like TDP-43 myo-granules are a functional feature of healthy skeletal muscle regeneration and suggest that heightened assembly or decreased clearance of myo-granules could be the source of potentially toxic cytoplasmic TDP-43 amyloid aggregates common to neuromuscular disease.

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