Spinocerebellar ataxia type 3 (SCA3, also called Machado-Joseph disease) is a neurodegenerative disease caused by CAG repeat expansion in the ATXN3 gene. This results in polyglutamine expansion within the ataxin-3 protein, conferring the protein toxic properties including the propensity to misfold, aggregate, and form toxic inclusions within neurons. Ataxin-3 functions as a deubiquitinase, meaning it edits ubiquitin linkages on proteins and thus regulates the degradation, protein-protein interactions, and functions of proteins. How polyglutamine expansion in ataxin-3 alters its deubiquitinase function and contributes to disease remains unclear. To identify proteins that may be differently deubiquitinated by polyglutamine-expanded ataxin-3 and therefore possibly involved in SCA3 pathogenesis, we immunoprecipitated K48-ubiquitinated proteins in Neuro-2A cells expressing wild-type or polyglutamine-expanded human ataxin-3, or no human ataxin-3, and performed LC-MS/MS proteomic analysis. Interestingly, proteomic analysis revealed ‘RNA-binding proteins’ as the largest class of dysregulated proteins in cells expressing polyglutamine-expanded compared to wild-type human ataxin-3. We selected three RNA-binding proteins (matrin-3, PABPC1, and ELAVL1) for further validation in cell, zebrafish, and mouse models of SCA3. We discovered that the abundance of matrin-3 protein is altered in the brain of SCA3 mice, and in cells expressing wild-type or polyglutamine-expanded human ataxin-3, compared to deubiquitinase inactive ataxin-3, and we determined that matrin-3 and ataxin-3 proteins co-interact. We are now continuing to investigate how the dysregulation of RNA-binding proteins such as matrin-3 in SCA3 may result in altered RNA processing and contribute to disease pathogenesis. Dysregulation of RNA-binding proteins and the resulting abnormalities in RNA processing, splicing, and polyadenylation represent a significant disease mechanism in motor neuron disease (a related neurodegenerative disease) [1]. Dysregulation of RNA-binding proteins is also an emerging area of interest in polyglutamine diseases [2] but remains largely unexplored for SCA3. Therefore, the findings presented here provide novel insights for a field of growing interest.