Date of Award

Spring 1-1-2017

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

First Advisor

Robert T. Batey

Second Advisor

Ravinder Singh

Third Advisor

Deborah S. Wuttke

Fourth Advisor

Shelley Copley

Fifth Advisor

Thomas Perkins

Abstract

Recent developments in the comprehensive identification of the RNA-binding protein (RBP) repertoire has accelerated discovery of new RBPs. According to these studies, 20% of both known and novel RNA-binding proteins are highly disordered. Moreover, analysis of the human mRNA interactome revealed most disease related mutations are found within intrinsically disordered RNA-binding domains (RBDs). For most of these proteins, their RNA-binding properties are poorly characterized. Thus, deciphering intrinsically disordered RBD-RNA interactions on a molecular scale is essential to understanding their impact upon human physiology and diseases.

RGG/RG (arginine/glycine) domains are the second most common RNA binding domain in the human genome, yet their RNA-binding properties have not been well understood. Proteins containing RGG/RG domains regulate all aspects of RNA metabolism including transcription, processing, nucleocytoplasmic shuttling and translation. Proteins such as Fused in Sarcoma (FUS), Fragile X mental retardation (FMRP) and hnRNP U, bind a majority of the cellular transcriptome such that their recognition of RNAs has been considered to be non-specific or “promiscuous”.

Here, I report a detailed analysis of the RNA-binding characteristics of the RGG/RG domains from FUS, FMRP and hnRNP U. While previous studies of FUS focused on RNA binding by the RRM and zinc finger (ZnF) domains, my analysis showed RNA binding activity is driven by the RGG/RG domains. Further, I observed a strong synergy between the RRM and adjacent RGG/RG domains to achieve RNA binding affinities of the full-length FUS. To better characterize RNA-binding properties of RGG/RG domains, we have analyzed RGG/RG domains of FUS, FMRP and hnRNP U in vitro against a spectrum of different RNAs with well-defined structural and sequence features. These experiments revealed that RGG/RG domains have different degrees of preference for binding to RNAs but share consistent trends in their selectivity towards RNAs with complex secondary structure. Thus, the binding behavior of RGG domains is best described as “degenerate specificity” reflecting that RGG/RG domains interact with a broad spectrum of RNAs that contain frequently observed sequence/structural elements. This mode of specificity is likely further facilitated by the intrinsically disordered nature of RGG/RG domains that enable them to adopt multiple conformations to adaptively bind RNA.

Share

COinS