RNA-protein interactions are of increasing interest in chemistry and biology. In human cells, over 25,000 long non-coding RNAs have been recently been described and proposed to function in a diverse array of cellular processes, from epigenetic control of gene expression to metabolic regulation. Many prior studies have shown correlations between the overexpression or underexpression of long non-coding RNAs and human disease processes, but few studies have so far investigated the specific molecular basis of the interactions between long non-coding RNAs and proteins and how the binding of these factors can control cellular functions. Human long non-coding RNAs with known functions include Xist, Malat1, and Gas5. Using a quantitative stable isotope labeling proteomics analysis method and RNA antisense capture techniques, direct and specific molecular interactions were identified between long non-coding RNAs and their protein partners compared to control cellular RNAs. The results reveal that each long non-coding RNA has a specific set of protein interaction partners required for its function in the cell. We use electrophoretic mobility shift assays and competitive inhibition experiments to determine the binding specificity and affinity for novel non-coding RNA and protein interactions. Competitive binding of lncRNA fragments and controls are used to determine the specificity of protein interactions and compare the affinity of canonical RNA-binding domains for individual long non-coding RNAs.<br/>

Biochemical and molecular approaches to identify the specificity of long non-coding RNA and protein interactions

2019 Fall National Meeting

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