A retroelement-derived mammalian ARC protein exhibits selective RNA recognition and nucleic acid chaperone functions

Activity-regulated cytoskeleton-associated protein (ARC) is an RNA-binding protein that also serves as a central hub for neuronal protein-protein interactions. It is essential for intercellular signaling and contributes to synaptic plasticity. ARC includes Gag-like sequences of Ty3/Gypsy retrotransposons and retains the ability to self-assemble into capsid-like structures containing Arc mRNA. Here, we employ an integrative approach to provide the first detailed in vitro analysis of ARC-RNA interactions. Using quantitative binding assays, RNA structure mapping, and ribonucleoprotein (RNP) footprinting, complemented by extensive computational analyses, we identified Arc mRNA regions specifically and non-specifically bound by ARC, as well as ARC amino acid residues involved in RNA interactions. We show that ARC recognizes RNA sequence and structure. A specific GC-rich motif is common to all bound RNA sequences, and the binding preferentially occurs near highly stable, solvent-exposed helices in the 5' region of Arc mRNA. Surprisingly, the conserved coding sequence seems more relevant to binding specificity than the 5'-untranslated region. Our predictions suggest that ARC binding to RNA through positively charged regions of matrix and capsid domains exposes an oligomerization motif, enhancing binding cooperativity. We also provide evidence that ARC acts as a nucleic acid chaperone and can locally destabilize Arc mRNA structure.