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

This project aims to characterize the structural features of Arc mRNA and its derived transcripts (F1, F1delhUTR, and F1delUTR), along with their interactions with rat ARC protein. High-resolution structural information for RNA in both unbound and protein-bound states was obtained using SHAPE-MaP technology. In brief, RNA was modified with the SHAPE reagent (NAI-treated samples) or mock-treated with DMSO (DMSO-treated samples). After modification, SHAPE adduct locations were detected by reverse transcription with specific primers and mutational profiling (MaP), an error-prone reverse transcription method. Then, samples were converted into sequencing libraries and sequenced on the PE250 or PE150 Illumina system. Experiments were performed with two biological replicates (rep1, rep2). To achieve sufficient sequencing depth in some cases, 2-3 rounds of library sequencing were performed. The resulting data provide valuable insights into the conformational dynamics of RNA, its modulation upon protein binding, and the identification of protein-binding sites.