Global analysis of RNA secondary structure conservation between two metazoans. Global analysis of RNA secondary structure conservation between two metazoans

The secondary structure of RNA is necessary for its maturation, regulation, and processing. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we identify evolutionarily conserved features of RNA secondary structure in metazoans by applying our high-throughput, sequencing-based, structure-mapping approach to Drosophila melanogaster and Caenorhabditis elegans. This analysis reveals key structural patterns across protein-coding transcripts that indicate RNA folding is influential to protein translation and microRNA-mediated targeting and/or regulation of mRNAs in animals. Additionally, we uncover a novel population of highly base-paired RNAs, many of which are likely functional, long, non-coding RNAs. Finally, we identify and characterize ~180 structural motifs of mRNAs that are under positive or negative selection in these metazoans, thereby revealing a large set of RNA structures that are likely functional. Overall, our findings highlight the significance of secondary structure within RNA molecules, and provide the first comprehensive evidence of widespread RNA secondary structure conservation in animals. Overall design: Double-stranded (dsRNA) specific RNA sequencing (dsRNA-seq) and single-stranded (ssRNA) specific RNA sequencing (ssRNA-seq) in Drosophila DL1 cells and C. elegans mixed stage N2 worms. Each of the four samples (dsRNA/Dmel, ssRNA/Dmel, dsRNA/Cel, and ssRNA/Cel) was sequenced separately on both Illumina GA-IIx and Hiseq2000, giving a total of eight datasets. Two corresponding smRNA libraries (smRNA-seq) of the same DL1 cells and mixed stage N2 worms are also presented.