Stable, intronic RNAs explain preservation of introns in Cyanidioschyzon merolae

Despite recent work identifying functional roles for introns, we lack a broad understanding of why some introns are preserved while others are removed. Here, we use the thermophilic red alga, Cyanidioschyzon merolae, as a model to investigate why only 39 of the approximately 2000 ancestral introns were preserved in this lineage. We observe that 23 of the 39 introns encode stable RNAs, 11 of which represent a novel class of non-coding RNA (ncRNA), which we call stable intronically-encoded RNAs (sieRNAs). These novel ncRNAs are expressed constitutively under normal growth conditions and are conserved in other extremophilic algae. One sieRNA, Q270, is predicted to stabilize a chloroplast polycistronic transcript encoding 17 ribosomal protein genes through direct antisense base pairing. Strikingly, all sieRNAs are polyadenylated under heat stress with long tails ranging from 50-200 nucleotides long, linking them to a potential heat stress response that may be critical for heat adaptation. Furthermore, DMS-MaP chemical probing revealed that some sieRNAs contain three-way junctions, a common RNA regulatory element, while others undergo accessibility shifts between in vivo and in vitro conditions, indicative of cellular interactions. Our findings suggest that introns in C. merolae are preserved to encode ncRNAs and suggest that introns may serve as hosts for regulatory RNAs across eukaryotes.