Deep Sequencing Reveals Unique Small RNA Repertoire that are regulated during head regeneration in the Cnidarian Hydra magnipapillata

Small noncoding RNAs such as miRNAs, piRNAs and endo-siRNAs fine tune gene expression and regulate many cellular processes like development, differentiation, cell cycle, self renewal regeneration and protection against genomic pathogens through post-transcriptional regulation. Hydra is a cnidarian model system with robust regenerative capacity. In this study we have profiled small noncoding RNAs in Hydra magnipapillata and have investigated changes in small RNA expression pattern during head regeneration. Deep sequencing of hydra small RNA libraries reveals a unique repertoire of small RNAs in hydra. We have identified 129 miRNA loci in hydra; 126 of these miRNAs are unique to hydra and less than 50% are conserved across two different strains of H. vulgaris tested in this study, indicating a highly dynamic nature of hydra miRNAs. We have also identified siRNAs that have precursors with perfect stem loop structure and arise from inverted repeats. The most abundant small RNAs in hydra are piRNAs and they map to transposable elements, annotated transcriptome as well as unique noncoding regions on the genome. A significant number of piRNAs that map to transposable elements and annotated transcriptome have ping-pong signature suggesting this mechanism of piRNA biosynthesis arose early in evolution. Further, we also identified miRNAs and piRNAs that are differentially expressed during hydra head regeneration. Our study elaborates different classes of small RNAs, which might have a potential role in orchestrating the gene expression essential for hydra regeneration.