Comparative profiling of sperm small RNAs in cnidarians highlights potential for paternal inheritance

Small RNAs in mature sperm are crucial regulators of gene expression following fertilization during early development in bilaterians. However, the presence and functions of sperm-derived small RNAs remain poorly understood in early-diverging (i.e., non-bilaterian) metazoans. In this study, we characterize three classes of small RNAs-microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and tRNA-derived RNAs (tDRs)-in sperm from three phylogenetically and ecologically distinct species from the early-diverging phylum Cnidaria: the sea anemone Nematostella vectensis, the temperate stony coral Astrangia poculata, and the reef-building tropical coral Acropora hyacinthus. All three classes of small RNAs examined were present in sperm from these cnidarians. Most miRNAs were species-specific; however, target prediction analysis revealed enriched putative targets involved in conserved developmental and signaling pathways. piRNAs overlapped with transposable elements and genic regions, indicating a potential dual role in genomic maintenance and gene expression regulation. Characterization of tDRs demonstrated that 5 prime-terminal fragments constituted the primary structural type across the three species, driven by high accumulation of specific isoacceptors including 5 prime-tDR-GlyGCC. Together, these findings provide the first evidence that cnidarian sperm carry a rich repertoire of small RNAs, including both conserved and species-specific types. Their presence suggests that paternal small RNAs contribute important regulatory information to the zygote in cnidarians, implicating paternal small RNAs as possible mediators of epigenetic inheritance in this early-branching metazoan phylum.