Global characterization and target identification of piRNAs and endo-siRNAs in mouse gametes and zygotes

•The expression profiles of rasRNAs are different in oocytes and spermatozoa.•The major piRNA group found in gametes was derived from tRNA and rRNA processing.•mRNAs are identified as potential targets of piRNAs in gametes and zygotes.•The “ping-pong” amplification of piRNAs is not restricted to male gametogenesis.

A set of small RNAs known as rasRNAs (repeat-associated small RNAs) have been related to the down-regulation of Transposable Elements (TEs) to safeguard genome integrity. Two key members of the rasRNAs group are piRNAs and endo-siRNAs. We have performed a comparative analysis of piRNAs and endo-siRNAs present in mouse oocytes, spermatozoa and zygotes, identified by deep sequencing and bioinformatic analysis. The detection of piRNAs and endo-siRNAs in the spermatozoa and revealed also in zygotes, hints to their potential delivery to oocytes during fertilization. However, a comparative assessment of the three cell types indicates that both piRNAs and endo-siRNAs are mainly maternally inherited. Finally, we have assessed the role of the different rasRNA molecules in connection with amplification processes by way of the “ping-pong cycle”. Our results suggest that the ping-pong cycle can act on other rasRNAs, such as tRNA- and rRNA-derived fragments, thus not only being restricted to TEs during gametogenesis.