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

Abstract

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.

Diversity and functional convergence of small noncoding RNAs in male germ cell differentiation and fertilization

“…This indicates that small RNAs derived from rRNA processing interact with PIWI proteins. The rRNA-derived piRNAs were highly accumulated in spermatozoa as we also previously reported (García-López et al 2014). Although some authors support that PIWI proteins and piRNAs are depleted in late spermatogenesis stages (Zhao et al 2013), others have hypothesized that spermatozoa piRNAs play important roles during fertilization and embryonic genome activation (Krawetz et al 2011).…”

“…This could imply cross-talk between translational and interfering pathways (Sobala and Hutvagner 2011). The alternative roles of some piRNAs as potential regulators of mRNAs have been recently reported (García-López et al 2014) and experimentally confirmed in species such as Aplysia (Rajasethupathy et al 2012) and silkworm (Kiuchi et al 2014). Some new examples of this convergent role and expanded function among diverse piRNAs are described here.…”

“…5). In general, germline rasRNAs have been included into two major categories: piRNAs and endo-siRNAs (Yang et al 2010;García-López et al 2014) sharing functions as safeguards of genome integrity but differing in their biogenesis pathways. First, we classified as piRNAs the small sequences detected by NGS identical to those previously reported in the RNA database (RNAdb) (Supplemental Fig.…”

Endo-siRNA deficiency results in oocyte maturation failure and apoptosis in porcine oocytes

“…Small RNAs are involved in RNA interference (RNAi) and include three classes: microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi interacting RNAs (piRNAs; García-López et al 2014). There are both endogenous siRNAs (endo-siRNAs) and exogenous siRNAs (exo-siRNAs).…”

RNA interference in early branching metazoans

“…Plants and brown algae also possess miRNA systems, however all three are considered analogous, having independently evolved following co-option of components of the shared eukaryotic endo-siRNA system (Jones- Rhoades et al 2006, Axtell et al 2011, Tarver et al 2012. Of the three RNAi systems, endo-siRNAs have received the least attention in animals, possibly due to their perceived lesser importance in vertebrates, although a renewed interest appears to be developing (Flemr et al 2013, Werner et al 2014, García-López et al 2014, Svoboda 2014. In fact, the capacity for artificial knockdown of target gene expression by hijacking the machinery of the endosiRNA pathway has long been known to be an effective strategy for experimental RNA interference in some vertebrate cell types (Wianny and Zernicka-Goetz 2000, Svoboda et al 2000, Elbashir et al 2001.…”