499robust RNAi in mouse (Svoboda et al. 2000 ; Wianny and Zernicka-Goetz 2000 ),
bovine (Paradis et al. 2005 ), porcine (Anger et al. 2004 ), and ovine (Yan et al.
2010 ) oocytes.
So far, the only evidence for functional importance of endogenous RNAi in
vertebrates comes from the mouse oocyte model, which represents a notable
exception in terms of siRNA biogenesis. Mouse oocytes express a unique trun-
cated Dicer isoform, which lacks the autoinhibitory N-terminal helicase domain
and is efficiently producing endo-siRNAs (Flemr et al. 2013 ). This Dicer isoform
evolved because of a retrotransposon insertion, which functions as an oocyte-
specific promoter and is found only in the Muridae family (Flemr et al. 2013 ). As
a consequence, mouse oocytes contain relatively high amounts of endo-siRNAs;
most of them are retrotransposon-derived, but many originate from processed
pseudogenes. The latter endo-siRNAs appear to functionally substitute for miR-
NAs in terms of regulation of endogenous genes (Tam et al. 2008 ; Watanabe
et al. 2008 ). Importantly, endo-siRNAs in mouse oocytes appear essential for
normal meiotic progression (Flemr et al. 2013 ; Tam et al. 2008 ; Watanabe et al.
2008 ; Kaneda et al. 2009 ). This likely reflects endo-siRNA-mediated mRNA
degradation during Phase 0 of clearance of maternal mRNAs (see also
Sect. 10.2.2.2). At the same time, the unique presence of the truncated Dicer
isoform in the Muridae family and rapid evolution of processed pseudogenes
suggest that an essential role for endogenous RNAi during meiotic maturation is
presumably restricted to mice and closely related species.
Taken together, except in the mouse model, endogenous RNAi in vertebrate
oocytes does not appear to be a significant pathway. Endo-siRNAs loaded on AGO
proteins do not have any known specific features, which would distinguish them
from miRNAs. Therefore, it is most likely that vertebrate maternal endo-siRNAs are
degraded together with miRNAs.
10.2.1.3 PIWI-Associated RNAs (piRNAs)
piRNAs are found mainly in germ cells. The piRNA pathway (reviewed in Weick
and Miska 2014 ) differs in several ways from miRNA/RNAi pathways. Briefly,
piRNA complex biogenesis involves PIWI proteins (a specific clade of Argonaute
protein family, which is expressed during gametogenesis) but not Dicer. piRNAs are
longer (24–30 nucleotides) than miRNAs, and they are chemically modified at their
3 ′ end by 2′O-methylation. piRNAs originate from distinct genomic regions and
come in two flavors—one represented by retrotransposon-derived piRNAs, which
help to maintain genome integrity. The second flavor is represented by piRNAs
derived from non-repetitive sequences; they are overrepresented in a unique piRNA
population called pachytene piRNAs, which are essential for spermatogenesis, but
their exact function is still being debated (Weick and Miska 2014 ).
piRNA pathway mutants often have sterile phenotypes, which underscore the
functional importance of piRNAs for germline development. In the zebrafish, PIWI
proteins are essential for both spermatogenesis and oogenesis (Houwing et al.
10 Clearance of Parental Products