GSE62416
Transcriptome analysis in mouse late spermatocyte deficient in pachytene piRNAs (MIWI-immunoprecipitated RNAs)
The eukaryotic genome has vast intergenic regions containing transposons, pseudogenes and other repetitive sequences. They produce numerous long non-coding RNAs (lncRNAs) and PIWI-interacting RNAs (piRNAs), yet the functions of the vast intergenic regions remain largely unknown. Mammalian piRNAs are abundantly expressed in late spermatocytes and round spermatids. Their expression coincides with the widespread expression of lncRNAs from the genome of these cells. Here, we show that piRNAs mediate the degradation of a large number of mRNAs and lncRNAs in mouse late spermatocytes. In particular, they have a large impact on the lncRNA transcriptome, as a quarter of lncRNAs expressed in late spermatocytes are upregulated in mice deficient in piRNA pathway. Furthermore, our genomic and in vivo functional analyses reveal that retrotransposon sequences in the 3´UTR of mRNAs are potentially targeted by piRNAs for degradation. Similarly, a large number of spermatogenic cell-specific lncRNAs are degraded by piRNAs via retrotransposon sequences. Moreover, we show that pseudogenes regulate mRNA stability via the piRNA pathway. The degradation of mRNAs and lncRNAs by piRNAs requires MIWI and, at least in part, depends on its slicer activity. Together, these findings reveal the presence of the highly complex and global RNA regulatory network mediated by piRNAs with retrotransposons and pseudogenes as regulatory sequences. Overall design: RNA-seq of MIWI-immunoprecipitated RNAs from Late spermatocytes in Miw+/-, MiwiADH/-, Miwi-/-