We profiled the transcriptome of mouse and hamster oocytes. RNA-seq of mouse and hamster oocyte and early development

Retrotransposons are “copy-and-paste” insertional mutagens substantially contributing to the mammalian genome content. Many retrotransposons carry long terminal repeats (LTRs), which function during retrovirus-like reverse transcription and integration into the genome. We report an extraordinary impact of LTRs from the mammalian endogenous retrovirus-related (ERVL) family on gene expression in the germline and beyond. Most importantly, we identified 872 ERVL LTRs resembling a mobile gene remodeling platform supplying a promoter together with the first exons. ERVL LTRs activate transcription in a developmental stage-specific manner, alter protein-coding sequences, create novel non-coding RNAs or even support evolution of novel protein-coding genes. We also identified ERVL LTR-mediated gene remodeling in hamster, human and bovine oocytes. Thus, ERVL LTRs intertwine with mammalian gene regulation and genome evolution in such a unique and complex way that they appear as an integral functional part of genome evolution rather than dangerous parasites.