Abstract
Transposable elements comprise more than 45% of the human genome and long interspersed nuclear element 1 (LINE-1 or L1) is the only autonomous mobile element remaining active. Since its identification, it has been proposed that L1 contributes to the mobilization and amplification of other cellular RNAs and more recently, experimental demonstrations of this function has been described for many transcripts such as Alu, a nonautonomous mobile element, cellular mRNAs, or small noncoding RNAs. Detailed examination of the mobilization of various cellular RNAs revealed distinct pathways by which they could be recruited during retrotransposition; template choice or template switching. Here, by analyzing genomic structures and retrotransposition signatures associated with small nuclear RNA (snRNA) sequences, we identified distinct recruiting steps during the L1 retrotransposition cycle for the formation of snRNA-processed pseudogenes. Interestingly, some of the identified recruiting steps take place in the nucleus. Moreover, after comparison to other vertebrate genomes, we established that snRNA amplification by template switching is common to many LINE families from several LINE clades. Finally, we suggest that U6 snRNA copies can serve as markers of L1 retrotransposition dynamics in mammalian genomes.
Highlights
IntroductionKnown as transposons and retrotransposons, make up a large fraction of all eukaryotic genomes
Mobile elements, known as transposons and retrotransposons, make up a large fraction of all eukaryotic genomes
We identified 30-truncated small nuclear RNA (snRNA) pseudogenes that are followed by a poly(A) tract and flanked by Total Hitsa Hits Selectedb Hits Analyzed (TSD) (2 cases for U1, 1 for U5, and 2 for U6; all included in table 1, Poly(A))
Summary
Known as transposons and retrotransposons, make up a large fraction of all eukaryotic genomes. Non-LTR (long terminal repeat) retrotransposons are present in most eukaryotes and are divided into 28 clades based on phylogenetic analysis (Malik et al 1999; Eickbush and Malik 2002; Kapitonov et al 2009). L1 is believed to be the only autonomous mobile element remaining active, and it continues to have a mutagenic impact by various mechanisms including insertion, duplication, deletion, and recombination (Deininger et al 2003; Chen et al 2005; Babushok and Kazazian 2007; Jurka et al 2007; Muotri et al 2007; Cordaux and Batzer 2009; Xing et al 2009; Beck et al 2010; Ewing and Kazazian 2010; Huang et al 2010; Iskow et al 2010; O’Donnell and Burns 2010; Baillie et al 2011). Human endogenous retrovirus-K (HERV-K), an LTR retrotransposon, may theoretically be active as functional copies have the potential to exist in individual genomes (Dewannieux et al 2006; Ruprecht et al 2008; Hohn et al 2013)
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