title: U6 snRNA Pseudogenes: Markers of Retrotransposition Dynamics in Mammals.
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.
authors.affiliation: Institut de Génétique Humaine, CNRS, UPR 1142, Montpellier, France Institute for Research on Cancer and Aging, Nice (IRCAN), INSERM, U1081, CNRS UMR 7284, Nice, France.
authors.forename: Aurélien J
authors.initials: AJ
authors.lastname: Doucet
authors.affiliation: Institut de Génétique Humaine, CNRS, UPR 1142, Montpellier, France Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), UMR AGAP, Montpellier, France.
authors.forename: Gaëtan
authors.initials: G
authors.lastname: Droc
authors.affiliation: Institut de Génétique Humaine, CNRS, UPR 1142, Montpellier, France Institut de Génétique Humaine, CNRS, UPR 1142, Montpellier, France.
authors.forename: Oliver
authors.initials: O
authors.lastname: Siol
authors.affiliation: Institute for Regenerative Medicine and Biotherapy, INSERM, U1183, Montpellier, France.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Audoux
authors.affiliation: Institut de Génétique Humaine, CNRS, UPR 1142, Montpellier, France Institute for Regenerative Medicine and Biotherapy, INSERM, U1183, Montpellier, France nicolas.gilbert@inserm.fr.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Gilbert
mesh_terms: D000818:Animals; D001483:Base Sequence; D015894:Genome, Human; D006801:Humans; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics; D008322:Mammals / Q000235:genetics*; D008969:Molecular Sequence Data; D026723:Polyadenylation / Q000235:genetics; D011544:Pseudogenes / Q000235:genetics*; D012342:RNA, Small Nuclear / Q000235:genetics*; D018626:Retroelements / Q000235:genetics*; D013698:Templates, Genetic
chemical_list: D012342:RNA, Small Nuclear; D018626:Retroelements; C405486:U6 small nuclear RNA
keywords: long interspersed nuclear element; retrotransposon; small nuclear RNA