title: Functional repeat-derived RNAs often originate from retrotransposon-propagated ncRNAs.
abstract: The human genome is scattered with repetitive sequences, and the ENCODE project revealed that 60-70% of the genomic DNA is transcribed into RNA. As a consequence, the human transcriptome contains a large portion of repeat-derived RNAs (repRNAs). Here, we present a hypothesis for the evolution of novel functional repeat-derived RNAs from non-coding RNAs (ncRNAs) by retrotransposition. Upon amplification, the ncRNAs can diversify in sequence and subsequently evolve new activities, which can result in novel functions. Non-coding transcripts derived from highly repetitive regions can therefore serve as a reservoir for the evolution of novel functional RNAs. We base our hypothetical model on observations reported for short interspersed nuclear elements derived from 7SL RNA and tRNAs, α satellites derived from snoRNAs and SL RNAs derived from U1 small nuclear RNA. Furthermore, we present novel putative human repeat-derived ncRNAs obtained by the comparison of the Dfam and Rfam databases, as well as several examples in other species. We hypothesize that novel functional ncRNAs can derive also from other repetitive regions and propose Genomic SELEX as a tool for their identification.
authors.affiliation: Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Matylla-Kulinska
authors.forename: Hakim
authors.initials: H
authors.lastname: Tafer
authors.forename: Adam
authors.initials: A
authors.lastname: Weiss
authors.forename: Renée
authors.initials: R
authors.lastname: Schroeder
mesh_terms: D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D019244:RNA, Satellite / Q000235:genetics; D020733:RNA, Small Cytoplasmic / Q000235:genetics; D012342:RNA, Small Nuclear / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics*; D018626:Retroelements / Q000235:genetics*; D018271:Signal Recognition Particle / Q000235:genetics
chemical_list: C115990:7SL RNA; D019244:RNA, Satellite; D020733:RNA, Small Cytoplasmic; D012342:RNA, Small Nuclear; D022661:RNA, Untranslated; D018626:Retroelements; D018271:Signal Recognition Particle; C405483:U1 small nuclear RNA; D012343:RNA, Transfer