U6 snRNA Pseudogenes: Markers of Retrotransposition Dynamics in Mammals

Molecular Biology and Evolution
Aurélien J DoucetNicolas Gilbert

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 serv...Continue Reading

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Citations

May 10, 2016·Mobile DNA·Dustin C Hancks, Haig H Kazazian
Apr 14, 2017·Viruses·Magdalena Regina Kubiak, Izabela Makałowska
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Dec 6, 2020·Proceedings of the National Academy of Sciences of the United States of America·Katsumi YamaguchiHaig H Kazazian

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Datasets Mentioned

BETA
M14486

Methods Mentioned

BETA
immunoprecipitation
2′-phosphotransferase

Software Mentioned

BLAST ( Basic Local Alignment Search Tool
Apache
EMBOSS wordmatch
JQuery
ProRNAScan
WebLogo
BLAST
Ensembl
EMBOSS
Ajax

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