Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles

Long INterspersed Elements (LINE-1s, L1s) are responsible for over one million retrotransposon insertions and 8000 processed pseudogenes (PPs) in the human genome. An active L1 encodes two proteins (ORF1p and ORF2p) that bind with L1 RNA and form L1-ribonucleoprotein particles (RNPs). Although it is...

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Bibliographic Details
Published in:Human molecular genetics 2013-09, Vol.22 (18), p.3730-3748
Main Authors: Mandal, Prabhat K, Ewing, Adam D, Hancks, Dustin C, Kazazian, Jr, Haig H
Format: Article
Language:English
Subjects:
Gene Expression
HEK293 Cells
High-Throughput Nucleotide Sequencing
Humans
Long Interspersed Nucleotide Elements - genetics
Open Reading Frames
Pseudogenes
Retroelements
Ribonucleoproteins - genetics
Ribonucleoproteins - metabolism
RNA - genetics
RNA - metabolism
RNA-Binding Proteins - genetics
RNA-Binding Proteins - metabolism
RNA-Directed DNA Polymerase - genetics
RNA-Directed DNA Polymerase - metabolism
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Summary:Long INterspersed Elements (LINE-1s, L1s) are responsible for over one million retrotransposon insertions and 8000 processed pseudogenes (PPs) in the human genome. An active L1 encodes two proteins (ORF1p and ORF2p) that bind with L1 RNA and form L1-ribonucleoprotein particles (RNPs). Although it is believed that the RNA-binding property of ORF1p is critical to recruit other mobile RNAs to the RNP, the identity of recruited RNAs is largely unknown. Here, we used crosslinking and immunoprecipitation followed by deep sequencing to identify RNA components of L1-RNPs. Our results show that in addition to retrotransposed RNAs [L1, Alu and SINE-VNTR-Alu (SVA)], L1-RNPs are enriched with cellular mRNAs, which have PPs in the human genome. Using purified L1-RNPs, we show that PP-source RNAs preferentially serve as ORF2p templates in a reverse transcriptase assay. In addition, we find that exogenous ORF2p binds endogenous ORF1p, allowing reverse transcription of the same PP-source RNAs. These data demonstrate that interaction of a cellular RNA with the L1-RNP is an inside track to PP formation.
ISSN:0964-6906
1460-2083
DOI:10.1093/hmg/ddt225