ArticlePloS one2016
Novel Role of 3'UTR-Embedded Alu Elements as Facilitators of Processed Pseudogene Genesis and Host Gene Capture by Viral Genomes.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Transposable element expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineages.Nature communications · 2025Article
- Identification of a minimal Alu domain required for retrotransposition.Nucleic acids research · 2025Article
- Human cytomegalovirus harnesses host L1 retrotransposon for efficient replication.Nature communications · 2024Article
- SARS-CoV-2 helicase might interfere with cellular nonsense-mediated RNA decay: insights from a bioinformatics study.BMC genomic data · 2023Article
- ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements.Nucleic acids research · 2023Article
- TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments.Bioinformatics (Oxford, England) · 2022Article
- Discovery of the first PD-1 ligand encoded by a pathogen.Frontiers in immunology · 2022Article
- A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients.Nature communications · 2021Article
- How Chaotic Is Genome Chaos?Cancers · 2021Review
- Divergent Traits and Ligand-Binding Properties of the Cytomegalovirus CD48 Gene Family.Viruses · 2020Article
- Subversion of natural killer cell responses by a cytomegalovirus-encoded soluble CD48 decoy receptor.PLoS pathogens · 2019Article
- Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts.Computational and structural biotechnology journal · 2019Review
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Authors and funding
3 authors.
Funding
Abstract
Since the discovery of the high abundance of Alu elements in the human genome, the interest for the functional significance of these retrotransposons has been increasing. Primate Alu and rodent Alu-like elements are retrotransposed by a mechanism driven by the LINE1 (L1) encoded proteins, the same machinery that generates the L1 repeats, the processed pseudogenes (PPs), and other retroelements. Apart from free Alu RNAs, Alus are also transcribed and retrotranscribed as part of cellular gene transcripts, generally embedded inside 3' untranslated regions (UTRs). Despite different proposed hypotheses, the functional implication of the presence of Alus inside 3'UTRs remains elusive. In this study we hypothesized that Alu elements in 3'UTRs could be involved in the genesis of PPs. By analyzing human genome data we discovered that the existence of 3'UTR-embedded Alu elements is overrepresented in genes source of PPs. In contrast, the presence of other retrotransposable elements in 3'UTRs does not show this PP linked overrepresentation. This research was extended to mouse and rat genomes and the results accordingly reveal overrepresentation of 3'UTR-embedded B1 (Alu-like) elements in PP parent genes. Interestingly, we also demonstrated that the overrepresentation of 3'UTR-embedded Alus is particularly significant in PP parent genes with low germline gene expression level. Finally, we provide data that support the hypothesis that the L1 machinery is also the system that herpesviruses, and possibly other large DNA viruses, use to capture host genes expressed in germline or somatic cells. Altogether our results suggest a novel role for Alu or Alu-like elements inside 3'UTRs as facilitators of the genesis of PPs, particularly in lowly expressed genes. Moreover, we propose that this L1-driven mechanism, aided by the presence of 3'UTR-embedded Alus, may also be exploited by DNA viruses to incorporate host genes to their viral genomes.
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