ArticleBMC genomics2016
Conserved 3' UTR stem-loop structure in L1 and Alu transposons in human genome: possible role in retrotransposition.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Characterization of Hairpin Loops and Cruciforms Across 118,019 Genomes Spanning the Tree of Life.Genome biology and evolution · 2026Article
- Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication.Microbiology and molecular biology reviews : MMBR · 2022Review
- The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology.International journal of molecular sciences · 2022Review
- Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites.RNA biology · 2021Article
- Widespread Exaptation of L1 Transposons for Transcription Factor Binding in Breast Cancer.International journal of molecular sciences · 2021Article
- Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation.Development (Cambridge, England) · 2020Review
- Recognition of 3'-end L1, Alu, processed pseudogenes, and mRNA stem-loops in the human genome using sequence-based and structure-based machine-learning models.Scientific reports · 2019Article
- Structure, clustering and functional insights of repeats configurations in the upstream promoter region of the human coding genes.BMC genomics · 2018Article
- LINE- and Alu-containing genomic instability hotspot at 16q24.1 associated with recurrent and nonrecurrent CNV deletions causative for ACDMPV.Human mutation · 2018Article
- Biology ofCurrent genomics · 2018Article
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2 authors.
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Abstract
backgroundIn the process of retrotransposition LINEs use their own machinery for copying and inserting themselves into new genomic locations, while SINEs are parasitic and require the machinery of LINEs. The exact mechanism of how a LINE-encoded reverse transcriptase (RT) recognizes its own and SINE RNA remains unclear. However it was shown for the stringent-type LINEs that recognition of a stem-loop at the 3'UTR by RT is essential for retrotransposition. For the relaxed-type LINEs it is believed that the poly-A tail is a common recognition element between LINE and SINE RNA. However polyadenylation is a property of any messenger RNA, and how the LINE RT recognizes transposon and non-transposon RNAs remains an open question. It is likely that RNA secondary structures play an important role in RNA recognition by LINE encoded proteins.
resultsHere we selected a set of L1 and Alu elements from the human genome and investigated their sequences for the presence of position-specific stem-loop structures. We found highly conserved stem-loop positions at the 3'UTR. Comparative structural analyses of a human L1 3'UTR stem-loop showed a similarity to 3'UTR stem-loops of the stringent-type LINEs, which were experimentally shown to be recognized by LINE RT. The consensus stem-loop structure consists of 5-7 bp loop, 8-10 bp stem with a bulge at a distance of 4-6 bp from the loop. The results show that a stem loop with a bulge exists at the 3'-end of Alu. We also found conserved stem-loop positions at 5'UTR and at the end of ORF2 and discuss their possible role.
conclusionsHere we presented an evidence for the presence of a highly conserved 3'UTR stem-loop structure in L1 and Alu retrotransposons in the human genome. Both stem-loops show structural similarity to the stem-loops of the stringent-type LINEs experimentally confirmed as essential for retrotransposition. Here we hypothesize that both L1 and Alu RNA are recognized by L1 RT via the 3'-end RNA stem-loop structure. Other conserved stem-loop positions in L1 suggest their possible functions in protein-RNA interactions but to date no experimental evidence has been reported.
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