ArticleRNA (New York, N.Y.)2016
The domain structure and distribution of Alu elements in long noncoding RNAs and mRNAs.
Article in RNA (New York, N.Y.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
19 citing papers in PubMed, 29 citations in OpenAlex.
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- A sequence context-based approach for classifying tumor structural variants without paired normal samples.Cell reports methods · 2025Article
- Comparison of germline and somatic structural variants in cancers reveal systematic differences in variant generating and selection processes.bioRxiv : the preprint server for biology · 2024Article
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- Strand asymmetries across genomic processes.Computational and structural biotechnology journal · 2023Review
- Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-CodingNon-coding RNA · 2022Article
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- Pseudogene ACTBP2 increases blood-brain barrier permeability by promoting KHDRBS2 transcription through recruitment of KMT2D/WDR5 in AβCell death discovery · 2021Article
- Retrotransposons as Drivers of Mammalian Brain Evolution.Life (Basel, Switzerland) · 2021Review
- Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences.Nucleic acids research · 2021Article
- PABPC1-induced stabilization of BDNF-AS inhibits malignant progression of glioblastoma cells through STAU1-mediated decay.Cell death & disease · 2020Article
- An IntronicFrontiers in genetics · 2020Article
- Roles of Transposable Elements in the Different Layers of Gene Expression Regulation.International journal of molecular sciences · 2019Review
- Article
- Cytokines and Long Noncoding RNAs.Cold Spring Harbor perspectives in biology · 2018Review
- Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1.Scientific reports · 2018Article
- Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Immunobiology of Long Noncoding RNAs.Annual review of immunology · 2017Review
- ALS and FTD: an epigenetic perspective.Acta neuropathologica · 2016Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Approximately 75% of the human genome is transcribed and many of these spliced transcripts contain primate-specific Alu elements, the most abundant mobile element in the human genome. The majority of exonized Alu elements are located in long noncoding RNAs (lncRNAs) and the untranslated regions of mRNA, with some performing molecular functions. To further assess the potential for Alu elements to be repurposed as functional RNA domains, we investigated the distribution and evolution of Alu elements in spliced transcripts. Our analysis revealed that Alu elements are underrepresented in mRNAs and lncRNAs, suggesting that most exonized Alu elements arising in the population are rare or deleterious to RNA function. When mRNAs and lncRNAs retain exonized Alu elements, they have a clear preference for Alu dimers, left monomers, and right monomers. mRNAs often acquire Alu elements when their genes are duplicated within Alu-rich regions. In lncRNAs, reverse-oriented Alu elements are significantly enriched and are not restricted to the 3' and 5' ends. Both lncRNAs and mRNAs primarily contain the Alu J and S subfamilies that were amplified relatively early in primate evolution. Alu J subfamilies are typically overrepresented in lncRNAs, whereas the Alu S dimer is overrepresented in mRNAs. The sequences of Alu dimers tend to be constrained in both lncRNAs and mRNAs, whereas the left and right monomers are constrained within particular Alu subfamilies and classes of RNA. Collectively, these findings suggest that Alu-containing RNAs are capable of forming stable structures and that some of these Alu domains might have novel biological functions.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.