ArticleNucleic acids research2013
Transcriptome-wide expansion of non-coding regulatory switches: evidence from co-occurrence of Alu exonization, antisense and editing.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 36 citations in OpenAlex.
- A 280 bp SINE insertion within the pig PLA2G16 could potentially modify gene expression through integration with its transcript.Journal of applied genetics · 2025Article
- Recent insights into crosstalk between genetic parasites and their host genome.Briefings in functional genomics · 2024Review
- Alu RNA fold links splicing with signal recognition particle proteins.Nucleic acids research · 2023Article
- Exonized Alu repeats in the 3'UTR of a CYP20A1_Alu-LT transcript act as a miRNA sponge.BMC research notes · 2023Article
- The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology.International journal of molecular sciences · 2022Review
- The 'Alu-ome' shapes the epigenetic environment of regulatory elements controlling cellular defense.Nucleic acids research · 2022Article
- Article
- Antisense RNAs during early vertebrate development are divided in groups with distinct features.Genome research · 2021Article
- Multiple Alu Exonization in 3'UTR of a Primate-Specific Isoform of CYP20A1 Creates a Potential miRNA Sponge.Genome biology and evolution · 2021Article
- The angiotensin-I-converting enzyme insertion/deletion in polymorphic element codes for an AluYa5 RNA that downregulates gene expression.The pharmacogenomics journal · 2018Review
- Natural antisense transcripts drive a regulatory cascade controlling c-MYC transcription.RNA biology · 2017Article
- Frequency of Alu insertions within the ACE and PR loci in Northwestern Mexicans.BMC research notes · 2017Article
- Identification of RNA Polymerase III-Transcribed SINEs at Single-Locus Resolution from RNA Sequencing Data.Non-coding RNA · 2017Review
- Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection.Scientific reports · 2016Article
- Retrotransposon-associated long non-coding RNAs in mice and men.Pflugers Archiv : European journal of physiology · 2016Review
- Alu Elements as Novel Regulators of Gene Expression in Type 1 Diabetes Susceptibility Genes?Genes · 2015Article
- The RNA-centred view of the synapse: non-coding RNAs and synaptic plasticity.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2014Review
- One hundred million adenosine-to-inosine RNA editing sites: hearing through the noise.BioEssays : news and reviews in molecular, cellular and developmental biology · 2014Article
- The persistent contributions of RNA to eukaryotic gen(om)e architecture and cellular function.Cold Spring Harbor perspectives in biology · 2014Review
- Physiology of the read-write genome.The Journal of physiology · 2014Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Non-coding RNAs from transposable elements of human genome are gaining prominence in modulating transcriptome dynamics. Alu elements, as exonized, edited and antisense components within same transcripts could create novel regulatory switches in response to different transcriptional cues. We provide the first evidence for co-occurrences of these events at transcriptome-wide scale through integrative analysis of data sets across diverse experimental platforms and tissues. This involved the following: (i) positional anchoring of Alu exonization events in the UTRs and CDS of 4663 transcript isoforms from RefSeq mRNAs and (ii) mapping on to them A→I editing events inferred from ∼7 million ESTs from dbEST and antisense transcripts identified from virtual serial analysis of gene expression tags represented in Cancer Genome Anatomy Project next-generation sequencing data sets across 20 tissues. We observed significant enrichment of these events in the 3'UTR as well as positional preference within the embedded Alus. More than 300 genes had co-occurrence of all these events at the exon level and were significantly enriched in apoptosis and lysosomal processes. Further, we demonstrate functional evidence of such dynamic interactions between Alu-mediated events in a time series data from Integrated Personal Omics Profiling during recovery from a viral infection. Such 'single transcript-multiple fate' opportunity facilitated by Alu elements may modulate transcriptional response, especially during stress.
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