ArticleGenome research2019
Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Article
- Uncertainty-aware benchmarking reveals ambiguous transcripts in mRNA-lncRNA classification.bioRxiv : the preprint server for biology · 2026Article
- LncRNA PVT1 in human cancers: genomic complexity, isoforms, functional elements, mechanism of action, subcellular localization and possible role as a therapeutic target.Molecular cancer · 2026Review
- Long noncoding RNA regulation of immunity.Nature immunology · 2026Review
- Transposable element expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineages.Nature communications · 2025Article
- The Regulatory Role of LncRNAs in Modulating Autophagy and Drug Resistance in Non-Small-Cell Lung Cancer: Focus on Targeted Therapeutic Approaches.Biomolecules · 2025Review
- Zygotic activation of transposable elements during zebrafish early embryogenesis.Nature communications · 2025Article
- Decoding subcellular RNA localization one molecule at a time.Genome biology · 2025Review
- Targeting and engineering long non-coding RNAs for cancer therapy.Nature reviews. Genetics · 2024Review
- The Human Developing Cerebral Cortex Is Characterized by an Elevated De Novo Expression of Long Noncoding RNAs in Excitatory Neurons.Molecular biology and evolution · 2024Article
- Selection on synonymous sites: the unwanted transcript hypothesis.Nature reviews. Genetics · 2024Review
- Functional identification of cis-regulatory long noncoding RNAs at controlled false discovery rates.Nucleic acids research · 2024Article
- Large-scale functional inference for skin-expressing lncRNAs using expression and sequence information.JCI insight · 2023Article
- Conserved structured domains in plant non-coding RNA enod40, their evolution and recruitment of sequences from transposable elements.NAR genomics and bioinformatics · 2023Article
- LncRNA ARGI Contributes to Virus-Induced Pancreatic β Cell Inflammation Through Transcriptional Activation of IFN-Stimulated Genes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Review
- A transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification.Cardiovascular research · 2023Article
- Tumour mutations in long noncoding RNAs enhance cell fitness.Nature communications · 2023Article
- Generalized nuclear localization of retroelement transcripts.Mobile DNA · 2022Article
- Developmental dynamics of RNA translation in the human brain.Nature neuroscience · 2022Article
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6 authors.
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Abstract
The sequence domains underlying long noncoding RNA (lncRNA) activities, including their characteristic nuclear enrichment, remain largely unknown. It has been proposed that these domains can originate from neofunctionalized fragments of transposable elements (TEs), otherwise known as RIDLs (repeat insertion domains of lncRNA), although just a handful have been identified. It is challenging to distinguish functional RIDL instances against a numerous genomic background of neutrally evolving TEs. We here show evidence that a subset of TE types experience evolutionary selection in the context of lncRNA exons. Together these comprise an enrichment group of 5374 TE fragments in 3566 loci. Their host lncRNAs tend to be functionally validated and associated with disease. This RIDL group was used to explore the relationship between TEs and lncRNA subcellular localization. By using global localization data from 10 human cell lines, we uncover a dose-dependent relationship between nuclear/cytoplasmic distribution and evolutionarily conserved L2b, MIRb, and MIRc elements. This is observed in multiple cell types and is unaffected by confounders of transcript length or expression. Experimental validation with engineered transgenes shows that these TEs drive nuclear enrichment in a natural sequence context. Together these data reveal a role for TEs in regulating the subcellular localization of lncRNAs.
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