SynthesisGenome biology2014
Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions.
Synthesis in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
60 citing papers in PubMed, 98 citations in OpenAlex.
- Review
- Genomic sequence evolution underlying human neocortical interareal diversification.Genome biology · 2026Article
- Transposable Element Dysregulation in Hepatocellular Carcinoma: Epigenetic Mechanisms, Immune Remodeling, and Translational Opportunities.Journal of hepatocellular carcinoma · 2026Review
- Alternative splicing: from tumorigenesis to neoantigen-mediated cancer immunotherapy.Biomarker research · 2025Review
- A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types.Nature communications · 2025Article
- Transposable element expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineages.Nature communications · 2025Article
- Conserved structured domains in plant non-coding RNA enod40, their evolution and recruitment of sequences from transposable elements.NAR genomics and bioinformatics · 2023Article
- TDP-43 Epigenetic Facets and Their Neurodegenerative Implications.International journal of molecular sciences · 2023Review
- Review
- Overview of mJournal of cancer research and clinical oncology · 2023Review
- Long non-coding RNAs: definitions, functions, challenges and recommendations.Nature reviews. Molecular cell biology · 2023Review
- Generalized nuclear localization of retroelement transcripts.Mobile DNA · 2022Article
- Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Transposable Elements in Pluripotent Stem Cells and Human Disease.Frontiers in genetics · 2022Review
- The control of polycomb repressive complexes by long noncoding RNAs.Wiley interdisciplinary reviews. RNA · 2021Review
- Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells.Nucleic acids research · 2021Article
- Binding patterns of RNA-binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements.NAR genomics and bioinformatics · 2021Article
- CircRNAs and their regulatory roles in cancers.Molecular medicine (Cambridge, Mass.) · 2021Review
- HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness.eLife · 2021Article
- Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundTransposable elements (TEs) have significantly influenced the evolution of transcriptional regulatory networks in the human genome. Post-transcriptional regulation of human genes by TE-derived sequences has been observed in specific contexts, but has yet to be systematically and comprehensively investigated. Here, we study a collection of 75 CLIP-Seq experiments mapping the RNA binding sites for a diverse set of 51 human proteins to explore the role of TEs in post-transcriptional regulation of human mRNAs and lncRNAs via RNA-protein interactions.
resultsWe detect widespread interactions between RNA binding proteins (RBPs) and many families of TE-derived sequence in the CLIP-Seq data. Further, alignment coverage peaks on specific positions of the TE consensus sequences, illuminating a diversity of TE-specific RBP binding motifs. Evidence of binding and conservation of these motifs in the nonrepetitive transcriptome suggests that TEs have generally appropriated existing sequence preferences of the RBPs. Depletion assays for numerous RBPs show that TE-derived binding sites affect transcript abundance and splicing similarly to nonrepetitive sites. However, in a few cases the effect of RBP binding depends on the specific TE family bound; for example, the ubiquitously expressed RBP HuR confers transcript stability unless bound to an Alu element.
conclusionsOur meta-analysis suggests a widespread role for TEs in shaping RNA-protein regulatory networks in the human genome.
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Registered trials
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.