ArticleGenome biology2020
Polymorphic mobile element insertions contribute to gene expression and alternative splicing in human tissues.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed, 39 citations in OpenAlex.
- Whole-genome sequencing implicates rare, low-frequency and structural non-coding variation at themedRxiv : the preprint server for health sciences · 2026Article
- Quantitative Control of Transposable Elements: From Genome Plasticity to Immune Regulatory Circuits.Cell biochemistry and function · 2026Review
- Inverted Alu repeats in loop-out exon skipping across hominoid evolution.Nucleic acids research · 2026Article
- Variability of transposable elements in six genetic isolates from North-Eastern Italy and their relationship with alcohol consumption, tobacco use and BMI.BMC genomics · 2025Article
- Diversity and consequences of structural variation in the human genome.Nature reviews. Genetics · 2025Review
- Polymorphic transposable elements contribute to variation in recombination landscapes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
- Construction of the porcine genome mobile element variations and investigation of its role in population diversity and gene expression.Journal of animal science and biotechnology · 2024Article
- Alternative splicing of transposable elements in human breast cancer.bioRxiv : the preprint server for biology · 2024Article
- Varying recombination landscapes between individuals are driven by polymorphic transposable elements.bioRxiv : the preprint server for biology · 2024Article
- Investigating mobile element variations by statistical genetics.Human genome variation · 2024Review
- Article
- Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue.Genetics · 2023Article
- Review
- The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation.Genome research · 2023Article
- Structural Variations Contribute to the Genetic Etiology of Autism Spectrum Disorder and Language Impairments.International journal of molecular sciences · 2023Article
- Article
- Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk.Nature genetics · 2023Article
- Evolutionarily recent retrotransposons contribute to schizophrenia.Translational psychiatry · 2023Article
- Evolutionarily recent retrotransposons contribute to schizophrenia.Research square · 2023Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundMobile elements are a major source of structural variants in the human genome, and some mobile elements can regulate gene expression and transcript splicing. However, the impact of polymorphic mobile element insertions (pMEIs) on gene expression and splicing in diverse human tissues has not been thoroughly studied. The multi-tissue gene expression and whole genome sequencing data generated by the Genotype-Tissue Expression (GTEx) project provide a great opportunity to systematically evaluate the role of pMEIs in regulating gene expression in human tissues.
resultsUsing the GTEx whole genome sequencing data, we identify 20,545 high-quality pMEIs from 639 individuals. Coupling pMEI genotypes with gene expression profiles, we identify pMEI-associated expression quantitative trait loci (eQTLs) and splicing quantitative trait loci (sQTLs) in 48 tissues. Using joint analyses of pMEIs and other genomic variants, pMEIs are predicted to be the potential causal variant for 3522 eQTLs and 3717 sQTLs. The pMEI-associated eQTLs and sQTLs show a high level of tissue specificity, and these pMEIs are enriched in the proximity of affected genes and in regulatory elements. Using reporter assays, we confirm that several pMEIs associated with eQTLs and sQTLs can alter gene expression levels and isoform proportions, respectively.
conclusionOverall, our study shows that pMEIs are associated with thousands of gene expression and splicing variations, indicating that pMEIs could have a significant role in regulating tissue-specific gene expression and transcript splicing. Detailed mechanisms for the role of pMEIs in gene regulation in different tissues will be an important direction for future studies.
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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.