ArticleGenome biology2007
Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 140 papers.
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140 citing papers in PubMed, 233 citations in OpenAlex.
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- Analysis of a Novel Human Protein, ORF3, Encoded by Spacer rDNA.Journal of molecular evolution · 2025Article
- Reactivation of retrotransposable elements is associated with environmental stress and ageing.Nature reviews. Genetics · 2025Review
- Charting the regulatory landscape of TP53 on transposable elements in cancer.Genome research · 2025Article
- Transposon-derived introns as an element shaping the structure of eukaryotic genomes.Mobile DNA · 2024Review
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- Recent insights into crosstalk between genetic parasites and their host genome.Briefings in functional genomics · 2024Review
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- Alu RNA fold links splicing with signal recognition particle proteins.Nucleic acids research · 2023Article
- Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana.Nature communications · 2023Article
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- Conserved microRNAs and Flipons Shape Gene Expression during Development by Altering Promoter Conformations.International journal of molecular sciences · 2023Article
- Distinct composition and amplification dynamics of transposable elements in sacred lotus (Nelumbo nucifera Gaertn.).The Plant journal : for cell and molecular biology · 2022Article
- Antisense Oligonucleotide Rescue of Deep-Intronic Variants Activating Pseudoexons in the 6-Pyruvoyl-Tetrahydropterin Synthase Gene.Nucleic acid therapeutics · 2022Article
- Meta-Analysis Suggests That Intron Retention Can Affect Quantification of Transposable Elements from RNA-Seq Data.Biology · 2022Article
- Article
- The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology.International journal of molecular sciences · 2022Review
80 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTransposed elements (TEs) have a substantial impact on mammalian evolution and are involved in numerous genetic diseases. We compared the impact of TEs on the human transcriptome and the mouse transcriptome.
resultsWe compiled a dataset of all TEs in the human and mouse genomes, identifying 3,932,058 and 3,122,416 TEs, respectively. We than extracted TEs located within human and mouse genes and, surprisingly, we found that 60% of TEs in both human and mouse are located in intronic sequences, even though introns comprise only 24% of the human genome. All TE families in both human and mouse can exonize. TE families that are shared between human and mouse exhibit the same percentage of TE exonization in the two species, but the exonization level of Alu, a primate-specific retroelement, is significantly greater than that of other TEs within the human genome, leading to a higher level of TE exonization in human than in mouse (1,824 exons compared with 506 exons, respectively). We detected a primate-specific mechanism for intron gain, in which Alu insertion into an exon creates a new intron located in the 3' untranslated region (termed 'intronization'). Finally, the insertion of TEs into the first and last exons of a gene is more frequent in human than in mouse, leading to longer exons in human.
conclusionOur findings reveal many effects of TEs on these two transcriptomes. These effects are substantially greater in human than in mouse, which is due to the presence of Alu elements in human.
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