ArticleGenome biology and evolution2011
Effect of the transposable element environment of human genes on gene length and expression.
Article in Genome biology and evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
What it found
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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.
The trial behind it
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
21 citing papers in PubMed, 1 synthesis or guideline pooled it, 35 citations in OpenAlex.
- The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content.BMC biology · 2021Pooled it
- Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism.Genome biology and evolution · 2026Article
- Emerging Functions of the Repeat Genome in Nuclear Structure: A View from the Human Karyotype.Annual review of genomics and human genetics · 2025Review
- Rewiring of SINE-MIR enhancer topology and Esrrb modulation in expanded and naive pluripotency.Genome biology · 2025Article
- Article
- Spatial organization of transcribed eukaryotic genes.Nature cell biology · 2022Article
- ZNF768 links oncogenic RAS to cellular senescence.Nature communications · 2021Article
- The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality.Genome biology and evolution · 2021Article
- Review
- MIR sequences recruit zinc finger protein ZNF768 to expressed genes.Nucleic acids research · 2019Article
- Genome-Wide Identification of Microsatellites and Transposable Elements in the Dromedary Camel Genome Using Whole-Genome Sequencing Data.Frontiers in genetics · 2019Article
- Article
- MIR retrotransposon sequences provide insulators to the human genome.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Differential regulation of genes by retrotransposons in rice promoters.Plant molecular biology · 2015Article
- Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression.Mobile DNA · 2014Article
- Compound cis-regulatory elements with both boundary and enhancer sequences in the human genome.Bioinformatics (Oxford, England) · 2013Article
- Evolutionary rate of human tissue-specific genes are related with transposable element insertions.Genetica · 2012Article
- Gene properties and chromatin state influence the accumulation of transposable elements in genes.PloS one · 2012Article
- Transposon-derived and satellite-derived repetitive sequences play distinct functional roles in Mammalian intron size expansion.Evolutionary bioinformatics online · 2012Article
- Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Independent lines of investigation have documented effects of both transposable elements (TEs) and gene length (GL) on gene expression. However, TE gene fractions are highly correlated with GL, suggesting that they cannot be considered independently. We evaluated the TE environment of human genes and GL jointly in an attempt to tease apart their relative effects. TE gene fractions and GL were compared with the overall level of gene expression and the breadth of expression across tissues. GL is strongly correlated with overall expression level but weakly correlated with the breadth of expression, confirming the selection hypothesis that attributes the compactness of highly expressed genes to selection for economy of transcription. However, TE gene fractions overall, and for the L1 family in particular, show stronger anticorrelations with expression level than GL, indicating that GL may not be the most important target of selection for transcriptional economy. These results suggest a specific mechanism, removal of TEs, by which highly expressed genes are selectively tuned for efficiency. MIR elements are the only family of TEs with gene fractions that show a positive correlation with tissue-specific expression, suggesting that they may provide regulatory sequences that help to control human gene expression. Consistent with this notion, MIR fractions are relatively enriched close to transcription start sites and associated with coexpression in specific sets of related tissues. Our results confirm the overall relevance of the TE environment to gene expression and point to distinct mechanisms by which different TE families may contribute to gene regulation.
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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.