ArticleGenome biology2006
Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns.
Article in Genome biology, 2006. 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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Who cites it
27 citing papers in PubMed, 31 citations in OpenAlex.
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- The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality.Genome biology and evolution · 2021Article
- DNA methylation of a PLPP3 MIR transposon-based enhancer promotes an osteogenic programme in calcific aortic valve disease.Cardiovascular research · 2018Article
- Regulatory activities of transposable elements: from conflicts to benefits.Nature reviews. Genetics · 2017Review
- Whole-genome expression analysis of mammalian-wide interspersed repeat elements in human cell lines.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Genomic landscape of human, bat, and ex vivo DNA transposon integrations.Molecular biology and evolution · 2014Article
- Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression.Mobile DNA · 2014Article
- Visualized computational predictions of transcriptional effects by intronic endogenous retroviruses.PloS one · 2013Article
- The ant genomes have been invaded by several types of mariner transposable elements.Die Naturwissenschaften · 2012Article
- Evolutionary rate of human tissue-specific genes are related with transposable element insertions.Genetica · 2012Article
- The role of Transposable Elements in shaping the combinatorial interaction of Transcription Factors.BMC genomics · 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
- Effect of the transposable element environment of human genes on gene length and expression.Genome biology and evolution · 2011Article
- Genes devoid of full-length transposable element insertions are involved in development and in the regulation of transcription in human and closely related species.Journal of molecular evolution · 2010Article
- Article
- Paucity and preferential suppression of transgenes in late replication domains of the D. melanogaster genome.BMC genomics · 2010Article
- The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important.Genome research · 2010Article
- Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements.Nucleic acids research · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTransposable elements (TEs) represent more than 45% of the human and mouse genomes. Both parasitic and mutualistic features have been shown to apply to the host-TE relationship but a comprehensive scenario of the forces driving TE fixation within mammalian genes is still missing.
resultsWe show that intronic multispecies conserved sequences (MCSs) have been affecting TE integration frequency over time. We verify that a selective economizing pressure has been acting on TEs to decrease their frequency in highly expressed genes. After correcting for GC content, MCS density and intron size, we identified TE-enriched and TE-depleted gene categories. In addition to developmental regulators and transcription factors, TE-depleted regions encompass loci that might require subtle regulation of transcript levels or precise activation timing, such as growth factors, cytokines, hormones, and genes involved in the immune response. The latter, despite having reduced frequencies of most TE types, are significantly enriched in mammalian-wide interspersed repeats (MIRs). Analysis of orthologous genes indicated that MIR over-representation also occurs in dog and opossum immune response genes, suggesting, given the partially independent origin of MIR sequences in eutheria and metatheria, the evolutionary conservation of a specific function for MIRs located in these loci. Consistently, the core MIR sequence is over-represented in defense response genes compared to the background intronic frequency.
conclusionOur data indicate that gene function, expression level, and sequence conservation influence TE insertion/fixation in mammalian introns. Moreover, we provide the first report showing that a specific TE family is evolutionarily associated with a gene function category.
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