ArticleJournal of molecular evolution2005
Transposable element orientation bias in the Drosophila melanogaster genome.
Article in Journal of molecular evolution, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 27 citations in OpenAlex.
- Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome.Retrovirology · 2022Article
- On the Base Composition of Transposable Elements.International journal of molecular sciences · 2022Review
- Molecular functions of human endogenous retroviruses in health and disease.Cellular and molecular life sciences : CMLS · 2015Review
- Abundance and distribution of transposable elements in two Drosophila QTL mapping resources.Molecular biology and evolution · 2013Article
- Visualized computational predictions of transcriptional effects by intronic endogenous retroviruses.PloS one · 2013Article
- Gene properties and chromatin state influence the accumulation of transposable elements in genes.PloS one · 2012Article
- Retroelements and their impact on genome evolution and functioning.Cellular and molecular life sciences : CMLS · 2009Review
- Integration target site selection by a resurrected human endogenous retrovirus.Genes & development · 2009Article
- Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element.Nucleic acids research · 2008Article
- Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements.PLoS genetics · 2008Article
- Retrotransposons influence the mouse transcriptome: implication for the divergence of genetic traits.Genetics · 2007Article
- Multiple effects govern endogenous retrovirus survival patterns in human gene introns.Genome biology · 2006Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nonrandom distributions of transposable elements can be generated by a variety of genomic features. Using the full D. melanogaster genome as a model, we characterize the orientations of different classes of transposable elements in relation to the directionality of genes. DNA-mediated transposable elements are more likely to be in the same orientation as neighboring genes when they occur in the nontranscribed region's that flank genes. However, RNA-mediated transposable elements located in an intron are more often oriented in the direction opposite to that of the host gene. These orientation biases are strongest for genes with highly biased codon usage, probably reflecting the ability of such loci to respond to weak positive or negative selection. The leading hypothesis for selection against transposable elements in the coding orientation proposes that transcription termination poly(A) signal motifs within retroelements interfere with normal gene transcription. However, after accounting for differences in base composition between the strands, we find no evidence for global selection against spurious transcription termination signals in introns. We therefore conclude that premature termination of host gene transcription due to the presence of poly(A) signal motifs in retroelements might only partially explain strand-specific detrimental effects in the D. melanogaster genome.
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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.