ArticleNucleic acids research2017
TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers, 1 of them a synthesis that pooled it.
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Who cites it
80 citing papers in PubMed, 1 synthesis or guideline pooled it, 145 citations in OpenAlex.
- Infections by Transovarially Transmitted DMelSV in Drosophila Have No Impact on Ovarian Transposable Element Transcripts but Increase Their Amounts in the Soma.Genome biology and evolution · 2021Pooled it
- The impact of P-element-induced hybrid dysgenesis on the male germline in Drosophila simulans.Genetics · 2026Article
- Review
- Defective splicing of Y-chromosome-linked gigantic genes contributes to hybrid male sterility in Drosophila.Molecular biology and evolution · 2026Article
- Investigating the Physiological Regulation of Transposable Elements In Vivo: Nuclei Preparation from Primary Mouse Tissues for Epigenomic Analyses and Computational Approaches to Interrogate the Repeat Genome.Methods in molecular biology (Clifton, N.J.) · 2026Article
- TE-Seq: a transposable element annotation and RNA-Seq pipeline.Mobile DNA · 2025Article
- Long-read RNA sequencing of transposable elements from single cells using CELLO-seq.Nature protocols · 2025Review
- Gene and transposable element expression in response to stress in temperate and tropical populations of Drosophila.Mobile DNA · 2025Article
- Article
- Transposable element expression is associated with sex chromosome number in humans.PLoS genetics · 2025Article
- Exploring the Relationship of Transposable Elements and Ageing: Causes and Consequences.Genome biology and evolution · 2025Review
- LocusMasterTE: integrating long-read RNA sequencing improves locus-specific quantification of transposable element expression.Genome biology · 2025Article
- Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis.The plant genome · 2025Article
- Exploring the Potential of Malvidin and Echiodinin as Probable Antileishmanial Agents Through In Silico Analysis and In Vitro Efficacy.Molecules (Basel, Switzerland) · 2025Article
- MORE-RNAseq: a pipeline for quantifying retrotransposition-capable LINE1 expression based on RNA-seq data.Frontiers in bioinformatics · 2025Article
- Genomic Variability Survey inInternational journal of molecular sciences · 2024Article
- 3t-seq: automatic gene expression analysis of single-copy genes, transposable elements, and tRNAs from RNA-seq data.Briefings in bioinformatics · 2024Article
- Navigating the landscape of epitranscriptomics and host immunity.Genome research · 2024Review
- Effects of Arboviral Infections on Transposable Element Transcript Levels in Aedes aegypti.Genome biology and evolution · 2024Article
- Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae.G3 (Bethesda, Md.) · 2024Article
20 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Over recent decades, substantial efforts have been made to understand the interactions between host genomes and transposable elements (TEs). The impact of TEs on the regulation of host genes is well known, with TEs acting as platforms of regulatory sequences. Nevertheless, due to their repetitive nature it is considerably hard to integrate TE analysis into genome-wide studies. Here, we developed a specific tool for the analysis of TE expression: TEtools. This tool takes into account the TE sequence diversity of the genome, it can be applied to unannotated or unassembled genomes and is freely available under the GPL3 (https://github.com/l-modolo/TEtools). TEtools performs the mapping of RNA-seq data obtained from classical mRNAs or small RNAs onto a list of TE sequences and performs differential expression analyses with statistical relevance. Using this tool, we analyzed TE expression from five Drosophila wild-type strains. Our data show for the first time that the activity of TEs is strictly linked to the activity of the genes implicated in the piwi-interacting RNA biogenesis and therefore fits an arms race scenario between TE sequences and host control genes.
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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.