ArticleNucleic acids research2023
ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed, 30 citations in OpenAlex.
- Mapping the functional dark proteome in cancer.Nature reviews. Cancer · 2026Review
- TBP regulates transposable element expression in early mouse embryos.The EMBO journal · 2026Article
- Therapeutic Stress-Induced Remodeling of Transposable Elements and TE-Gene Chimeras in KYSE150 Esophageal Squamous Cell Carcinoma Cells.International journal of molecular sciences · 2026Article
- Transposable elements contribute to the evolution of host shift-related genes in cactophilicGenome research · 2026Article
- Male sterility in Drosophila hybrids revealed by a multi-generational transcriptomic analysis of genes and transposable elements in testes.BMC biology · 2026Article
- Transposable elements as drivers of genome evolution in Drosophila virilis.Nucleic acids research · 2026Article
- Transposable elements drive species-specific and tissue-specific transcriptomes in human development.Genome biology · 2025Article
- The Other Side of the Same Coin: Beyond the Coding Region in Amyotrophic Lateral Sclerosis.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Gene and transposable element expression in response to stress in temperate and tropical populations of Drosophila.Mobile DNA · 2025Article
- BMAL1-TRIM28 represses transposable elements independently of CLOCK in pluripotent cells.Nature communications · 2025Article
- Exploring the Relationship of Transposable Elements and Ageing: Causes and Consequences.Genome biology and evolution · 2025Review
- Limited impact of the siRNA pathway on transposable element expression in Aedes aegypti.BMC biology · 2025Article
- The transcription factor SRF regulates MERVL retrotransposons and gene expression during zygotic genome activation.Genes & development · 2025Article
- Architects and Partners: The Dual Roles of Non-coding RNAs in Gene Fusion Events.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Transposable Element (TE) insertion predictions from RNAseq inputs and TE impact on RNA splicing and gene expression in Drosophila brain transcriptomes.Mobile DNA · 2024Article
- Investigation of chimeric transcripts derived from LINE-1 and Alu retrotransposons in cerebellar tissues of individuals with autism spectrum disorder (ASD).Scientific reports · 2024Article
- Technology to the rescue: how to uncover the role of transposable elements in preimplantation development.Biochemical Society transactions · 2024Review
- Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes acrossGenome research · 2023Article
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 2 institutions in 2 countries.
Funding
Abstract
Transposable elements (TEs) produce structural variants and are considered an important source of genetic diversity. Notably, TE-gene fusion transcripts, i.e. chimeric transcripts, have been associated with adaptation in several species. However, the identification of these chimeras remains hindered due to the lack of detection tools at a transcriptome-wide scale, and to the reliance on a reference genome, even though different individuals/cells/strains have different TE insertions. Therefore, we developed ChimeraTE, a pipeline that uses paired-end RNA-seq reads to identify chimeric transcripts through two different modes. Mode 1 is the reference-guided approach that employs canonical genome alignment, and Mode 2 identifies chimeras derived from fixed or insertionally polymorphic TEs without any reference genome. We have validated both modes using RNA-seq data from four Drosophila melanogaster wild-type strains. We found ∼1.12% of all genes generating chimeric transcripts, most of them from TE-exonized sequences. Approximately ∼23% of all detected chimeras were absent from the reference genome, indicating that TEs belonging to chimeric transcripts may be recent, polymorphic insertions. ChimeraTE is the first pipeline able to automatically uncover chimeric transcripts without a reference genome, consisting of two running Modes that can be used as a tool to investigate the contribution of TEs to transcriptome plasticity.
Indexed as
Identifiers
What OpenQuestion holds
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.