ArticleGenome research2022
Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression.
Article in Genome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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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.
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Who cites it
53 citing papers in PubMed, 82 citations in OpenAlex.
- A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.Genome biology · 2026Article
- Transposable elements as evolutionary catalysts of ant macrodiversity.Science advances · 2026Article
- Recurrent ZC3H18 mutations stabilize oncogenic endogenous retroviral RNA.Cell reports · 2026Article
- Host-Parasite Interactions Revisited: Evidence of Horizontal Transfer of a Transposable Element Between a Snail and Its Parasite.Genome biology and evolution · 2026Article
- A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.bioRxiv : the preprint server for biology · 2026Article
- Transposable elements contribute to the evolution of host shift-related genes in cactophilicGenome research · 2026Article
- Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8.Nucleic acids research · 2026Article
- Diverging transposon activity among polar bear sub-populations inhabiting different climate zones.Mobile DNA · 2025Article
- Mix-and-match between transposable elements and zinc finger proteins fuels genic and regulatory innovation.Current opinion in genetics & development · 2025Review
- Insertion of an invading retrovirus regulates a novel color trait in swordtail fish.bioRxiv : the preprint server for biology · 2025Article
- BMAL1-TRIM28 represses transposable elements independently of CLOCK in pluripotent cells.Nature communications · 2025Article
- Transposon insertion causes ctnnb2 transcript instability that results in the maternal effect zebrafish ichabod (ich) mutation.Biochimica et biophysica acta. Gene regulatory mechanisms · 2025Article
- Thymol and menthol as anaesthetics for short transportation of zebrafish larva.Fish physiology and biochemistry · 2025Article
- An endogenous retroviral element co-opts an upstream regulatory sequence to achieve somatic expression and mobility.Nucleic acids research · 2025Article
- Gag proteins encoded by endogenous retroviruses are required for zebrafish development.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Zygotic activation of transposable elements during zebrafish early embryogenesis.Nature communications · 2025Article
- Transposable element dynamics in Xenopus laevis embryogenesis: a tale of two coexisting subgenomes.Mobile DNA · 2025Article
- The landscape of transposable element distribution in the genome of Neotropical fish Apareiodon sp. (Characiformes: Parodontidae).Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2025Article
- Environmentally induced variation in sperm sRNAs is linked to gene expression and transposable elements in zebrafish offspring.Heredity · 2025Article
- Multi-omics analysis reveals criticaliScience · 2025Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
Abstract
There is considerable interest in understanding the effect of transposable elements (TEs) on embryonic development. Studies in humans and mice are limited by the difficulty of working with mammalian embryos and by the relative scarcity of active TEs in these organisms. The zebrafish is an outstanding model for the study of vertebrate development, and over half of its genome consists of diverse TEs. However, zebrafish TEs remain poorly characterized. Here we describe the demography and genomic distribution of zebrafish TEs and their expression throughout embryogenesis using bulk and single-cell RNA sequencing data. These results reveal a highly dynamic genomic ecosystem comprising nearly 2000 distinct TE families, which vary in copy number by four orders of magnitude and span a wide range of ages. Longer retroelements tend to be retained in intergenic regions, whereas short interspersed nuclear elements (SINEs) and DNA transposons are more frequently found nearby or within genes. Locus-specific mapping of TE expression reveals extensive TE transcription during development. Although two-thirds of TE transcripts are likely driven by nearby gene promoters, we still observe stage- and tissue-specific expression patterns in self-regulated TEs. Long terminal repeat (LTR) retroelements are most transcriptionally active immediately following zygotic genome activation, whereas DNA transposons are enriched among transcripts expressed in later stages of development. Single-cell analysis reveals several endogenous retroviruses expressed in specific somatic cell lineages. Overall, our study provides a valuable resource for using zebrafish as a model to study the impact of TEs on vertebrate development.
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