ArticleGenome research2022
Epigenomic analysis reveals prevalent contribution of transposable elements to
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 19 papers.
What it found
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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
19 citing papers in PubMed, 25 citations in OpenAlex.
- Long-read assembly reveals vast transcriptional complexity in the placenta associated with metabolic and endocrine function.Nature communications · 2026Article
- Architectural and evolutionary features of TE-derived TSSs shape tissue-specific promoter activity in the human genome.Nature communications · 2026Article
- A developmentally regulated long-range enhancer-promoter contact mediates human neural development.bioRxiv : the preprint server for biology · 2026Article
- Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding.Genome research · 2025Article
- Snake Venom Peptide Fractions fromPharmaceuticals (Basel, Switzerland) · 2025Article
- Zygotic activation of transposable elements during zebrafish early embryogenesis.Nature communications · 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
- Integrative mRNA and miRNA Expression Profiles from Developing Zebrafish Head Highlight Brain-Preference Genes and Regulatory Networks.Molecular neurobiology · 2025Article
- Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes.Genome biology · 2025Article
- DNA Methylation of Somatic Tissues in Oysters is Influenced by Sex and Heredity.Marine biotechnology (New York, N.Y.) · 2025Article
- Binding of zebrafish lipovitellin and L1‑ORF2 increases the accessibility of L1‑ORF2 via interference with histone wrapping.International journal of molecular medicine · 2025Article
- HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation.Nature communications · 2024Article
- Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition.BMC biology · 2024Article
- Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes.bioRxiv : the preprint server for biology · 2024Article
- Pig H3K4me3, H3K27ac, and gene expression profiles reveal reproductive tissue-specific activity of transposable elements.Zoological research · 2024Article
- Gonadal transcriptome sequencing reveals sexual dimorphism in expression profiling of sex-related genes in Asian arowana (Frontiers in genetics · 2024Article
- Review
- Transposable Elements Co-Option in Genome Evolution and Gene Regulation.International journal of molecular sciences · 2023Review
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
Abstract
Transposable elements (TEs) encode regulatory elements that impact gene expression in multiple species, yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here, we systematically investigate the epigenomic and transcriptomic landscape of TEs across 11 adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE-derived transcriptional units expressed across tissues. Finally, we show that novel TE-derived promoters can initiate tissue-specific transcription of alternate gene isoforms. This work provides a comprehensive profile of TE activity across normal zebrafish tissues, shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.
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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.