ArticleBMC bioinformatics2019
Exploratory analysis of transposable elements expression in the C. elegans early embryo.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 24 citations in OpenAlex.
- Comparative Transcriptomics Reveals an Extracellular Worm Argonaute as an Ancestral Regulator of LTR Retrotransposons.Genome biology and evolution · 2026Article
- An endogenous retroviral element co-opts an upstream regulatory sequence to achieve somatic expression and mobility.Nucleic acids research · 2025Article
- Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis.The plant genome · 2025Article
- Expression of Transposable Elements throughout theNon-coding RNA · 2024Article
- AdvancingPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- LINE-1 regulates cortical development by acting as long non-coding RNAs.Nature communications · 2023Article
- Transposable elements drive the evolution of metazoan zinc finger genes.Genome research · 2023Article
- Article
- TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments.Bioinformatics (Oxford, England) · 2022Article
- Analysis of repeat elements in the Pristionchus pacificus genome reveals an ancient invasion by horizontally transferred transposons.BMC genomics · 2022Article
- Meta-Analysis Suggests That Intron Retention Can Affect Quantification of Transposable Elements from RNA-Seq Data.Biology · 2022Article
- Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea UrchinBiomedicines · 2021Article
- Region-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans.PLoS genetics · 2021Article
- Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest.Evolutionary applications · 2021Article
- Unraveling the features of somatic transposition in the Drosophila intestine.The EMBO journal · 2021Article
- Analysis of LINE1 Retrotransposons in Huntington's Disease.Frontiers in cellular neuroscience · 2021Article
- Measuring and interpreting transposable element expression.Nature reviews. Genetics · 2020Review
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundTransposable Elements (TE) are mobile sequences that make up large portions of eukaryote genomes. The functions they play within the complex cellular architecture are still not clearly understood, but it is becoming evident that TE have a role in several physiological and pathological processes. In particular, it has been shown that TE transcription is necessary for the correct development of mice embryos and that their expression is able to finely modulate transcription of coding and non-coding genes. Moreover, their activity in the central nervous system (CNS) and other tissues has been correlated with the creation of somatic mosaicisms and with pathologies such as neurodevelopmental and neurodegenerative diseases as well as cancers.
resultsWe analyzed TE expression among different cell types of the Caenorhabditis elegans (C. elegans) early embryo asking if, where and when TE are expressed and whether their expression is correlated with genes playing a role in early embryo development. To answer these questions, we took advantage of a public C. elegans embryonic single-cell RNA-seq (sc-RNAseq) dataset and developed a bioinformatics pipeline able to quantify reads mapping specifically against TE, avoiding counting reads mapping on TE fragments embedded in coding/non-coding transcripts. Our results suggest that i) canonical TE expression analysis tools, which do not discard reads mapping on TE fragments embedded in annotated transcripts, may over-estimate TE expression levels, ii) Long Terminal Repeats (LTR) elements are mostly expressed in undifferentiated cells and might play a role in pluripotency maintenance and activation of the innate immune response, iii) non-LTR are expressed in differentiated cells, in particular in neurons and nervous system-associated tissues, and iv) DNA TE are homogenously expressed throughout the C. elegans early embryo development.
conclusionsTE expression appears finely modulated in the C. elegans early embryo and different TE classes are expressed in different cell types and stages, suggesting that TE might play diverse functions during early embryo development.
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