ArticleCell reports methods2025
A single-cell transposable element atlas of human cell identity.
Article in Cell reports methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Review
- Longitudinal Repeatome Remodeling in Peripheral Blood Following Parkinson's Disease Diagnosis.Genes · 2026Article
- Smoking-induced dysregulation of transposable elements in the small airway epithelium.Respiratory research · 2026Article
- Article
- CDK9 Inhibition with enitociclib reveals influence on HERV and LINE RNA abundances in whole blood, T-, and B-Cell lines.BMC medical genomics · 2026Article
- Dynamic dosage changes in X-linked transposable elements during mammalian dosage compensation.Nature communications · 2025Article
- Strict retroelement regulation is frequently lost following cancer transformation and generates a promising reservoir of cancer biomarkers.Mobile DNA · 2025Article
- Deciphering lung adenocarcinoma evolution and the role of LINE-1 retrotransposition.bioRxiv : the preprint server for biology · 2025Article
- Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level.Genome research · 2024Article
- Endogenous retroelement expression in modeled airway epithelial repair.Microbes and infectionArticle
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18 authors.
Funding
Abstract
Single-cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex biological systems. However, most sequencing studies overlook the contribution of transposable element (TE) expression to the transcriptome. The quantification of locus-specific TE expression in scRNA-seq experiments is challenging due to their repetitive sequence content and poorly characterized annotations. Here, we developed a computational tool for single-cell transposable element locus-level analysis of scRNA sequencing (Stellarscope) that reassigns multimapped reads to specific genomic loci using an expectation maximization algorithm. Using Stellarscope, we built an atlas of TE expression in human PBMCs. We found that locus-specific TEs delineate cell types and define cell subsets not identified by standard mRNA expression profiles. Altogether, this study provides comprehensive insights into the influence of TEs in human biology at the single-cell level.
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