ArticleNature communications2021
Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 121 papers.
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Who cites it
121 citing papers in PubMed, 199 citations in OpenAlex.
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- IAPEz retrotransposons regulate the first lineage segregation in mouse pre-implantation development.Nucleic acids research · 2026Article
- Persistent viral infection in the Drosophila fat body is associated with immune activation at the single cell level.BMC genomics · 2026Article
- Response dynamics of discrete subiculum→retrosplenial cortex projections underlying trace fear conditioning.iScience · 2026Article
- Spatial Transcriptomics Unveils the Blueprint of Mammalian Lung Development.Genomics, proteomics & bioinformatics · 2026Article
- Single-cell epigenomics uncovers heterochromatin instability and transcription factor dysfunction during mouse brain aging.Cell reports · 2026Article
- Ultra-precision deconvolution of spatial transcriptomics decodes immune heterogeneity and fate-defining programs in tissues.Nature communications · 2026Article
- Epigenetic Deregulation of Transposable Elements Links Developmental Processes and Tumorigenesis.International journal of molecular sciences · 2026Review
- miR-203 facilitates timely cell fate transitions via epigenetic modulation during early embryogenesis.Science advances · 2026Article
- panHiTE: A comprehensive and accurate pipeline for TE detection in large-scale population genomes.Plant communications · 2026Article
- scTELL: a single-cell ATAC-seq tool for locus-specific transposable element identification in chromatin accessibility.Mobile DNA · 2026Article
61 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TEs) make up a majority of a typical eukaryote's genome, and contribute to cell heterogeneity in unclear ways. Single-cell sequencing technologies are powerful tools to explore cells, however analysis is typically gene-centric and TE expression has not been addressed. Here, we develop a single-cell TE processing pipeline, scTE, and report the expression of TEs in single cells in a range of biological contexts. Specific TE types are expressed in subpopulations of embryonic stem cells and are dynamically regulated during pluripotency reprogramming, differentiation, and embryogenesis. Unexpectedly, TEs are expressed in somatic cells, including human disease-specific TEs that are undetectable in bulk analyses. Finally, we apply scTE to single-cell ATAC-seq data, and demonstrate that scTE can discriminate cell type using chromatin accessibly of TEs alone. Overall, our results classify the dynamic patterns of TEs in single cells and their contributions to cell heterogeneity.
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