ArticleCommunications biology2022
SoloTE for improved analysis of transposable elements in single-cell RNA-Seq data using locus-specific expression.
Article in Communications biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed, 63 citations in OpenAlex.
- Reading the SINEs - functionality in noncoding RNA 'cheap genes'.RNA biology · 2026Review
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- Transposable Elements Are Dynamically Regulated in Medium Spiny Neurons and May Contribute to the Molecular and Behavioral Adaptations to Cocaine.Biological psychiatry · 2026Article
- Distinct Transposable Element Transcript Patterns in Microglia Across Aging and Alzheimer's Disease.Aging cell · 2026Article
- LINE-1 retrotransposons: Multifaceted functions and regulatory mechanisms in health and disease.Molecular therapy. Nucleic acids · 2026Review
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- Persistent viral infection in the Drosophila fat body is associated with immune activation at the single cell level.BMC genomics · 2026Article
- Single-cell epigenomics uncovers heterochromatin instability and transcription factor dysfunction during mouse brain aging.Cell reports · 2026Article
- Review
- Review
- TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution.Nucleic acids research · 2026Article
- Investigating the Physiological Regulation of Transposable Elements In Vivo: Nuclei Preparation from Primary Mouse Tissues for Epigenomic Analyses and Computational Approaches to Interrogate the Repeat Genome.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A conserved differentiation programme facilitates inhibitory neuron production in the developing mouse and human cerebellum.Development (Cambridge, England) · 2025Article
- Long-read RNA sequencing of transposable elements from single cells using CELLO-seq.Nature protocols · 2025Review
- Human Endogenous Retroviruses and Diseases.MedComm · 2025Review
- Single-Cell Transcriptome Patterns of Transposable Elements in Alzheimer's Disease.Molecular neurobiology · 2025Article
- Molecular cartography of the human down syndrome and trisomic mouse brain.Nature communications · 2025Article
- Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable Elements (TEs) contribute to the repetitive fraction in almost every eukaryotic genome known to date, and their transcriptional activation can influence the expression of neighboring genes in healthy and disease states. Single cell RNA-Seq (scRNA-Seq) is a technical advance that allows the study of gene expression on a cell-by-cell basis. Although a current computational approach is available for the single cell analysis of TE expression, it omits their genomic location. Here we show SoloTE, a pipeline that outperforms the previous approach in terms of computational resources and by allowing the inclusion of locus-specific TE activity in scRNA-Seq expression matrixes. We then apply SoloTE to several datasets to reveal the repertoire of TEs that become transcriptionally active in different cell groups, and based on their genomic location, we predict their potential impact on gene expression. As our tool takes as input the resulting files from standard scRNA-Seq processing pipelines, we expect it to be widely adopted in single cell studies to help researchers discover patterns of cellular diversity associated with TE expression.
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