ArticleGenome research2021
Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data.
Article in Genome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 60 citations in OpenAlex.
- Transposable Element Activation: A Hallmark of Cancer.Cancer discovery · 2026Review
- Transposable element expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineages.Nature communications · 2025Article
- A single-cell transposable element atlas of human cell identity.Cell reports methods · 2025Article
- Article
- The Somatic Mosaicism across Human Tissues Network.Nature · 2025Review
- Charting the regulatory landscape of TP53 on transposable elements in cancer.Genome research · 2025Article
- Efficient profiling of total RNA in single cells with STORM-seq.bioRxiv : the preprint server for biology · 2025Article
- Cell-Specific Transposable Element and Gene Expression Analysis Across Systemic Lupus Erythematosus Phenotypes.ACR open rheumatology · 2024Article
- Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level.Genome research · 2024Article
- IRescue: uncertainty-aware quantification of transposable elements expression at single cell level.Nucleic acids research · 2024Article
- HEMU: An integrated comparative genomics database and analysis platform for Andropogoneae grasses.Plant communications · 2024Article
- ADNP modulates SINE B2-derived CTCF-binding sites during blastocyst formation in mice.Genes & development · 2024Article
- Towards targeting transposable elements for cancer therapy.Nature reviews. Cancer · 2024Review
- HervD Atlas: a curated knowledgebase of associations between human endogenous retroviruses and diseases.Nucleic acids research · 2024Article
- Characterization of H3K9me3 and DNA methylation co-marked CpG-rich regions during mouse development.BMC genomics · 2023Article
- The transcriptional landscape of endogenous retroelements delineates esophageal adenocarcinoma subtypes.NAR cancer · 2023Article
- Immunogenicity in renal cell carcinoma: shifting focus to alternative sources of tumour-specific antigens.Nature reviews. Nephrology · 2023Review
- LINE-1 retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5' single-cell RNA-Seq.Nucleic acids research · 2023Article
- Pseudoalignment tools as an efficient alternative to detect repeated transposable elements in scRNAseq data.Bioinformatics (Oxford, England) · 2023Article
- Transposon control as a checkpoint for tissue regeneration.Development (Cambridge, England) · 2022Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Transposable elements (TEs) are an integral part of the host transcriptome. TE-containing noncoding RNAs (ncRNAs) show considerable tissue specificity and play important roles during development, including stem cell maintenance and cell differentiation. Recent advances in single-cell RNA-seq (scRNA-seq) revolutionized cell type-specific gene expression analysis. However, effective scRNA-seq quantification tools tailored for TEs are lacking, limiting our ability to dissect TE expression dynamics at single-cell resolution. To address this issue, we established a TE expression quantification pipeline that is compatible with scRNA-seq data generated across multiple technology platforms. We constructed TE-containing ncRNA references using bulk RNA-seq data and showed that quantifying TE expression at the transcript level effectively reduces noise. As proof of principle, we applied this strategy to mouse embryonic stem cells and successfully captured the expression profile of endogenous retroviruses in single cells. We further expanded our analysis to scRNA-seq data from early stages of mouse embryogenesis. Our results illustrated the dynamic TE expression at preimplantation stages and revealed 146 TE-containing ncRNA transcripts with substantial tissue specificity during gastrulation and early organogenesis.
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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.