ArticleNucleic acids research2021
Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 49 citations in OpenAlex.
- Single-oocyte full-length isoform sequencing unveils the impact of transposable elements on RNA diversity and stability.Nature communications · 2026Article
- Transposable element-gene chimera cartography, origination and role in enhancing transcriptome plasticity.Nature structural & molecular biology · 2026Article
- Dissecting the contribution of transposable elements to interphase chromosome structure.Genome biology · 2026Article
- Nanopore sequencing and multiomics reveal predictable non-coding RNA activation in DNA methylation deficient Arabidopsis thaliana.Communications biology · 2025Article
- HERVs and Epigenetic Regulators Transcriptional Expression After Chondrogenic Differentiation of Adipose Tissue-Derived Mesenchymal Stem Cells.Current issues in molecular biology · 2025Article
- Transposable element expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineages.Nature communications · 2025Article
- Zygotic activation of transposable elements during zebrafish early embryogenesis.Nature communications · 2025Article
- Long-read RNA sequencing enables full-length chimeric transcript annotation of transposable elements in lung adenocarcinoma.BMC cancer · 2025Article
- 20 years of stemness: From stem cells to hypertranscription and back.Stem cell reports · 2025Review
- The nuclear matrix stabilizes primed-specific genes in human pluripotent stem cells.Nature cell biology · 2025Article
- Transcriptome sequencing reveals the evolutionary histories and gene expression evolution in two related Pagurus species.PloS one · 2025Article
- Functional Bidirectionality of ERV-Derived Long Non-Coding RNAs in Humans.International journal of molecular sciences · 2024Review
- Novel function of U7 snRNA in the repression of HERV1/LTR12s and lincRNAs in human cells.Nucleic acids research · 2024Article
- HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation.Nature communications · 2024Article
- Profiling the role of m6A effectors in the regulation of pluripotent reprogramming.Human genomics · 2024Article
- ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements.Nucleic acids research · 2023Article
- The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation.Genome research · 2023Article
- Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes acrossGenome research · 2023Article
- ZFP92, a KRAB domain zinc finger protein enriched in pancreatic islets, binds to B1/Alu SINE transposable elements and regulates retroelements and genes.PLoS genetics · 2023Article
- Transposable Elements Co-Option in Genome Evolution and Gene Regulation.International journal of molecular sciences · 2023Review
Corrections and comments
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Authors and funding
23 authors at 6 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TEs) occupy nearly 40% of mammalian genomes and, whilst most are fragmentary and no longer capable of transposition, they can nevertheless contribute to cell function. TEs within genes transcribed by RNA polymerase II can be copied as parts of primary transcripts; however, their full contribution to mature transcript sequences remains unresolved. Here, using long and short read (LR and SR) RNA sequencing data, we show that 26% of coding and 65% of noncoding transcripts in human pluripotent stem cells (hPSCs) contain TE-derived sequences. Different TE families are incorporated into RNAs in unique patterns, with consequences to transcript structure and function. The presence of TE sequences within a transcript is correlated with TE-type specific changes in its subcellular distribution, alterations in steady-state levels and half-life, and differential association with RNA Binding Proteins (RBPs). We identify hPSC-specific incorporation of endogenous retroviruses (ERVs) and LINE:L1 into protein-coding mRNAs, which generate TE sequence-derived peptides. Finally, single cell RNA-seq reveals that hPSCs express ERV-containing transcripts, whilst differentiating subpopulations lack ERVs and express SINE and LINE-containing transcripts. Overall, our comprehensive analysis demonstrates that the incorporation of TE sequences into the RNAs of hPSCs is more widespread and has a greater impact than previously appreciated.
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