ArticleNature genetics2009
The regulated retrotransposon transcriptome of mammalian cells.
Article in Nature genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 469 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
469 citing papers in PubMed, 825 citations in OpenAlex.
- The therapeutic potential of transposable element activity modulation.EMBO molecular medicine · 2026Review
- Regulatory Evolution and the Genetic Basis of Human Brain Expansion.Journal of molecular evolution · 2026Review
- Cooperation, competition and enforcement in transposon evolution.Nature communications · 2026Article
- Transcriptional perturbation of LINE-1 elements reveals their cis-regulatory potential.EMBO reports · 2026Article
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- Identification and multi-omics analysis of extracellular vesicles from the plerocercoids of Spirometra mansoni (Cestoda: Diphyllobothriidae).Parasitology research · 2026Article
- Longitudinal Repeatome Remodeling in Peripheral Blood Following Parkinson's Disease Diagnosis.Genes · 2026Article
- Pervasive Transcription in the Human Genome Exceeds Background Noise.Genome biology and evolution · 2026Article
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- Transposable elements contribute to the evolution of host shift-related genes in cactophilicGenome research · 2026Article
- Single-Cell RNA-Seq Profiling of Transposable Element Expression in Human Peripheral Blood Cells During Viral Infections.International journal of molecular sciences · 2026Article
- Alterations of placental HERV expression as a result of gestational COVID-19 disease.Frontiers in microbiology · 2026Article
- Sleep and circadian regulation of DNA repair and retrotransposons in neuronal genome stability and neurodegenerative disease mechanisms.Frontiers in neuroscience · 2026Review
- Article
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- ADAR1 as a Placental Innate Immune Rheostat Sustaining the Homeostatic Balance of Intrinsic Interferon Response at the Maternal-Fetal Interface.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Subfamily-selective PCR primers for the human LINE1 L1PA lineage.Scientific reports · 2025Article
- Microglial deficiency in the ATRX chromatin remodeler elicits a viral mimicry immune response that impacts neuronal function and behavior.PLoS biology · 2025Article
- A 280 bp SINE insertion within the pig PLA2G16 could potentially modify gene expression through integration with its transcript.Journal of applied genetics · 2025Article
- OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide.Nature structural & molecular biology · 2025Article
409 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
22 authors at 5 institutions in 4 countries.
Funding
Abstract
Although repetitive elements pervade mammalian genomes, their overall contribution to transcriptional activity is poorly defined. Here, as part of the FANTOM4 project, we report that 6-30% of cap-selected mouse and human RNA transcripts initiate within repetitive elements. Analysis of approximately 250,000 retrotransposon-derived transcription start sites shows that the associated transcripts are generally tissue specific, coincide with gene-dense regions and form pronounced clusters when aligned to full-length retrotransposon sequences. Retrotransposons located immediately 5' of protein-coding loci frequently function as alternative promoters and/or express noncoding RNAs. More than a quarter of RefSeqs possess a retrotransposon in their 3' UTR, with strong evidence for the reduced expression of these transcripts relative to retrotransposon-free transcripts. Finally, a genome-wide screen identifies 23,000 candidate regulatory regions derived from retrotransposons, in addition to more than 2,000 examples of bidirectional transcription. We conclude that retrotransposon transcription has a key influence upon the transcriptional output of the mammalian genome.
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Registered trials
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.