ArticleNucleic acids research2022
Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 21 citations in OpenAlex.
- A LINE-1 retrotransposon promotes SEMA3C expression as a cis-regulatory enhancer to sustain breast cancer stem cell survival.Science China. Life sciences · 2026Article
- The nuclear cap-binding complex regulates subcellular RNA processing and surveillance of coding and noncoding RNAs.Nucleic acids research · 2026Article
- PervasivebioRxiv : the preprint server for biology · 2025Article
- Structural Homology Fails to Predict Secretion Efficiency inInternational journal of molecular sciences · 2025Article
- Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability.Science advances · 2025Article
- HervD Atlas: a curated knowledgebase of associations between human endogenous retroviruses and diseases.Nucleic acids research · 2024Article
- Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation.Molecular cell · 2023Article
- ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements.Nucleic acids research · 2023Article
- Symmetric inheritance of parental histones governs epigenome maintenance and embryonic stem cell identity.Nature genetics · 2023Article
- Globally elevated levels of histone H3 lysine 9 trimethylation in early infancy are associated with poor growth trajectory in Bangladeshi children.Clinical epigenetics · 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
- Transcriptional and reverse transcriptional regulation of host genes by human endogenous retroviruses in cancers.Frontiers in microbiology · 2022Review
- Transposable Elements in Pluripotent Stem Cells and Human Disease.Frontiers in genetics · 2022Review
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements are an abundant source of transcription factor binding sites, and favorable genomic integration may lead to their recruitment by the host genome for gene regulatory functions. However, it is unclear how frequent co-option of transposable elements as regulatory elements is, to which regulatory programs they contribute and how they compare to regulatory elements devoid of transposable elements. Here, we report a transcription initiation-centric, in-depth characterization of the transposon-derived regulatory landscape of mouse embryonic stem cells. We demonstrate that a substantial number of transposable element insertions, in particular endogenous retroviral elements, are associated with open chromatin regions that are divergently transcribed into unstable RNAs in a cell-type specific manner, and that these elements contribute to a sizable proportion of active enhancers and gene promoters. We further show that transposon subfamilies contribute differently and distinctly to the pluripotency regulatory program through their repertoires of transcription factor binding site sequences, shedding light on the formation of regulatory programs and the origins of regulatory elements.
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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.