ArticleCell stem cell2011
DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs.
Article in Cell stem cell, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 339 papers, 1 of them a synthesis that pooled it.
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.
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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
339 citing papers in PubMed, 1 synthesis or guideline pooled it, 534 citations in OpenAlex.
- Disrupting Mechanisms that Regulate Genomic Repeat Elements to Combat Cancer and Drug Resistance.Frontiers in cell and developmental biology · 2022Pooled it
- Dynamic regulation of H3K9 modifications in cancer: pathogenesis and targeted therapies.Biomarker research · 2026Review
- Methylome profiling of SetDB1-deficient ESCs reveals coordinated epigenetic cross-talk during pluripotency.Stem cell reports · 2026Article
- Retrotransposable element derepression distinguishes DNMT3A-mutant from TET2-mutant clonal haematopoiesis.GeroScience · 2026Article
- Targeting MORC2 activates transposable element-mediated viral mimicry and potentiates immune checkpoint blockade in triple-negative breast cancer.Molecular cancer · 2026Article
- SETDB1 promotes gastric cancer progression via UPR and mTOR pathway.Cancer cell international · 2026Article
- SETDB1 and HUSH modulate Xist RNA levels during establishment of X chromosome inactivation.Nature communications · 2026Article
- The Many Faces of SetDB1.Epigenomes · 2026Review
- Hat1 Orchestrates Heterochromatin Inheritance by Regulating Localization of H3K9 Methyltransferases.bioRxiv : the preprint server for biology · 2026Article
- RETRACTED: Endogenous Retroviruses as Regulators of Innate Immune Signaling and InflammationViruses · 2026Review
- Article
- SETDB1/ATF7IP regulate the precise genome engineering of HUSH-regulated genes.Epigenetics & chromatin · 2026Article
- Viral mimicry acts as a tumor suppressor in colitis.Nature communications · 2026Article
- Epigenetic mechanisms of retroviral regulation: a comparative review.Epigenetics & chromatin · 2026Review
- 3'-tRNA Fragments Target Domesticated LTR-Retrotransposons.bioRxiv : the preprint server for biology · 2026Article
- Genomic Perspective on Heterogeneity of Organs and Body Aging.Aging cell · 2026Review
- Endogenous retrovirus IAP forms virus-like particles and traffics across the maternal-fetal barrier.bioRxiv : the preprint server for biology · 2025Article
- H3K36 Methylation as a Guardian of Epigenome Integrity.Nature communications · 2025Article
- Intrinsic mechanotransduction during apical constriction licenses lineage competence in pluripotent stem cells.bioRxiv : the preprint server for biology · 2025Article
- Reprogramming of H3K36me2 guides lineage-specific post-implantation de novo DNA methylation.Nature cell biology · 2025Article
279 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
Abstract
DNA methylation and histone H3 lysine 9 trimethylation (H3K9me3) play important roles in silencing of genes and retroelements. However, a comprehensive comparison of genes and repetitive elements repressed by these pathways has not been reported. Here we show that in mouse embryonic stem cells (mESCs), the genes upregulated after deletion of the H3K9 methyltransferase Setdb1 are distinct from those derepressed in mESC deficient in the DNA methyltransferases Dnmt1, Dnmt3a, and Dnmt3b, with the exception of a small number of primarily germline-specific genes. Numerous endogenous retroviruses (ERVs) lose H3K9me3 and are concomitantly derepressed exclusively in SETDB1 knockout mESCs. Strikingly, ~15% of upregulated genes are induced in association with derepression of promoter-proximal ERVs, half in the context of "chimeric" transcripts that initiate within these retroelements and splice to genic exons. Thus, SETDB1 plays a previously unappreciated yet critical role in inhibiting aberrant gene transcription by suppressing the expression of proximal ERVs.
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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.