ArticleGenes & development2022
H3K9 trimethylation in active chromatin restricts the usage of functional CTCF sites in SINE B2 repeats.
Article in Genes & development, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 33 citations in OpenAlex.
- WAVE2 and REST/NRSF Regulate Clustered Gene Expression by Maintaining Heterochromatin Organization.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- Sequence design for three-dimensional genome folding using Akita Semifreddo.bioRxiv : the preprint server for biology · 2026Article
- The Many Faces of SetDB1.Epigenomes · 2026Review
- A beneficial environment promotes immune resilience through epigenetic regulation.Science advances · 2026Article
- H3K36 Methylation as a Guardian of Epigenome Integrity.Nature communications · 2025Article
- H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity.Genome research · 2025Article
- CTCF binding landscape is shaped by the epigenetic state of the N-terminal nucleosome in relation to CTCF motif orientation.Nucleic acids research · 2025Article
- Deciphering the role of histone modifications in memory and exhausted CD8 T cells.Scientific reports · 2025Article
- Histone methyltransferase SETDB1 safeguards mouse fetal hematopoiesis by suppressing activation of cryptic enhancers.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Histone H3.3 lysine 9 and 27 control repressive chromatin at cryptic enhancers and bivalent promoters.Nature communications · 2024Article
- SETDB1 regulates short interspersed nuclear elements and chromatin loop organization in mouse neural precursor cells.Genome biology · 2024Article
- An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors.Molecular systems biology · 2024Article
- ADNP modulates SINE B2-derived CTCF-binding sites during blastocyst formation in mice.Genes & development · 2024Article
- Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide.Molecular cell · 2024Article
- Cell-type differential targeting of SETDB1 prevents aberrant CTCF binding, chromatin looping, and cis-regulatory interactions.Nature communications · 2024Article
- The functions of SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) in biological process and disease.Epigenetics & chromatin · 2023Review
- Short tandem repeats are important contributors to silencer elements in T cells.Nucleic acids research · 2023Article
- Article
- Review
- 3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome.Cell · 2022Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Six methyltransferases divide labor in establishing genomic profiles of histone H3 lysine 9 methylation (H3K9me), an epigenomic modification controlling constitutive heterochromatin, gene repression, and silencing of retroelements. Among them, SETDB1 is recruited to active chromatin domains to silence the expression of endogenous retroviruses. In the context of experiments aimed at determining the impact of SETDB1 on stimulus-inducible gene expression in macrophages, we found that loss of H3K9me3 caused by SETDB1 depletion was associated with increased recruitment of CTCF to >1600 DNA binding motifs contained within SINE B2 repeats, a previously unidentified target of SETDB1-mediated repression. CTCF is an essential regulator of chromatin folding that restrains DNA looping by cohesin, thus creating boundaries among adjacent topological domains. Increased CTCF binding to SINE B2 repeats enhanced insulation at hundreds of sites and increased loop formation within topological domains containing lipopolysaccharide-inducible genes, which correlated with their impaired regulation in response to stimulation. These data indicate a role of H3K9me3 in restraining genomic distribution and activity of CTCF, with an impact on chromatin organization and gene regulation.
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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.