ArticleNature cell biology2021
CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells.
Article in Nature cell biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers, 1 of them a synthesis that pooled it.
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Who cites it
42 citing papers in PubMed, 1 synthesis or guideline pooled it, 64 citations in OpenAlex.
- An updated catalog ofFrontiers in molecular neuroscience · 2023Pooled it
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- Mechanisms coordinating exit from the stem cell state in mammals.Genes & development · 2026Review
- Motif grammar and transcriptional programs decouple CTCF binding from nucleosome phasing to control cell-type-specific chromatin insulation.Cell reports · 2026Article
- Bipartite DNA binding domain of transcription factor BCL11B binds clustered short DNA sequence motifs.bioRxiv : the preprint server for biology · 2026Article
- Article
- An upstream secondary DNA motif within the IL3 insulator CTCF binding site is required for enhancer-blocking insulator activity.PloS one · 2026Article
- Epigenetic drugs in cancer therapy: mechanisms, immune modulation, and therapeutic applications.Molecular biomedicine · 2025Review
- Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy.Genome research · 2025Article
- KIF2A stabilizes intercellular bridge microtubules to maintain mouse embryonic stem cell cytokinesis.The Journal of cell biology · 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
- Revealing long-range heterogeneous organization of nucleoproteins with 6mA footprinting by ipdTrimming.Genome biology · 2025Article
- Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation.Cell genomics · 2025Article
- Mature chromatin packing domains persist after RAD21 depletion in 3D.Science advances · 2025Article
- A negatively charged region within carboxy-terminal domain maintains proper CTCF DNA binding.iScience · 2024Article
- Identification of transcription factor co-binding patterns with non-negative matrix factorization.Nucleic acids research · 2024Article
- Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy.bioRxiv : the preprint server for biology · 2024Article
- Factors that determine cell type-specific CTCF binding in health and disease.Current opinion in genetics & development · 2024Review
- Machine learning enables pan-cancer identification of mutational hotspots at persistent CTCF binding sites.Nucleic acids research · 2024Article
- A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization.Molecular systems biology · 2024Article
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23 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The 11 zinc finger (ZF) protein CTCF regulates topologically associating domain formation and transcription through selective binding to thousands of genomic sites. Here, we replaced endogenous CTCF in mouse embryonic stem cells with green-fluorescent-protein-tagged wild-type or mutant proteins lacking individual ZFs to identify additional determinants of CTCF positioning and function. While ZF1 and ZF8-ZF11 are not essential for cell survival, ZF8 deletion strikingly increases the DNA binding off-rate of mutant CTCF, resulting in reduced CTCF chromatin residence time. Loss of ZF8 results in widespread weakening of topologically associating domains, aberrant gene expression and increased genome-wide DNA methylation. Thus, important chromatin-templated processes rely on accurate CTCF chromatin residence time, which we propose depends on local sequence and chromatin context as well as global CTCF protein concentration.
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