ArticleGenome biology2020
Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed, 128 citations in OpenAlex.
- Origins and consequences of oncogenic 3D chromatin remodelling.Nature reviews. Cancer · 2026Review
- Nested TAD hierarchy defines cohesion zones on replicated chromosomes.The EMBO journal · 2026Article
- Chromatin Accessibility Reveals Adaptive Regulatory Variation in a Keystone Freshwater Fish.Molecular ecology · 2026Article
- Epigenetics in development, disease, and therapy: from mechanisms to clinical interventions.Science China. Life sciences · 2026Review
- Evolution of CTCF binding sites in the human genome.Molecular biology and evolution · 2026Article
- Conserved 3D genome reorganization during DNA repair.Life science alliance · 2026Review
- Effects of topological domain disruption on transcriptional regulation are chromatin context dependent.Epigenetics & chromatin · 2026Article
- High-throughputbioRxiv : the preprint server for biology · 2025Article
- The emerging sequence grammar of 3D genome organisation.Human genetics · 2025Review
- Epigenetic regulators in cancer therapy and progression.NPJ precision oncology · 2025Review
- Genome-wide rules of transcription factor cooperativity revealed throughbioRxiv : the preprint server for biology · 2025Article
- Genome Mountaineering: Expanding Horizons of the 3D Genome for the Intrepid Evolutionary Adventurer.Genome biology and evolution · 2025Review
- A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs.BMC genomics · 2025Article
- Identification and Characterization of LINE and SINE Retrotransposons in the African Hedgehog (Genes · 2025Article
- CTCF-mediated insulation and chromatin environment modulate Car5b escape from X inactivation.BMC biology · 2025Article
- Pioneer factor GATA6 promotes colorectal cancer through 3D genome regulation.Science advances · 2025Article
- Widespread 3D genome reorganization precedes programmed DNA rearrangement inbioRxiv : the preprint server for biology · 2025Article
- Functional Validation of Noncoding Variants Associated With Nonsyndromic Orofacial Cleft.Human mutation · 2025Review
- An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes.Genome research · 2024Article
- Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion.Genome biology · 2024Article
23 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 3 institutions in 3 countries.
Funding
Abstract
backgroundCTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive.
resultsWe carry out an experimental and computational study that exploits the natural genetic variation across five closely related species to assess how CTCF binding patterns stably fixed by evolution in each species contribute to the establishment and evolutionary dynamics of TAD boundaries. We perform CTCF ChIP-seq in multiple mouse species to create genome-wide binding profiles and associate them with TAD boundaries. Our analyses reveal that CTCF binding is maintained at TAD boundaries by a balance of selective constraints and dynamic evolutionary processes. Regardless of their conservation across species, CTCF binding sites at TAD boundaries are subject to stronger sequence and functional constraints compared to other CTCF sites. TAD boundaries frequently harbor dynamically evolving clusters containing both evolutionarily old and young CTCF sites as a result of the repeated acquisition of new species-specific sites close to conserved ones. The overwhelming majority of clustered CTCF sites colocalize with cohesin and are significantly closer to gene transcription start sites than nonclustered CTCF sites, suggesting that CTCF clusters particularly contribute to cohesin stabilization and transcriptional regulation.
conclusionsDynamic conservation of CTCF site clusters is an apparently important feature of CTCF binding evolution that is critical to the functional stability of a higher-order chromatin structure.
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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.