ArticleBMC genomics2013
Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 73 citations in OpenAlex.
- Article
- Evolution of CTCF binding sites in the human genome.Molecular biology and evolution · 2026Article
- The nuclear structural protein NuMA is required for efficient DNA replication by ensuring association of core replication factors to replication forks.bioRxiv : the preprint server for biology · 2026Article
- STARR-CRAAVT: A platform to identify cell type-specific regulatory elements for next-generation gene therapy.iScience · 2026Article
- CTCF/cohesin-binding sites are susceptible to replication-associated DNA damage and genomic instability in cancer cells.iScience · 2026Article
- In Silico Analysis of Post-COVID-19 Condition (PCC) Associated SNP rs9367106 Predicts the Molecular Basis of Abnormalities in the Lungs and Brain Functions.International journal of molecular sciences · 2025Article
- Article
- Neural network modeling of differential binding between wild-type and mutant CTCF reveals putative binding preferences for zinc fingers 1-2.BMC genomics · 2022Article
- The Myc-associated zinc finger protein (MAZ) works together with CTCF to control cohesin positioning and genome organization.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Review
- Implication of a new function of human tDNAs in chromatin organization.Scientific reports · 2020Article
- CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity.BMC genetics · 2020Article
- Unraveling the Hierarchy ofMolecular and cellular biology · 2020Article
- The conserved DNMT1-dependent methylation regions in human cells are vulnerable to neurotoxicant rotenone exposure.Epigenetics & chromatin · 2020Article
- Shortened nuclear matrix attachment regions are sufficient for replication and maintenance of episomes in mammalian cells.Molecular biology of the cell · 2019Article
- The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist.Nature genetics · 2019Article
- Alternative FunctionalFrontiers in microbiology · 2019Article
- Genomic identification and functional analysis of essential genes in Caenorhabditis elegans.BMC genomics · 2018Article
- Intergenic and intronic DNA hypomethylated regions as putative regulators of imprinted domains.Epigenomics · 2018Article
- Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2018Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundRecent studies suggested that human/mammalian genomes are divided into large, discrete domains that are units of chromosome organization. CTCF, a CCCTC binding factor, has a diverse role in genome regulation including transcriptional regulation, chromosome-boundary insulation, DNA replication, and chromatin packaging. It remains unclear whether a subset of CTCF binding sites plays a functional role in establishing/maintaining chromatin topological domains.
resultsWe systematically analysed the genomic, transcriptomic and epigenetic profiles of the CTCF binding sites in 56 human cell lines from ENCODE. We identified ~24,000 CTCF sites (referred to as constitutive sites) that were bound in more than 90% of the cell lines. Our analysis revealed: 1) constitutive CTCF loci were located in constitutive open chromatin and often co-localized with constitutive cohesin loci; 2) most constitutive CTCF loci were distant from transcription start sites and lacked CpG islands but were enriched with the full-spectrum CTCF motifs: a recently reported 33/34-mer and two other potentially novel (22/26-mer); 3) more importantly, most constitutive CTCF loci were present in CTCF-mediated chromatin interactions detected by ChIA-PET and these pair-wise interactions occurred predominantly within, but not between, topological domains identified by Hi-C.
conclusionsOur results suggest that the constitutive CTCF sites may play a role in organizing/maintaining the recently identified topological domains that are common across most human cells.
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