ArticleGenome biology2009
CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed, 83 citations in OpenAlex.
- Motif grammar and transcriptional programs decouple CTCF binding from nucleosome phasing to control cell-type-specific chromatin insulation.Cell reports · 2026Article
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- CTCF binding landscape is shaped by the epigenetic state of the N-terminal nucleosome in relation to CTCF motif orientation.Nucleic acids research · 2025Article
- Identifying deleterious noncoding variation through gain and loss of CTCF binding activity.American journal of human genetics · 2025Article
- Motif distribution and DNA methylation underlie distinct Cdx2 binding during development and homeostasis.Nature communications · 2025Article
- Factors that determine cell type-specific CTCF binding in health and disease.Current opinion in genetics & development · 2024Review
- Atypical Modes of CTCF Binding Facilitate Tissue-Specific and Neuronal Activity-Dependent Gene Expression States.Molecular neurobiology · 2024Article
- The PTM profiling of CTCF reveals the regulation of 3D chromatin structure by O-GlcNAcylation.Nature communications · 2024Article
- DNA methylation-dependent and -independent binding of CDX2 directs activation of distinct developmental and homeostatic genes.bioRxiv : the preprint server for biology · 2024Article
- Cell-type differential targeting of SETDB1 prevents aberrant CTCF binding, chromatin looping, and cis-regulatory interactions.Nature communications · 2024Article
- G-quadruplexes associated with R-loops promote CTCF binding.Molecular cell · 2023Article
- DNA architectural protein CTCF facilitates subset-specific chromatin interactions to limit the formation of memory CD8Immunity · 2023Article
- Characterization of a new CCCTC-binding factor binding site as a dual regulator of Epstein-Barr virus latent infection.PLoS pathogens · 2023Article
- Benefiting from the intrinsic role of epigenetics to predict patterns of CTCF binding.Computational and structural biotechnology journal · 2023Article
- CLIMB: High-dimensional association detection in large scale genomic data.Nature communications · 2022Article
- Regulation ofMolecular and cellular biology · 2022Article
- CTCF: an R/bioconductor data package of human and mouse CTCF binding sites.Bioinformatics advances · 2022Article
- Genetic Background Influences Severity of Colonic Aganglionosis and Response to GDNF Enemas in theInternational journal of molecular sciences · 2021Article
- Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis.PLoS pathogens · 2021Article
- NPM1c impedes CTCF functions through cytoplasmic mislocalization in acute myeloid leukemia.Leukemia · 2020Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
backgroundCTCF (CCCTC-binding factor) is an evolutionarily conserved zinc finger protein involved in diverse functions ranging from negative regulation of MYC, to chromatin insulation of the beta-globin gene cluster, to imprinting of the Igf2 locus. The 11 zinc fingers of CTCF are known to differentially contribute to the CTCF-DNA interaction at different binding sites. It is possible that the differences in CTCF-DNA conformation at different binding sites underlie CTCF's functional diversity. If so, the CTCF binding sites may belong to distinct classes, each compatible with a specific functional role.
resultsWe have classified approximately 26,000 CTCF binding sites in CD4+ T cells into three classes based on their similarity to the well-characterized CTCF DNA-binding motif. We have comprehensively characterized these three classes of CTCF sites with respect to several evolutionary, genomic, epigenomic, transcriptomic and functional features. We find that the low-occupancy sites tend to be cell type specific. Furthermore, while the high-occupancy sites associate with repressive histone marks and greater gene co-expression within a CTCF-flanked block, the low-occupancy sites associate with active histone marks and higher gene expression. We found that the low-occupancy sites have greater conservation in their flanking regions compared to high-occupancy sites. Interestingly, based on a novel class-conservation metric, we observed that human low-occupancy sites tend to be conserved as low-occupancy sites in mouse (and vice versa) more frequently than expected.
conclusionsOur work reveals several key differences among CTCF occupancy-based classes and suggests a critical, yet distinct functional role played by low-occupancy sites.
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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.