ArticlePloS one2012
Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
117 citing papers in PubMed, 174 citations in OpenAlex.
- CLASH (Chromatin Loop Across-sample Score Harmonizer) quantifies the relative contributions of genetic variation, methylation, and CTCF occupancy on chromatin loop strength across individuals.bioRxiv : the preprint server for biology · 2026Article
- DREAM-Stellar: parallel and space efficient exact local alignment.BMC bioinformatics · 2026Article
- Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells.G3 (Bethesda, Md.) · 2026Article
- Runx2 downregulates Lpl expression through super-silencer formation to alter lipid metabolism in Zhu Schwann cells after nerve injury.Cellular & molecular biology letters · 2025Article
- Fragment dispersity index analysis of cfDNA fragments reveals chromatin accessibility and enables early cancer detection.Cell reports methods · 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
- Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation.Cell genomics · 2025Article
- Interplay between CTCF-binding and CTCF-lacking regulatory elements in generating an architectural stripe at the Igh locus.Nature communications · 2025Article
- Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues.Nature structural & molecular biology · 2025Article
- The Regulatory Role of CTCF in IL6 Gene Transcription Assessed in Breast Cancer Cell Lines.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Simultaneous profiling of chromatin-associated RNA at targeted DNA loci and RNA-RNA Interactions through TaDRIM-seq.Nature communications · 2025Article
- Repression of CADM1 transcription by HPV type 18 is mediated by three-dimensional rearrangement of promoter-enhancer interactions.PLoS pathogens · 2025Article
- Gaining insights into Alzheimer's disease by predicting chromatin spatial organization.Bioinformatics advances · 2025Article
- Machine and Deep Learning Methods for Predicting 3D Genome Organization.Methods in molecular biology (Clifton, N.J.) · 2025Review
- The chromatin tapestry as a framework for neurodevelopment.Genome research · 2024Review
- Identifying transcription factors with cell-type specific DNA binding signatures.BMC genomics · 2024Article
- Machine learning enables pan-cancer identification of mutational hotspots at persistent CTCF binding sites.Nucleic acids research · 2024Article
- Brain and cancer associated binding domain mutations provide insight into CTCF's relationship with chromatin and its ability to act as a chromatin organizer.Research square · 2024Article
- Intertwining roles of R-loops and G-quadruplexes in DNA repair, transcription and genome organization.Nature cell biology · 2024Review
- Atypical Modes of CTCF Binding Facilitate Tissue-Specific and Neuronal Activity-Dependent Gene Expression States.Molecular neurobiology · 2024Article
57 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromatin insulators are DNA elements that regulate the level of gene expression either by preventing gene silencing through the maintenance of heterochromatin boundaries or by preventing gene activation by blocking interactions between enhancers and promoters. CCCTC-binding factor (CTCF), a ubiquitously expressed 11-zinc-finger DNA-binding protein, is the only protein implicated in the establishment of insulators in vertebrates. While CTCF has been implicated in diverse regulatory functions, CTCF has only been studied in a limited number of cell types across human genome. Thus, it is not clear whether the identified cell type-specific differences in CTCF-binding sites are functionally significant. Here, we identify and characterize cell type-specific and ubiquitous CTCF-binding sites in the human genome across 38 cell types designated by the Encyclopedia of DNA Elements (ENCODE) consortium. These cell type-specific and ubiquitous CTCF-binding sites show uniquely versatile transcriptional functions and characteristic chromatin features. In addition, we confirm the insulator barrier function of CTCF-binding and explore the novel function of CTCF in DNA replication. These results represent a critical step toward the comprehensive and systematic understanding of CTCF-dependent insulators and their versatile roles in the human genome.
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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.