ArticleBMC genomics2016
CTCF-mediated chromatin loops enclose inducible gene regulatory domains.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 68 citations in OpenAlex.
- Cross-cell-line conservation-resolved interactions reveal conservation-dependent relationships among CTCF loops.BMC genomics · 2026Article
- Identification of cis-regulatory elements provides insights into tissue-specific gene regulation in the sheep genome.Nature communications · 2026Article
- TF-loop: deciphering the transcription factor regulatory language for CTCF-mediated chromatin loop based on BERT.Briefings in bioinformatics · 2026Article
- Virus-human chromatin interactions reorganise 3D genome and hijack KDM5B for promoting metastasis in nasopharyngeal carcinoma.Nature communications · 2025Article
- DeSUMOylation of chromatin-bound proteins limits the rapid transcriptional reprogramming induced by daunorubicin in acute myeloid leukemias.Nucleic acids research · 2023Article
- Exploring the impact of dexamethasone on gene regulation in myeloma cells.Life science alliance · 2023Article
- Inferring CTCF-binding patterns and anchored loops across human tissues and cell types.Patterns (New York, N.Y.) · 2023Article
- An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics.Science advances · 2023Article
- Remembering through the genome: the role of chromatin states in brain functions and diseases.Translational psychiatry · 2023Review
- Functional annotation of the animal genomes: An integrated annotation resource for the horse.PLoS genetics · 2023Review
- MINE is a method for detecting spatial density of regulatory chromatin interactions based on a multi-modal network.Cell reports methods · 2023Article
- Integrating extrusion complex-associated pattern to predict cell type-specific long-range chromatin loops.iScience · 2022Article
- Cathepsin B Gene Knockout Improves Behavioral Deficits and Reduces Pathology in Models of Neurologic Disorders.Pharmacological reviews · 2022Review
- The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation.Science advances · 2022Article
- Three-dimensional loop extrusion.Biophysical journal · 2021Article
- Pig genome functional annotation enhances the biological interpretation of complex traits and human disease.Nature communications · 2021Article
- Complex small-world regulatory networks emerge from the 3D organisation of the human genome.Nature communications · 2021Article
- The roles of inducible chromatin and transcriptional memory in cellular defense system responses to redox-active pollutants.Free radical biology & medicine · 2021Review
- Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research.Nature communications · 2021Article
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Corrections and comments
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe CCTC-binding factor (CTCF) protein is involved in genome organization, including mediating three-dimensional chromatin interactions. Human patient lymphocytes with mutations in a single copy of the CTCF gene have reduced expression of enhancer-associated genes involved in response to stimuli. We hypothesize that CTCF interactions stabilize enhancer-promoter chromatin interaction domains, facilitating increased expression of genes in response to stimuli. Here we systematically investigate this model using computational analyses.
resultsWe use CTCF ChIA-PET data from the ENCODE project to show that CTCF-associated chromatin loops have a tendency to enclose regions of enhancer-regulated stimulus responsive genes, insulating them from neighboring regions of constitutively expressed housekeeping genes. To facilitate cell type-specific CTCF loop identification, we develop an algorithm to predict CTCF loops from ChIP-seq data alone by exploiting the CTCF motif directionality in loop anchors. We apply this algorithm to a hundred ENCODE cell line datasets, confirming the universality of our observations as well as identifying a general distinction between primary and immortal cells in loop-enclosed gene content. Finally, we combine the existing evidence to propose a model for the formation of CTCF loops in which partner sites are brought together by chromatin template reeling through stationary RNA polymerases, consistent with the transcription factory hypothesis.
conclusionsWe provide computational evidence that CTCF-mediated chromatin interactions enclose domains of stimulus responsive enhancer-regulated genes, insulating them from nearby housekeeping genes.
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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.