ArticleNature communications2021
Loop competition and extrusion model predicts CTCF interaction specificity.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
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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
34 citing papers in PubMed, 46 citations in OpenAlex.
- TF-loop: deciphering the transcription factor regulatory language for CTCF-mediated chromatin loop based on BERT.Briefings in bioinformatics · 2026Article
- Epigenetic Regulation of Higher-Order Chromatin Structure (HOCS) and Its Implication in Human Diseases.Cancers · 2026Review
- The 3D Genome Structure of a Blcap-Linked Silencer Loop Regulates Terminal Differentiation During Lens Fiber Cell Denucleation.Investigative ophthalmology & visual science · 2025Article
- Non-local modeling of enhancer-promoter interactions, a correspondence on "LOCO-EPI: Leave-one-chromosome-out (LOCO) as a benchmarking paradigm for deep learning based prediction of enhancer-promoter interactions".Applied intelligence (Dordrecht, Netherlands) · 2025Article
- CXCL Gene Clusters Regulated by Enhancer-Mediated DNA Looping Alteration in Pancreatic Cancer Cells.Journal of cellular and molecular medicine · 2025Article
- CTCF-anchored chromatin loop dynamics during human meiosis.BMC biology · 2025Article
- Integrating Single-Molecule Sequencing and Deep Learning to Predict Haplotype-Specific 3D Chromatin Organization in a Mendelian Condition.bioRxiv : the preprint server for biology · 2025Article
- Linking DNA-packing density distribution and TAD boundary locations.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- FLT1 and other candidate fetal haemoglobin modifying loci in sickle cell disease in African ancestries.Nature communications · 2025Article
- Gaining insights into Alzheimer's disease by predicting chromatin spatial organization.Bioinformatics advances · 2025Article
- Multifaceted role of CTCF in X-chromosome inactivation.Chromosoma · 2024Review
- YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle.Nature genetics · 2024Article
- Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals.Nature communications · 2024Article
- Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.Genome research · 2024Article
- TF-EPI: an interpretable enhancer-promoter interaction detection method based on Transformer.Frontiers in genetics · 2024Article
- MicroRNAs provide negative feedback and stability in gene regulatory network models of cell-state transitions.Frontiers in epigenetics and epigenomics · 2024Article
- Involvement of CCCTC-binding factor in epigenetic regulation of cancer.Molecular biology reports · 2023Review
- Explainable artificial intelligence for omics data: a systematic mapping study.Briefings in bioinformatics · 2023Review
- Inferring CTCF-binding patterns and anchored loops across human tissues and cell types.Patterns (New York, N.Y.) · 2023Article
- Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.Nature genetics · 2023Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Three-dimensional chromatin looping interactions play an important role in constraining enhancer-promoter interactions and mediating transcriptional gene regulation. CTCF is thought to play a critical role in the formation of these loops, but the specificity of which CTCF binding events form loops and which do not is difficult to predict. Loops often have convergent CTCF binding site motif orientation, but this constraint alone is only weakly predictive of genome-wide interaction data. Here we present an easily interpretable and simple mathematical model of CTCF mediated loop formation which is consistent with Cohesin extrusion and can predict ChIA-PET CTCF looping interaction measurements with high accuracy. Competition between overlapping loops is a critical determinant of loop specificity. We show that this model is consistent with observed chromatin interaction frequency changes induced by CTCF binding site deletion, inversion, and mutation, and is also consistent with observed constraints on validated enhancer-promoter interactions.
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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.