ArticleeLife2018
Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver.
Article in eLife, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 85 citations in OpenAlex.
- A compendium of chromatin interaction maps in the Giant Panda genome.Communications biology · 2026Article
- HDI-STARR-seq Identifies Functional GH-regulated Sex-Biased Hepatocyte Enhancers Linked to Liver Metabolism and Disease.bioRxiv : the preprint server for biology · 2026Article
- Immune signaling as a determinant of cellular identity and tissue function.Frontiers in immunology · 2026Review
- Single Nucleus MultiOmics Links Novel Transcription Factor Motifs to Murine Hepatic Sex Differences in Chromatin Accessibility and Metabolic Dysfunction-Associated Steatotic Liver Disease.bioRxiv : the preprint server for biology · 2025Article
- CTCF-anchored chromatin loop dynamics during human meiosis.BMC biology · 2025Article
- Essential roles of CTCF binding sites at TAD boundaries in modulating chromatin interactions and transcriptional regulation at theFrontiers in immunology · 2025Article
- HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo.BMC genomics · 2024Article
- An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes.Genome research · 2024Article
- SMC3 contributes to heart development by regulating super-enhancer associated genes.Experimental & molecular medicine · 2024Article
- CatLearning: highly accurate gene expression prediction from histone mark.Briefings in bioinformatics · 2024Article
- Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet.Journal of animal science and biotechnology · 2024Article
- Article
- Plasma Growth Hormone Pulses Induce Male-biased Pulsatile Chromatin Opening and Epigenetic Regulation in Adult Mouse Liver.bioRxiv : the preprint server for biology · 2023Article
- Transposable elements in mammalian chromatin organization.Nature reviews. Genetics · 2023Review
- Article
- Inferring CTCF-binding patterns and anchored loops across human tissues and cell types.Patterns (New York, N.Y.) · 2023Article
- Low-affinity CTCF binding drives transcriptional regulation whereas high-affinity binding encompasses architectural functions.iScience · 2023Article
- Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries.Genome research · 2023Article
- Integrating extrusion complex-associated pattern to predict cell type-specific long-range chromatin loops.iScience · 2022Article
- Cohesin and CTCF complexes mediate contacts in chromatin loops depending on nucleosome positions.Biophysical journal · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
CTCF and cohesin are key drivers of 3D-nuclear organization, anchoring the megabase-scale Topologically Associating Domains (TADs) that segment the genome. Here, we present and validate a computational method to predict cohesin-and-CTCF binding sites that form intra-TAD DNA loops. The intra-TAD loop anchors identified are structurally indistinguishable from TAD anchors regarding binding partners, sequence conservation, and resistance to cohesin knockdown; further, the intra-TAD loops retain key functional features of TADs, including chromatin contact insulation, blockage of repressive histone mark spread, and ubiquity across tissues. We propose that intra-TAD loops form by the same loop extrusion mechanism as the larger TAD loops, and that their shorter length enables finer regulatory control in restricting enhancer-promoter interactions, which enables selective, high-level expression of gene targets of super-enhancers and genes located within repressive nuclear compartments. These findings elucidate the role of intra-TAD cohesin-and-CTCF binding in nuclear organization associated with widespread insulation of distal enhancer activity.
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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.