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(2021)", "@id": "/publications/509198f5-37e4-4e6f-8205-e5de14e36e56/", "date_published": "2021-02", "uuid": "509198f5-37e4-4e6f-8205-e5de14e36e56", "authors": ["Kubo N", "Ishii H", "Xiong X", "Bianco S", "Meitinger F", "Hu R", "Hocker JD", "Conte M", "Gorkin D", "Yu M", "Li B", "Dixon JR", "Hu M", "Nicodemi M", "Zhao H", "Ren B"], "abstract": "The CCCTC-binding factor (CTCF) works together with the cohesin complex to drive  the formation of chromatin loops and topologically associating domains, but its role in gene regulation has not been fully defined. Here, we investigated the effects of acute CTCF loss on chromatin architecture and transcriptional programs in mouse embryonic stem cells undergoing differentiation to neural precursor cells. We identified CTCF-dependent enhancer-promoter contacts genome-wide and found that they disproportionately affect genes that are bound by CTCF at the promoter and are dependent on long-distance enhancers. Disruption of promoter-proximal CTCF binding reduced both long-range enhancer-promoter contacts and transcription, which were restored by artificial tethering of CTCF to the promoter. Promoter-proximal CTCF binding is correlated with the transcription of  over 2,000 genes across a diverse set of adult tissues. Taken together, the results of our study show that CTCF binding to promoters may promote long-distance enhancer-dependent transcription at specific genes in diverse cell  types.", "title": "Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation.", "ID": "PMID:33398174", "@type": ["Publication", "Item"], "status": "current", "display_title": "Kubo N et al. 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Here, we investigated the effects of acute CTCF loss on chromatin architecture and transcriptional programs in mouse embryonic stem cells undergoing differentiation to neural precursor cells. We identified CTCF-dependent enhancer-promoter contacts genome-wide and found that they disproportionately affect genes that are bound by CTCF at the promoter and are dependent on long-distance enhancers. Disruption of promoter-proximal CTCF binding reduced both long-range enhancer-promoter contacts and transcription, which were restored by artificial tethering of CTCF to the promoter. Promoter-proximal CTCF binding is correlated with the transcription of  over 2,000 genes across a diverse set of adult tissues. Taken together, the results of our study show that CTCF binding to promoters may promote long-distance enhancer-dependent transcription at specific genes in diverse cell  types.", "status": "current", "journal": "Nature structural & molecular biology", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "MboI", "combined": "Enzyme: MboI"}, "experiment_summary": "in situ Hi-C on F123-CASTx129 (Tier 2) with MboI", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBS8OV52KV/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing doubling_number", "Biosample missing passage_number", "Biosample missing morphology_image", "Biosample is a stem cell line with unknown passage number missing karyotype"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}