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(2021)", "display_title": "Huang H et al. (2021) PMID:34002095", "@type": ["Publication", "Item"], "authors": ["Huang H", "Zhu Q", "Jussila A", "Han Y", "Bintu B", "Kern C", "Conte M", "Zhang Y", "Bianco S", "Chiariello AM", "Yu M", "Hu R", "Tastemel M", "Juric I", "Hu M", "Nicodemi M", "Zhuang X", "Ren B"], "@id": "/publications/4f766397-5ead-416e-b891-1c95391dcd77/", "uuid": "4f766397-5ead-416e-b891-1c95391dcd77", "date_published": "2021-07", "title": "CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.", "journal": "Nature genetics", "abstract": "Insulators play a critical role in spatiotemporal gene regulation in animals. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here we  explore the sequence requirements of CTCF-mediated transcriptional insulation using a sensitive insulator reporter in mouse embryonic stem cells. We find that  insulation potency depends on the number of CTCF-binding sites in tandem. Furthermore, CTCF-mediated insulation is dependent on upstream flanking sequences at its binding sites. CTCF-binding sites at topologically associating domain boundaries are more likely to function as insulators than those outside topologically associating domain boundaries, independently of binding strength. We demonstrate that insulators form local chromatin domain boundaries and weaken  enhancer-promoter contacts. Taken together, our results provide genetic, molecular and structural evidence connecting chromatin topology to the action of  insulators in the mammalian genome.", "ID": "PMID:34002095", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"date_published": "2021-07", "@type": ["Publication", "Item"], "uuid": "4f766397-5ead-416e-b891-1c95391dcd77", "ID": "PMID:34002095", "authors": ["Huang H", "Zhu Q", "Jussila A", "Han Y", "Bintu B", "Kern C", "Conte M", "Zhang Y", "Bianco S", "Chiariello AM", "Yu M", "Hu R", "Tastemel M", "Juric I", "Hu M", "Nicodemi M", "Zhuang X", "Ren B"], "abstract": "Insulators play a critical role in spatiotemporal gene regulation in animals. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here we  explore the sequence requirements of CTCF-mediated transcriptional insulation using a sensitive insulator reporter in mouse embryonic stem cells. We find that  insulation potency depends on the number of CTCF-binding sites in tandem. Furthermore, CTCF-mediated insulation is dependent on upstream flanking sequences at its binding sites. CTCF-binding sites at topologically associating domain boundaries are more likely to function as insulators than those outside topologically associating domain boundaries, independently of binding strength. We demonstrate that insulators form local chromatin domain boundaries and weaken  enhancer-promoter contacts. Taken together, our results provide genetic, molecular and structural evidence connecting chromatin topology to the action of  insulators in the mammalian genome.", "short_attribution": "Huang H et al. (2021)", "@id": "/publications/4f766397-5ead-416e-b891-1c95391dcd77/", "display_title": "Huang H et al. (2021) PMID:34002095", "title": "CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.", "status": "current", "journal": "Nature genetics", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "H3K4me3", "combined": "Target: H3K4me3"}, "experiment_summary": "PLAC-seq against H3K4me3 on F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSFXJHF19/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing Cell Culture Details"], "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": []}