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Another notable difference is that a filter is applied to remove reads with MAPQ scores below 30 prior to mcool file generation."}], "@id": "/experiments-hi-c/4DNEXIH9RYFN/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "1214bcd0-54b7-471d-9d5e-9c7ad65aa72f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "in situ Hi-C on CH12 with MboI - 4DNEXIH9RYFN", "external_references": [{"ref": "GEO:GSM3138979", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138979"}], "experiment_sets": [{"status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNES7C6LBWI", "uuid": "227520f7-0c41-47e9-a82c-c5486ad3ca17", "@id": "/experiment-set-replicates/4DNES7C6LBWI/", "experimentset_type": "replicate", "display_title": "4DNES7C6LBWI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"short_attribution": "Vian L et al. (2018)", "@id": "/publications/89ec268b-d05c-4841-8806-a49fb0d99e78/", "date_published": "2018-04-26", "uuid": "89ec268b-d05c-4841-8806-a49fb0d99e78", "authors": ["Vian L", "Pekowska A", "Rao SSP", "Kieffer-Kwon KR", "Jung S", "Baranello L", "Huang SC", "El Khattabi L", "Dose M", "Pruett N", "Sanborn AL", "Canela A", "Maman Y", "Oksanen A", "Resch W", "Li X", "Lee B", "Kovalchuk AL", "Tang Z", "Nelson S", "Di Pierro M", "Cheng RR", "Machol I", "St Hilaire BG", "Durand NC", "Shamim MS", "Stamenova EK", "Onuchic JN", "Ruan Y", "Nussenzweig A", "Levens D", "Aiden EL", "Casellas R"], "abstract": "Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian genomes. However, extrusion has not been visualized in  vivo, and thus, its functional impact and energetics are unknown. Using ultra-deep Hi-C, we show that loop domains form by a process that requires cohesin ATPases. Once formed, however, loops and compartments are maintained for  hours without energy input. Strikingly, without ATP, we observe the emergence of  hundreds of CTCF-independent loops that link regulatory DNA. We also identify architectural \"stripes,\" where a loop anchor interacts with entire domains at high frequency. Stripes often tether super-enhancers to cognate promoters, and in B cells, they facilitate Igh transcription and recombination. Stripe anchors represent major hotspots for topoisomerase-mediated lesions, which promote chromosomal translocations and cancer. In plasmacytomas, stripes can deregulate Igh-translocated oncogenes. We propose that higher organisms have coopted cohesin extrusion to enhance transcription and recombination, with implications for tumor development.", "title": "The Energetics and Physiological Impact of Cohesin Extrusion.", "ID": "PMID:29706548", "@type": ["Publication", "Item"], "status": "current", "display_title": "Vian L et al. (2018) PMID:29706548", "journal": "Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"title": "The Energetics and Physiological Impact of Cohesin Extrusion.", "date_published": "2018-04-26", "display_title": "Vian L et al. (2018) PMID:29706548", "short_attribution": "Vian L et al. (2018)", "authors": ["Vian L", "Pekowska A", "Rao SSP", "Kieffer-Kwon KR", "Jung S", "Baranello L", "Huang SC", "El Khattabi L", "Dose M", "Pruett N", "Sanborn AL", "Canela A", "Maman Y", "Oksanen A", "Resch W", "Li X", "Lee B", "Kovalchuk AL", "Tang Z", "Nelson S", "Di Pierro M", "Cheng RR", "Machol I", "St Hilaire BG", "Durand NC", "Shamim MS", "Stamenova EK", "Onuchic JN", "Ruan Y", "Nussenzweig A", "Levens D", "Aiden EL", "Casellas R"], "ID": "PMID:29706548", "@type": ["Publication", "Item"], "uuid": "89ec268b-d05c-4841-8806-a49fb0d99e78", "@id": "/publications/89ec268b-d05c-4841-8806-a49fb0d99e78/", "abstract": "Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian genomes. However, extrusion has not been visualized in  vivo, and thus, its functional impact and energetics are unknown. Using ultra-deep Hi-C, we show that loop domains form by a process that requires cohesin ATPases. Once formed, however, loops and compartments are maintained for  hours without energy input. Strikingly, without ATP, we observe the emergence of  hundreds of CTCF-independent loops that link regulatory DNA. We also identify architectural \"stripes,\" where a loop anchor interacts with entire domains at high frequency. Stripes often tether super-enhancers to cognate promoters, and in B cells, they facilitate Igh transcription and recombination. Stripe anchors represent major hotspots for topoisomerase-mediated lesions, which promote chromosomal translocations and cancer. In plasmacytomas, stripes can deregulate Igh-translocated oncogenes. We propose that higher organisms have coopted cohesin extrusion to enhance transcription and recombination, with implications for tumor development.", "status": "current", "journal": "Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "MboI", "combined": "Enzyme: MboI"}, "experiment_summary": "in situ Hi-C on CH12 with MboI", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSR9ZILUX/", "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": []}