EXPERIMENT_TITLE: GSM4331884: Synchronised G1 R1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: HindIII-based Hi-C libraries were captured using SureSelect target enrichment system, using a custom-designed RNA bait library and paired-end blockers. Promoter-based ligated products were isolated and amplified PCHiC libraries were constructed using HindIII as described in (Schoenfelder et al. 2018 and Wutz et al. 2017). PCHiC
STUDY_DESCRIPTOR_STUDY_ABSTRACT: It is currently assumed that 3D chromosomal organisation plays a central role in transcriptional control. However, recent evidence shows that steady-state transcription of only a minority of genes is affected by depletion of architectural proteins such as cohesin and CTCF. Here, we have used Capture Hi-C to interrogate the dynamics of chromosomal contacts of all human gene promoters upon rapid architectural protein degradation. We show that promoter contacts lost in these conditions tend to be long-range, with at least one interaction partner localising in the vicinity of topologically associated domain (TAD) boundaries. In contrast, many shorter-range chromosomal contacts, particularly those that connect active promoters with each other and with active enhancers remain unaffected by cohesin and CTCF depletion. We demonstrate that the effects of cohesin depletion on nascent transcription can be explained by changes in the connectivity of their enhancers. Jointly, these results provide a mechanistic explanation to the limited, but consistent effects of cohesin and CTCF on steady-state transcription and point towards the existence of alternative enhancer-promoter pairing mechanisms that are independent of these proteins. Overall design: PCHiC was performed on HeLa kyoto cells in which SCC1 and separately CTCF were raplidly and selectively depleted using an Auxin inducible degron. Additionally, PCHiC was performed on synchronised cells in G1, G2 and Mitosis. Lastly, PCHiC was performed on triple RNAi inhibited cells for WAPL, PDS5A and PDS5B
SAMPLE_TITLE: Synchronised G1 R1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HeLa synchronised interphase"}, {"TAG": "strain", "VALUE": "Kyoto"}, {"TAG": "type", "VALUE": "15h release after thymidine"}, {"TAG": "treatment", "VALUE": "contol (interphase)"}]
Pool_Member_@attributes_sample_title: Synchronised G1 R1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Synchronised G1 R1
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