EXPERIMENT_TITLE: GSM7509215: WT +dTAG+PCI; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were cross-linked in falcon tube. The DNA was fragmented, biotynilated at both ends, and ligated at newly blunted ends together. Biotinylated DNA was captured and prepared for paired-end Illumina sequencing. Libraries were prepared for sequencing using standard Illumina protocols.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Cohesin connects CTCF binding sites and other genomic loci in cis to form chromatin loops, and replicated DNA molecules in trans to mediate sister chromatid cohesion. Whether cohesin uses distinct or related mechanisms to perform these functions is unknown. Here we describe a cohesin hinge mutant, which can extrude DNA into loops but is unable to mediate cohesion. Our results suggest that the latter defect arises during cohesion establishment. The observation that cohesin's cohesion and loop extrusion activities can be separated indicates that cohesin uses distinct mechanisms to perform these two functions. Unexpectedly, the same hinge mutant can also not be stopped by CTCF boundaries as well as wildtype cohesin. This suggests that cohesion establishment and cohesin's interaction with CTCF boundaries depend on related mechanisms and raises the possibility that both require transient hinge opening to entrap DNA inside the cohesin ring. Overall design: Hi-C to analyze the effect of mutations on chromatin architectures in different conditions
SAMPLE_TITLE: WT +dTAG+PCI
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HeLa Kyoto"}, {"TAG": "cell line", "VALUE": "HeLa Kyoto"}, {"TAG": "cell type", "VALUE": "human cervical cancer cells"}, {"TAG": "genotype", "VALUE": "SMC1-AID-mKate2/SCC1-Halo-P2A-Tir1/FKBP-WAPL SMC1-WT"}, {"TAG": "treatment", "VALUE": "doxycycline (+)/Auxin (+)/dTAG(+)/PCI(+)"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: WT +dTAG+PCI
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