EXPERIMENT_TITLE: GSM2747749: Hi-C: Scc1-AID control + auxin, 120 min; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: ChIP-Seq: Cells were cross-linked and scrapped of the plate. The DNA was fragmented and the protein of interest was immunoprecipitated with indicated antibodies; Adaptors were ligated to the 5' and 3' ends and the library was prepared for Illumina sequencing by a qPCR amplification step. ChIP as well as Hi-C libraries were prepared for sequencing using standard Illumina protocols.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Mammalian genomes are organized into compartments, topologically-associating domains (TADs) and loops to facilitate gene regulation and other chromosomal functions. Compartments are formed by nucleosomal interactions, but how TADs and loops are generated is unknown. It has been proposed that cohesin forms these structures by extruding loops until it encounters CTCF, but direct evidence for this hypothesis is missing. Here we show that cohesin suppresses compartments but is essential for TADs and loops, that CTCF defines their boundaries, and that WAPL and its PDS5 binding partners control the length of chromatin loops. In the absence of WAPL and PDS5 proteins, cohesin passes CTCF sites with increased frequency, forms extended chromatin loops, accumulates in axial chromosomal positions (vermicelli) and condenses chromosomes to an extent normally only seen in mitosis. These results show that cohesin has an essential genome-wide function in mediating long-range chromatin interactions and support the hypothesis that cohesin creates these by loop extrusion, until it is delayed by CTCF in a manner dependent on PDS5 proteins, or until it is released from DNA by WAPL. Overall design: Analysis of chromatin structure by HiC and ChIP-Seq upon RNAi depletion and auxin-inducible degron (AID) systems.
SAMPLE_TITLE: Hi-C: Scc1-AID control + auxin, 120 min
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "cervical carcinoma"}, {"TAG": "cell type", "VALUE": "HeLa Kyoto"}, {"TAG": "RNAi", "VALUE": "n.a."}, {"TAG": "genotype", "VALUE": "w.t."}, {"TAG": "chip antibody", "VALUE": "n.a."}]
Pool_Member_@attributes_sample_title: Hi-C: Scc1-AID control + auxin, 120 min
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C: Scc1-AID control + auxin, 120 min
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