EXPERIMENT_TITLE: GSM5953598: DpnII Hi-C on HeLa S3 async with DMSO or Camp treatment: Camp R1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: For each Hi-C library, approximately 1-5 million cells were used as input. Cells were crosslinked for 10 minutes at room temperature in a final concentration of 1% formaldehyde. Glycine was added to quench crosslinking and pellets were frozen at -80C until Hi-C library generation. Hi-C was performed as described in Belagzhal et al, 2017, Methods. Restriction enzyme: DpnII
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The topological state of chromosomes determines their mechanical properties, dynamics, and function. Recent work indicated that interphase chromosomes are largely free of entanglements. Here, we use Hi-C, polymer simulations and multi-contact 3C, and propose that, in contrast, mitotic chromosomes are self-entangled. We explore how a mitotic self-entangled state is converted into an unentangled interphase state during mitotic exit. Most mitotic entanglements are removed during anaphase/telophase, with remaining ones removed during early G1, in a Topoisomerase II-dependent process. Polymer models suggest a two-stage disentanglement pathway: first, decondensation of mitotic chromosomes with remaining condensin loops produces entropic forces that bias Topoisomerase II activity towards decatenation. At the second stage, the loops are released, and formation of new entanglements is prevented by lower Topoisomerase II activity, allowing the establishment of unentangled and territorial G1 chromosomes. When mitotic entanglements are not removed, in experiment and models, a normal interphase state cannot be acquired. Overall design: Hi-C and MC-3C experiments in HeLa S3 and Hi-C experiments in HCT116 + Rad21-mAC cell lines. Hi-C experiments have 1-3 replicates each, MC-3C experiments have 3 replicates each.
SAMPLE_TITLE: DpnII Hi-C on HeLa S3 async with DMSO or Camp treatment: Camp R1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "uterine/cervical adenocarcinoma cell line"}, {"TAG": "cell line", "VALUE": "HeLa-S3 (CCL-2.2)"}, {"TAG": "tissue", "VALUE": "uterine/cervical adenocarcinoma cell line"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: DpnII Hi-C on HeLa S3 async with DMSO or Camp treatment: Camp R1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: DpnII Hi-C on HeLa S3 async with DMSO or Camp treatment: Camp R1
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