EXPERIMENT_TITLE: GSM2913119: Hap1-CAPH2KO; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C was performed essentially as previously described (Rao et al., 2014). Briefly, for each template roughly 10 million cells were crosslinked using 2% formaldehyde. In nucleus restriction was performed using MboI. Restriction overhangs were filled in with biotinylated nucleotides followed by blunt-end ligation. A streptavidin pull-down was performed to enrich for ligated sequences. Pulled-down DNA was end-repaired and an A-overhang was added. Sequencing adapters were ligated to the DNA samples to create sequencing libraries.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Condensin is a conserved SMC complex that uses its ATPase machinery to structure genomes, but how it does so is largely unknown. We show that condensin's ATPase has a dual role in chromosome condensation. Mutation of one ATPase site impairs condensation, while mutating the second site results in hyperactive condensin that compacts DNA faster than wild type, both in vivo and in vitro. Whereas one site drives loop formation, the second site is involved in the formation of more stable higher-order Z loop structures. Using hyperactive condensin I, we reveal that condensin II is not intrinsically needed for the shortening of mitotic chromosomes. Condensin II rather is required for a straight chromosomal axis and enables faithful chromosome segregation by counteracting the formation of ultrafine DNA bridges. SMC complexes with distinct roles for each ATPase site likely reflect a universal principle that enables these molecular machines to intricately control chromosome architecture. Overall design: Hi-C was performed in control, Caph2KO, AS2LV, AS1LV, AS2LV/LV, SMC2WT/? and CAPH2KO-AS2LV cell lines in technical replicates.
SAMPLE_TITLE: Hap1-CAPH2KO
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Hap1-CAPH2KO"}, {"TAG": "cell type", "VALUE": "Hap1"}]
Pool_Member_@attributes_sample_title: Hap1-CAPH2KO
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hap1-CAPH2KO
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