EXPERIMENT_TITLE: GSM7593941: Human sperm DGC biol. rep. 4; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Samples were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Hi-C was performed according to the previously described in situ Hi-C protocol (Rao et al., Cell 2014). Hi-C libraries were prepared according to the previously described in situ Hi-C protocol (Rao et al., Cell 2014).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Paternal genomes are compacted during spermiogenesis and de-compacted following fertilization. These processes are fundamental for inheritance but incompletely understood. We analyzed these processes in the frog Xenopus laevis, whose sperm can be assembled into functional pronuclei in egg extracts in vitro. In such extracts, cohesin extrudes DNA into loops, but in vivo cohesin only assembles topologically-associating domains (TADs) at the mid-blastula transition (MBT). Why cohesin assembles TADs only at this stage is unknown. We first analyzed genome architecture in frog sperm and compared it to human and mouse. Our results indicate that sperm genome organization is conserved between frogs and humans and occurs without formation of TADs. TADs can be detected in mouse sperm samples, as reported, but these structures might originate from somatic chromatin contaminations. We therefore discuss the possibility that the absence of TADs might be a general feature of vertebrate sperm. To analyze sperm genome remodeling upon fertilization, we reconstituted male pronuclei in Xenopus egg extracts. In pronuclei, chromatin compartmentalization increases but cohesin does not accumulate at CTCF sites and assemble TADs. However, if pronuclei are formed in the presence of exogenous CTCF, CTCF binds to its consensus sites, cohesin accumulates at these and forms short-range chromatin loops, which are preferentially anchored at CTCF's N-terminus. These results indicate that TADs are only assembled at MBT because before this stage CTCF sites are not occupied and cohesin only forms short-range chromatin loops. Overall design: Hi-C in human, mouse and Xenopus laevis sperm, pronuclei generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract and Xenopus laevis XL177 cells.
SAMPLE_TITLE: Human sperm DGC biol. rep. 4
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "human sperm isolated from ejaculate by discontinuous density gradient centrifugation (DGC)"}, {"TAG": "tissue", "VALUE": "human sperm isolated from ejaculate by discontinuous density gradient centrifugation (DGC)"}, {"TAG": "cell type", "VALUE": "human sperm"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: Human sperm DGC biol. rep. 4
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Human sperm DGC biol. rep. 4
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