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Series GSE237050 Query DataSets for GSE237050
Status Public on Oct 25, 2023
Title Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei
Organisms Xenopus laevis; Homo sapiens; Mus musculus
Experiment type Other
Summary 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.
Contributor(s) Jessberger G, Várnai C, Stocsits RR, Tang W, Stary G, Peters JM
Citation(s) 38129077
Submission date Jul 11, 2023
Last update date Jan 24, 2024
Contact name Roman R Stocsits
Organization name IMP - Research Institute of Molecular Pathology
Lab Jan-Michael Peters' Lab
Street address Campus-Vienna-Biocenter 1
City Vienna
ZIP/Postal code 1030
Country Austria
Platforms (5)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL18936 Illumina HiSeq 2500 (Xenopus laevis)
Samples (19)
GSM7593932 Frog XL177 nuclei ULSS-crosslinking replicate 1
GSM7593933 Frog XL177 nuclei PBS-crosslinking
GSM7593934 Human sperm swim-up replicate 1
This SubSeries is part of SuperSeries:
GSE237051 Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei
BioProject PRJNA993637

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Supplementary file Size Download File type/resource
GSE237050_RAW.tar 12.9 Gb (http)(custom) TAR (of HIC)
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Raw data are available in SRA
Processed data provided as supplementary file

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