Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei
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ABSTRACT:
PROVIDER: PRJNA993638 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25233844.fastq.gz | Fastqsanger.gz | |||
| SRR25233845.fastq.gz | Fastqsanger.gz | |||
| SRR25233846.fastq.gz | Fastqsanger.gz | |||
| SRR25233847.fastq.gz | Fastqsanger.gz | |||
| SRR25233848.fastq.gz | Fastqsanger.gz |
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Project description: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.
2023-10-25 | GSE237050 | GEO
Project description: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.
2023-10-25 | GSE237049 | GEO
Project description:Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei
| PRJNA993630 | ENA
Project description:Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei
| PRJNA993637 | ENA
Project description: Not available
| S-EPMC10760524 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-10-25 | GSE237051 | GEO
Project description:Embryogenesis begins with a zygote, a single cell with two pronuclei that separately enclose maternal and paternal chromosomes. The functional significance of the separation of parental chromosomes into distinct pronuclei remains unexplored, despite the fact that one-pronuclear biparental zygotes are used clinically. Here, using a combination of mouse zygote manipulation, quantitative imaging and theoretical approaches, we show a cytoplasm-mediated competition mechanism between separate parental pronuclei. This mechanism limits pronuclear volume and prevents the loss of epigenetic marks, including maternally inherited trimethylated histones. One-pronuclear biparental zygotes lack this mechanism, resulting in a reduced rate of development to term. This low developmental potential can be rescued by competition-based or drug-based restoration of epigenetic marks. In human zygotes, epigenetic loss correlates with pronuclear volume. This study provides insight into strategies to improve the clinical use of one-pronuclear biparental zygotes.
2026-02-26 | GSE231732 | GEO
Project description:Eukaryotic genomes are compacted into loops and topologically associating domains (TADs), which contribute to transcription, recombination and genomic stability. Cohesin extrudes DNA into loops that are thought to lengthen until it encounters CTCF boundaries. Little is known whether loop extrusion is impeded by macromolecular machines. We demonstrate that the replicative helicase MCM is a barrier that restricts loops and TADs in G1 phase. Single-nucleus Hi-C of one-cell embryos revealed that MCM loading reduces CTCF-anchored loops and increases TAD boundary insulation, suggesting loop extrusion is impeded before reaching CTCF. Single-molecule imaging provides evidence that MCM are physical barriers that constrain cohesin translocation in vitro. Simulations are consistent with MCM as abundant, random barriers with low permeability. We conclude that distinct loop extrusion barriers contribute to shaping 3D genomes.
2022-03-07 | GSE155971 | GEO
Project description:It has been demonstrated previously that the reprogramming factors are sequestered in the pronuclei of zygote after fertilization, as the enucleated zygotes at interphase cannot support the development of cloned embryos whereas the enucleated zygotes at M-phase can reprogram somatic cells to full pluripotency. However, it remains unknown whether the parental pronucleus, derived either from the sperm or oocyte, possesses the similar reprogramming ability. Here, we provide evidence demonstrating that the parental pronuclei are asymmetric in reprogramming and the reprogramming factors reside mainly in the male pronucleus. As a result, only the female pronucleus-depleted mouse zygotes enucleated at M-phase of mitosis can support the somatic cell reprogramming, the derivation of chromosome transfer embryonic stem (ctES) cells with full pluripotency and the full term development of cloned embryos. In striking contrast, the male pronucleus-depleted zygotes enucleated at M-phase of mitosis fail to support the pre-implantation development of somatic cell cloned embryos. Furthermore, we demonstrated that the distinct epigenetic reprogramming ability of the parental pronucleus might contribute directly to the developmental difference of somatic cloned embryos. Our study highlights the developmental asymmetry of parental pronuclei in reprogramming.
2014-12-30 | GSE49148 | GEO
Project description:The mammalian genome is sequentially partitioned from chromosomes into looped chromatin regions termed Topologically Associating Domains (TADs), and then into numerous smaller sub-TAD loops, each bounded and insulated by CTCF and Cohesin. The sub-TADs encompass enhancers, promoters and often multiple genes but whether promoter-enhancer interactions and gene regulation are broadly restricted to within the sub-TAD loops has not been functionally determined. Here we identify “Gene Unit Sub-TADs” or GUSTs as a class of sub-TADs that confine promoter-enhancer interactions and demarcate functional gene regulatory regions. We depleted Estrogen-related receptor β (Esrrb), which binds to the Mediator co-activator complex, to impair the activity of enhancers controlling 245 mouse embryonic stem cell genes. We find that most Esrrb-responsive enhancers lack significant Cohesin binding but instead correlate with Mediator binding. Esrrb depletion causes reduced Mediator binding, decreased nascent RNA expression and diminished promoter-enhancer looping. In 88% of the cases examined, the effects of Esrrb depletion are restricted to enhancers and target genes within GUSTs. In some GUSTs, active genes lay alongside inactive ones but are distinguished by their proximal promoter chromatin accessibility, explaining further the specificity of enhancer-promoter interactions within GUSTs. Our data indicate that GUSTs represent functional gene regulons in mammalian genomes.
2018-10-19 | GSE115340 | GEO