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Three-dimensional genome structures of single mammalian sperm [bulk Hi-C]

ABSTRACT: Three-dimensional genome structures of single mammalian sperm [bulk Hi-C]

PROVIDER: PRJNA1160231 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30645656_1.fastq.gz	Fastqsanger.gz
	SRR30645656_2.fastq.gz	Fastqsanger.gz
	SRR30645657_1.fastq.gz	Fastqsanger.gz
	SRR30645657_2.fastq.gz	Fastqsanger.gz

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Similar Datasets

Three-dimensional genome structures of single mammalian sperm [bulk Hi-C]

Project description:The three-dimensional (3D) organization of chromosomes is crucial for packaging a large mammalian genome into a confined nucleus and ensuring proper nuclear functions in somatic cells. However, the packaging of the much more condensed sperm genome is fundamentally different and not as well understood. In this study, we resolved the 3D whole-genome structures of a single mammalian sperm cell using an enhanced chromosome conformation capture assay. The reconstructed genome structures accurately delineate the species-specific nuclear morphologies for both human and mouse sperm. We discovered that sperm genomes are divided into chromosomal territories and A/B compartments, similarly as somatic cells. However, neither human nor mouse sperm chromosomes contain topologically associating domains or chromatin loops. These results suggest that the fine-scale chromosomal organization of mammalian sperm fundamentally differs from that of somatic cells.

2025-03-09 | GSE277018 | GEO

Three-dimensional genome structures of single mammalian sperm

Project description:Three-dimensional genome structures of single mammalian sperm

| PRJNA1160276 | ENA

Three-dimensional genome structures of single mammalian sperm [GAM]

2025-03-09 | GSE277016 | GEO

Three-dimensional genome structures of single mammalian sperm [scHi-C]

2025-03-09 | GSE276999 | GEO

Three-dimensional genome structures of single mammalian sperm [GAM]

Project description:Three-dimensional genome structures of single mammalian sperm [GAM]

| PRJNA1160225 | ENA

Three-dimensional genome structures of single mammalian sperm [scHi-C]

Project description:Three-dimensional genome structures of single mammalian sperm [scHi-C]

| PRJNA1160215 | ENA

Single-cell three dimensional genome structures of rice egg, sperm, and unicellular zygote

Project description:Chromatin conformation capture assays, such as 3C and Hi-C, allow for studies of three-dimensional (3D) genome structures in bulk samples through proximity ligation of DNA. However, the difference between cells can only be observed by single-cell measurements that avoid ensemble averaging3, 4,5. To study 3D chromatin organization and dynamics before and after fertilization in flowering plants, we analyzed the 3D genomes of rice egg, sperm, and unicellular zygote as well as shoot cells. We show that chromatin architectures of rice egg and sperm are comparable to that of somatic cells and are reorganized after fertilization in unicellular zygote. The rice single cell 3D genomes display specific features of chromosome compartments and configuration of telomeres/centromeres compared to those shown in mammalian single cells. Active and silent chromatin domains gather to form multiple foci in the nuclear space. Notably, the 3D genomes of egg, unicellular zygote, and shoot cells contain a compact silent center (CSC), which is absent in sperm. CSC is dynamically reorganized after fertilization and is likely to be involved in gene regulation related to zygotic genome activation (ZGA). Our results reveal specific 3D genome features of plant gametes and unicellular zygote and provide a spatial chromatin basis for ZGA and gene expression in plant.

2019-05-26 | GSE123109 | GEO

Single-cell three dimensional genome structures of rice egg, sperm, and unicellular zygote

Project description:Single-cell three dimensional genome structures of rice egg, sperm, and unicellular zygote

| PRJNA507566 | ENA

Three-dimensional genome structures of single mammalian sperm

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-03-08 | GSE277040 | GEO

Hi-C map of the three-dimensional genome organization

Project description:The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intra-chromosome interaction rates than neighboring regions and which represent a dominant local structural feature of genome conformation in A. thaliana. These regions appear as positive strips on two-dimensional representations of chromatin interaction and they are enriched in epigenetic marks H3K27me3, H3.1 and H3.3. We also identify over 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not the dominant feature of A. thaliana genome packing, we found over 1,000 regions that have properties of TAD boundaries, and a similar number of regions similar to the interior of TADs. These insulator-like, TAD-boundary-like, and TAD-interior-like regions show strong enrichment for distinct epigenetic marks, and correlate with gene transcription levels. We conclude that epigenetic modifications, gene density, and transcriptional activity all contribute to shaping the local structure of the A. thaliana nuclear genome.

2014-09-24 | E-MTAB-4438 | biostudies-arrayexpress

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