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Single-cell Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

ABSTRACT: Single-cell Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

PROVIDER: PRJNA317616 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3343950_1.fastq.gz	Fastqsanger.gz
	SRR3343950_2.fastq.gz	Fastqsanger.gz
	SRR3343960_1.fastq.gz	Fastqsanger.gz
	SRR3343960_2.fastq.gz	Fastqsanger.gz
	SRR3343970_1.fastq.gz	Fastqsanger.gz

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Single-cell Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

Project description:Chromatin is reorganized and reprogrammed after fertilization to produce a totipotent zygote with the potential to generate a new organism. In mammals, the maternal genome inherited through the oocyte and the paternal genome provided by sperm coexist as separate haploid nuclei in interphase of the first cell cycle. How these two epigenetically distinct genomes are spatially organized remains poorly understood. Existing chromosome conformation capture-based methods are inapplicable to oocytes and zygotes due to paucity of material. To study the three-dimensional organization of chromatin in rare cell types, we developed a simplified single-cell Hi-C (sscHi-C) protocol that provides 100-fold more contacts per cell than a previous method. Using sscHi-C, we show that chromatin architecture is uniquely reorganized during the oocyte-to-zygote transition. We found that major features of chromosome organization, compartments, domains and loops are all present in individual cells, with noticeable cell-to-cell variation and differences between male and female nuclei in zygotes. Compartments detected in male nuclei are notably absent from female nuclei, indicating these are the first mammalian interphase nuclei lacking this higher-order structure. While compartments in single cells closely resemble compartments from the cell population, TADs manifest themselves as contact domains (CDs) that differ from cell to cell, nevertheless averaging into TADs in pooled data. Finally, scaling of contact probability with genomic separations suggests that chromosome conformations in oocyte and zygote nuclei are fundamentally different and each are distinct from the global organization of chromosomes in other interphase cells. We conclude that chromatin organization of zygote nuclei is unique and can serve as the chromatin "ground state" of a totipotent cell.

2017-03-23 | GSE80006 | GEO

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition.

Project description:Chromatin is reprogrammed after fertilization to produce a totipotent zygote with the potential to generate a new organism. The maternal genome inherited from the oocyte and the paternal genome provided by sperm coexist as separate haploid nuclei in the zygote. How these two epigenetically distinct genomes are spatially organized is poorly understood. Existing chromosome conformation capture-based methods are not applicable to oocytes and zygotes owing to a paucity of material. To study three-dimensional chromatin organization in rare cell types, we developed a single-nucleus Hi-C (high-resolution chromosome conformation capture) protocol that provides greater than tenfold more contacts per cell than the previous method. Here we show that chromatin architecture is uniquely reorganized during the oocyte-to-zygote transition in mice and is distinct in paternal and maternal nuclei within single-cell zygotes. Features of genomic organization including compartments, topologically associating domains (TADs) and loops are present in individual oocytes when averaged over the genome, but the presence of each feature at a locus varies between cells. At the sub-megabase level, we observed stochastic clusters of contacts that can occur across TAD boundaries but average into TADs. Notably, we found that TADs and loops, but not compartments, are present in zygotic maternal chromatin, suggesting that these are generated by different mechanisms. Our results demonstrate that the global chromatin organization of zygote nuclei is fundamentally different from that of other interphase cells. An understanding of this zygotic chromatin 'ground state' could potentially provide insights into reprogramming cells to a state of totipotency.

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Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation (Hi-C)

Project description:Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation (Hi-C)

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Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation (Hi-C)

Project description:Aging is associated with a progressive decline in cellular function. To reset the aged cellular phenotype, various reprogramming approaches, including mechanical routes, have been proposed. However, the epigenetic mechanisms underlying cellular rejuvenation are poorly understood. We studied the transcriptional and genome-wide chromatin organization changes in young, aged and mechanically rejuvenated fibroblasts using RNA-seq and Hi-C experiments. The mechanically rejuvenated aged fibroblasts, that had reset their transcription to a younger cell state, showed a reorganization of the inter-chromosomal contacts and lamina-associated domains. Interestingly, the observed chromatin reorganization correlated with the transcriptional changes. Immunofluorescence experiments in the rejuvenated state confirmed increased contractility and reduced chromosome copy number variations, similar to younger fibroblasts. In addition, the rejuvenated contractile properties were maintained over multiple cell passages. Taken together, our results provide a multi-scale characterization of the chromatin reorganization that accompanies cellular aging and rejuvenation.

2024-03-20 | GSE237268 | GEO

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Project description:Inherited mitochondrial DNA (mtDNA) diseases transmit maternally and cause severe phenotypes. Since no effective treatment or genetic screening is available, nuclear genome transfer between patients’ and healthy eggs to replace mutant mtDNAs holds promises. Since polar body contains very few mitochondria and share same genomic material as oocyte, here we perform polar body transfer to prevent the transmission of inherited mtDNA variants. We compare the value of different germline genome transfer (spindle-chromosome, pronuclear, first and second polar body) in a mouse model. Reconstructed embryos support normal fertilization and produce live offspring. Strikingly, genetic analysis confirms F1 generation after polar body transfer possesses minimal donor mtDNA carry-over compared with spindle-chromosome (low/medium carry-over) and pronuclear (medium/high carry-over) transfer. Moreover, mtDNA genotype remains stable in F2 generation of progeny after polar body transfer. Our preclinical model demonstrates polar body transfer holds great potential in preventing the transmission of inherited mtDNA diseases. The objective of the present study was to detect genomic aberrations between PB1 and its counterpart, spindle-chromosome complex in human MII oocyte, PB2 and female pronucleus in human zygote at a single-cell level.

2014-06-19 | E-GEOD-56676 | biostudies-arrayexpress

HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [Capture Hi-C]

Project description:We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. To determine whether distal REs come into contact with promoters, instead of using a classical Hi-C, we further combined Hi-C with a capture enrichment step. We generated a biotinylated RNA bait library specifically targeting 212,735 promoter regions and performed a capture Hi-C after 0h, 1h and 6h after stress.

2023-01-03 | GSE206356 | GEO

HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [Hi-C]

Project description:We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. To map the three-dimensional chromatin interactions we performed in situ Hi-C, a genome-wide method that detects DNA-DNA physical interactions.

2023-01-03 | GSE206360 | GEO

Chemical-Induced Phase Transition and Global Conformational Reorganization of Chromatin [Hi-C]

Project description:Chemical-Induced Phase Transition and Global Conformational Reorganization of Chromatin [Hi-C]

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Capture of TAD reorganization endows variant patterns of gene transcription (Hi-C)

Project description:Capture of TAD reorganization endows variant patterns of gene transcription (Hi-C)

| PRJNA962583 | ENA

Granulosa cell mevalonate pathway abnormalities contribute to oocyte meiotic defects and aneuploidy [Hi-C]

Project description:The mechanisms of oocyte meiotic defects and low competence during ovarian aging remains elusive for decades. Using Hi-C (genome-wide chromatin conformation capture) and Smart RNA-seq of oocytes from 6- weeks or 10- months aged ovaries, the abnormal loose chromatin structures and disturbing expression of meiosis associated genes at metaphase I phase were disclosed. Furthermore, the transcriptomic landscape of granulosa cells (GCs) surrounding oocytes from young and aged ovaries reveled that oocyte meiotic maturation was accompanied with a robust increased expression of genes involved with the mevalonate (MVA) pathway in GCs from young ovaries but these genes expression was not upregulated to counterpart level in GCs from aged ovaries.The inhibitor of MVA pathway of GCs, Statins significantly decreased polar body extrusion rate and increased the rate of irregularly assembled spindles and misaligned chromosomes remarkably in oocytes of culumus-oocyte complex (COCs) from young ovaries . Correspondingly, the activitor of MVA pathway of GCs, Geranylgeraniol ameliorated ovarian reserve and reduced meiotic defects in oocytes of COCs from aged ovaries. Mechanistically, MVA pathway activation in GCs culminated oocyte meiotic maturation by upregulating EGF signaling via LH receptor on GCs surrounding oocytes. Together, MVA pathway is a promising therapeutic target for prompting quality of oocytes from aged ovaries.

2023-02-26 | GSE175830 | GEO

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