Active DNA Demethylation Regulates Plant Gamete and Zygote Genome Reprogramming
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ABSTRACT:
ORGANISM(S): Oryza sativa Japonica Group
PROVIDER: GSE143923 | GEO | 2020/02/08
REPOSITORIES: GEO
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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
Project description:The epigenomes of mammalian sperm and oocytes, characterized by gamete-specific 5-methylcytosine (5mC) patterns, are reprogrammed in early embryogenesis to establish full developmental potential. It is broadly accepted that the paternal genome is actively demethylated in the zygote while the maternal genome undergoes passive demethylation thanks to DNA replication over the subsequent cleavage divisions. Here we reveal that both maternal and paternal genomes undergo widespread active and passive demethylation in the pronuclear zygote before the first mitotic division. Whereas the passive demethylation requires DNA replication, the active demethylation relies on enzymatic oxidation of 5mC, as deletion of the DNA dioxygenase, Tet3, but not the inhibition of replication, blocks the active demethylation. At actively demethylated loci, 5mCs appear to be processed to unmodified cytosines in a manner independent of the DNA glycosylase TDG. These observations suggest the occurrence of genuine active demethylation in both parental genomes following fertilization. An extra supportive Tet3 knock-out female pronuclear sample related to experiment Series GSE56650.
2016-09-01 | E-GEOD-60777 | biostudies-arrayexpress
Project description:The epigenomes of mammalian sperm and oocytes, characterized by gamete-specific 5-methylcytosine (5mC) patterns, are reprogrammed in early embryogenesis to establish full developmental potential. It is broadly accepted that the paternal genome is actively demethylated in the zygote while the maternal genome undergoes passive demethylation thanks to DNA replication over the subsequent cleavage divisions. Here we reveal that both maternal and paternal genomes undergo widespread active and passive demethylation in the pronuclear zygote before the first mitotic division. Whereas the passive demethylation requires DNA replication, the active demethylation relies on enzymatic oxidation of 5mC, as deletion of the DNA dioxygenase, Tet3, but not the inhibition of replication, blocks the active demethylation. At actively demethylated loci, 5mCs appear to be processed to unmodified cytosines in a manner independent of the DNA glycosylase TDG. These observations suggest the occurrence of genuine active demethylation in both parental genomes following fertilization.
2016-09-01 | GSE60777 | GEO
Project description:DNA methylation is highly dynamic during mammalian embryogenesis. It is broadly accepted that the paternal genome is actively depleted of global cytosine methylation at fertilization, followed by passive depletion that reaches a minimum at the blastocyst stage. However, this model is based on limited data, and to date no base-resolution maps exist to support and refine it. Here, we generated genome-scale DNA methylation maps in mouse gametes and through post-implantation embryogenesis. We find that the oocyte already exhibits global hypomethylation, most prominently at specific subfamilies of LINE-1 and LTR-containing retro-elements, which are disparate between gametes and resolve to lower methylation values in zygote. Surprisingly, the oocyte contributes a unique set of Differentially Methylated Regions (DMRs), including many CpG Island promoter regions, that are maintained in the early embryo but are lost at the onset of embryonic specification and absent in somatic cells. In contrast, sperm contributed methylation includes retrotransposons that become completely methylated after the blastocyst stage. Our data provide a complete genome-scale, base-resolution timeline of DNA methylation in the pre-specified embryo, when this epigenetic modification is most dynamic and before returning to the canonical somatic pattern. Comparison of DNA methylation patterns in mouse gametes and through embryogenesis using Reduced Representation Bisulfite Sequencing (RRBS)
2012-03-28 | E-GEOD-34864 | biostudies-arrayexpress
Project description:PGC7 is a primordial germ cell (PGCs)-specific protein involved in epigenetic chromatin reprogramming in the zygote following fertilization. TET3 is a dioxygenase that catalyzes the conversion of the modified genomic base 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) and plays a key role in epigenetic chromatin reprogramming in the zygote following fertilization. PGC7 participates in protection of DNA methylation in the maternal pronucleus by preventing conversion of 5mC to 5hmC by TET3 oxidization subsequent DNA demethylation. Thus we tested the co-localization of PGC7 and TET3 in specific loci by ChIP-seq assays.
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Project description:The goal of the present study is to analyze the characteristics of maternal to zygotic transition (MZT) in Arabidopsis. The maternal-to-zygotic transition (MZT) is an essential developmental turning point during the alternation of generations in both plants and animals. In animals, early embryogenesis is maternally controlled and zygotic genome activation (ZGA) starts much later. However, in plants, the timing of MZT and parental contributions to the zygotic transcriptome remain unclear. To address above mentioned questions, we selected Arabidopsis as model plant for the analysis. Regarding to the characteristics of MZT, egg cells, embryos including spherical zygote, elongated zygote, 1-cell embryo and 32-cell embryo were isolated and collected for RNA sequencing. Hybrid zygotes at two representative stages from the reciprocal crosses between polymorphic Arabidopsis Columbia (Col) and Landsberg erecta (Ler) accessions were also sequenced for investigating the parental contributions. We demonstrate that plant MZT occurs during the zygote stage and is a two-step process, first involving rapid maternal transcript degradation and, second, large-scale de novo transcription. Parental contributions to the zygotic transcriptome are stage dependent over the course of zygote development; the spherical zygote is characterized by a maternally dominated transcriptome, whereas the elongated zygote genome shows equal parental contributions.
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Project description:Zygotic repair of paternal genome is a key event after fertilization. Spermatozoa accumulate DNA single and double strand breaks during spermatogenesis and can suffer additional damage before fertilization by different factors, including cryopreservation. Fertilization with DNA damaged spermatozoa (DDS) is considered to promote implantation failures and abortions, but also long term effects in the progeny that could be related to a defective repair. Base excision repair (BER) pathway is considered the most active in zygotic DNA repair, but healthy oocytes contain enzymes for all repairing pathways. In this study the effects of the inhibition of the BER pathway in the zygote, were analyzed on the progeny obtained after fertilization with differentially DDS. Massive gene expression (37.394 transcripts) was analyzed after hatching using microarrays. Trout oocytes are easily fertilized with DDS and the high prolificacy allows obtaining live progeny even with a high rate of abortions. Results showed that DDS, even if increased the number of abortions, provided normal progeny. Nevertheless, the zygotic inhibition of PARP, upstream the BER pathway, result 810 differentially expressed genes (DEGs) after hatching. DEGs are related to DNA repair, apoptosis, telomere maintenance or growth and development, revealing a scenario of impaired DNA damage signalization and repair. Down-regulation of the apoptotic cascade was noticed, suggesting a selection of embryos tolerant to residual DNA damage during embryo development. Our results suggest a high zygotic capacity to repair paternal DNA damage and reveals changes in the progeny from defective repairing zygotes whose long term consequences should be deeply analyzed Gene expression was analyzed in trout larvae one day after hatching obtained from differentially DNA damaged sperm with or without zygotic inhibition of the BER pathway of DNA repair. Eggs from two females were pooled and fertilized with sperm fresh (F samples) or cryopreserved using different procedures (LDL and EY samples). Ten min later two batches from each sperm kind were treated with 3-aminobenzamide (3AB) to inhibit the PARP activity. Ten larvae per each one of the 6 treatments (3sperm kind x 2 zygotic treatments) were analyzed after pooling RNA. Four replicates per treatment were done fertilizing eggs from the same females with sperm from 4 different males.
2014-10-29 | E-GEOD-52217 | biostudies-arrayexpress
Project description:We found that the DNA methylation heterogeneity was largely programmed by the initial DNA methylation state in zygote by building a mathematical model. Further, to clarify the causality of transcriptional expression heterogeneity and DNA methylation heterogeneity, we disrupted DNA methylation status during mouse early embryogenesis by knocked out (KO) DNA methylation-related genes Dppa3 in gamete cells. Then we performed single cell RNA-seq on each cell of the KO embryos in 4-cell stage and 8-cell stage.
2020-10-10 | E-MTAB-9360 | biostudies-arrayexpress
Project description:Zygotic repair of paternal genome is a key event after fertilization. Spermatozoa accumulate DNA single and double strand breaks during spermatogenesis and can suffer additional damage before fertilization by different factors, including cryopreservation. Fertilization with DNA damaged spermatozoa (DDS) is considered to promote implantation failures and abortions, but also long term effects in the progeny that could be related to a defective repair. Base excision repair (BER) pathway is considered the most active in zygotic DNA repair, but healthy oocytes contain enzymes for all repairing pathways. In this study the effects of the inhibition of the BER pathway in the zygote, were analyzed on the progeny obtained after fertilization with differentially DDS. Massive gene expression (37.394 transcripts) was analyzed after hatching using microarrays. Trout oocytes are easily fertilized with DDS and the high prolificacy allows obtaining live progeny even with a high rate of abortions. Results showed that DDS, even if increased the number of abortions, provided normal progeny. Nevertheless, the zygotic inhibition of PARP, upstream the BER pathway, result 810 differentially expressed genes (DEGs) after hatching. DEGs are related to DNA repair, apoptosis, telomere maintenance or growth and development, revealing a scenario of impaired DNA damage signalization and repair. Down-regulation of the apoptotic cascade was noticed, suggesting a selection of embryos tolerant to residual DNA damage during embryo development. Our results suggest a high zygotic capacity to repair paternal DNA damage and reveals changes in the progeny from defective repairing zygotes whose long term consequences should be deeply analyzed
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Project description:Fertilization triggers a global erasure of 5-methylcytosine from paternal DNA as part of extensive epigenetic reprogramming during the transition from gametic specialization to totipotency. This active removal has been shown to involve oxidation by TET3, but the targeting of this pathway and the wider context of demethylation remain poorly understood. We optimized a novel technique for whole-genome bisulfite sequencing and applied it to wild-type and TET3-deficient zygotes, using SNPs to access paternal alleles. As the great majority of sperm-contributed methylation lies outside the CpG islands (CGIs) and promoters analysed to date, these genome-wide methylation profiles allow paternal methylation trajectories in the zygote to be comprehensively examined for the first time. This global view revealed that in addition to pervasive loss of methylation from intergenic sequences and most repetitive elements, gene bodies constitute a major target of zygotic demethylation. Methylation loss is associated with zygotic genome activation, and at gene bodies is also linked to increased transcriptional noise in the early embryo. Our data maps the primary contribution of oxidative demethylation to a subset of gene bodies and single-copy intergenic sequences, and implicates the action of redundant pathways at many loci. We further uncover a novel function for TET3 in protection from de novo methylation at CGIs and promoters. This work adds new breadth to our understanding of the molecular events involved in reprogramming gametic identity following fertilization. Three independent collections of zygotes were performed for each genotype (control and TET3 deletion), giving a total of 225 control and 237 TET3 deletion zygotes, of which 120 and 129 were derived from 129S2/SvHsd studs for control and TET3 samples, respectively. Zygotes were pooled and whole-genome bisulfite libraries were prepared using a post-bisulfite adaptor tagging strategy optimized from (Miura et al. Nucleic Acids Research 2012, 40:e136)
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