Single Cell DNA Methylome Sequencing of Human Preimplantation Embryos
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PROVIDER: PRJNA321024 | ENA |
REPOSITORIES: ENA
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Project description:Although the DNA methylome of human early embryos has been analyzed, some of the key features have not been addressed to date. Here, we performed single-cell DNA methylome sequencing for human preimplantation embryos and found that tens of thousands of genomic loci exhibited de novo DNA methylation. This finding indicates that genome-wide DNA methylation reprogramming during preimplantation development is a dynamic balance between strong global demethylation and significant focused re-methylation. Furthermore, the demethylation of the paternal genome is much faster and thorough than that of the maternal genome. From the 2-cell to post-implantation stage, methylation of the paternal genome is consistently lower than that on the maternal genome. We also showed that the genetic lineage of the early blastomeres could be traced by DNA methylation analysis. Our work paves the way for deciphering the secrets of DNA methylation reprogramming in human early embryos.
2017-12-19 | GSE81233 | GEO
Project description:RNA m6A methylome in mouse oocytes and preimplantation embryos
| PRJNA791403 | ENA
Project description:Single-cell RNA sequencing of Monodelphis domestica preimplantation embryos
2020-08-19 | E-MTAB-7515 | biostudies-arrayexpress
Project description:DNA methylation (5mC) is central to cellular identity and the global erasure of 5mC from the parental genomes during preimplantation mammalian development. This process is critical to reset the methylome of terminally differentiated gametes to the become pluripotent cells in the blastocyst. While active and passive modes of demethylation have both been suggested to play a role in this process, the relative contribution of these two mechanisms to genome-wide 5mC erasure remains unclear. Here, we report a new high-throughput single-cell method (scMspJI-seq) that enables strand-specific quantification of 5mC, thereby allowing us to systematically probe the dynamics of global demethylation. First, when applied to hybrid mouse embryonic stem cells, we identified substantial cell-to-cell strand-specific 5mC heterogeneity with a small group of cells displaying asymmetric levels of 5mCpG between the two DNA strands of a chromosome and suggesting loss of maintenance methylation. Next, using scMspJI-seq in preimplantation mouse development, we discovered that maintenance methylation is active till the 16-cell stage followed by passive demethylation in a fraction of cells within 2 the early blastocyst at the 32-cell stage of development. Finally, we found that human preimplantation embryos qualitatively show slower yet similar demethylation dynamics as mouse preimplantation embryos. Collectively, these results demonstrate that scMspJI-seq is a sensitive and cost effective method to map the strand-specific genome- wide patterns of 5mC in single cells, thereby enabling quantitative investigation of methylation dynamics in developmental systems.
2020-02-13 | GSE139984 | GEO
Project description:In total, 240 single blastomeres from nine top-quality day-4 embryos frozen at day 3 of development and four fresh top-quality day-4 embryos that had one-cell biopsy on day 3 for preimplantation genetic diagnosis (PGD) were collected. Blastomeres' DNA was amplified using SurePlex DNA Amplification System (BlueGnome, Cambridge, UK) . Array-CGH was carried out using 24Sure Cytochip microarrays following the standard protocol (BlueGnome, www.cytochip.com). BAC array-CGH on single blastomeres amplified by SurePlex amplification Kit.
2013-04-05 | E-GEOD-39518 | biostudies-arrayexpress
Project description:We used ATLAS-seq to comprehensively map the genomic location of LINE-1 elements belonging to the youngest and potentially polymorphic subfamily (L1HS-Ta). This was performed in single-cells of 2 preimplantation embryos (E3 and E6) as well as from the remaining inner cell mass (denoted T). In brief, single cells were isolated from the inner cell mass of preimplantation embryos by laser drilling and micromanipulation. Whole-genome Multiple Displacement Amplification was performed on each isolated single cells, as well as on the remaining cells of the inner cell mass as a population (samples labelled 'T'). Then we applied ATLAS-seq to map L1HS-Ta retrotransposons. This approach relies on the random mechanical fragmentation of the genomic DNA to ensure high-coverage, ligation of adapter sequences, suppression PCR-amplification of L1HS-Ta element junctions, and Ion Torrent sequencing using single-end 400 bp read chemistry. A notable aspect of ATLAS-seq is that we can obtain both L1 downstream and upstream junctions (3'- and 5'-ATLAS-seq libraries, respectively), for full-length L1 elements.
2023-09-30 | E-MTAB-8616 | biostudies-arrayexpress
Project description:N6-methyladenosine (m6A), the most prevalent internal modification in eukaryotic messenger RNA, plays diverse regulatory roles in many biological processes and is involved in a variety of physiological behaviors. Here we present the m6A methylome maps of mouse oocytes and preimplantation embryos by a low-input approach picoMeRIP-seq. We revealed that m6A was largely and dynamically deposited on maternal and zygotic RNAs during maternal-to-zygotic transition (MZT), especially on those encoding the factors essential for cell fate determination. m6A frequently marked the maternally-derived RNAs to be degraded and the genes that were activated during zygotic genome activation. Moreover, the RNAs derived from retrotransposons, such as MTA and MERVL, were heavily occupied by m6A. Collectively, our results provide a foundation for future studies exploring the regulatory roles of m6A in mammalian early embryo development.
2023-02-10 | GSE192440 | GEO
Project description:The culture conditions of the early preimplantation embryos affects the DNA methylation landscape of the resulting blastocysts.
2015-10-07 | GSE69173 | GEO
Project description:In total, 240 single blastomeres from nine top-quality day-4 embryos frozen at day 3 of development and four fresh top-quality day-4 embryos that had one-cell biopsy on day 3 for preimplantation genetic diagnosis (PGD) were collected. Blastomeres' DNA was amplified using SurePlex DNA Amplification System (BlueGnome, Cambridge, UK) . Array-CGH was carried out using 24Sure Cytochip microarrays following the standard protocol (BlueGnome, www.cytochip.com).
2013-04-05 | GSE39518 | GEO
Project description:The early stages of mammalian embryonic development involve the participation and cooperation of numerous complex processes, including nutritional, genetic, and epigenetic mechanisms. However, in embryos cultured in vitro, a developmental block occurs that affects embryo development and the efficiency of culture. Although the block period is reported to involve the transcriptional repression of maternal genes and transcriptional activation of zygotic genes, how epigenetic factors regulate developmental block is still unclear. In this study, we systematically analyzed whole-genome methylation levels during five stages of sheep oocyte and preimplantation embryo development using SC-WGBS technology. Then, we examined several million CpG sites in individual cells at each evaluated developmental stage to identify the methylation changes that take place during the development of sheep preimplantation embryos. Our results showed that two strong waves of methylation changes occurred, namely, demethylation at the 8- to 16-cell stage and methylation at the 16- to 32-cell stage. Analysis of DNA methylation patterns in different functional regions revealed a stable hypermethylation status in 3'UTRs and gene bodies; however, significant differences were observed in intergenic and promoter regions at different developmental stages. Changes in methylation at different stages of preimplantation embryo development were also compared to investigate the molecular mechanisms involved in sheep embryo development at the methylation level. In conclusion, we report a detailed analysis of the DNA methylation dynamics during the development of sheep preimplantation embryos. Our results provide an explanation for the complex regulatory mechanisms underlying the embryo developmental block based on changes in DNA methylation levels.
2021-12-15 | GSE190746 | GEO