Understanding DNA methylation reprogramming dynamics during preimplantation development using single-cell sequencing

使用单细胞测序了解植入前发育过程中的 DNA 甲基化重编程动态

• 批准号: 10430197
• 负责人: Siddharth Subhas Dey
• 金额: $ 27.81万
• 依托单位: UNIVERSITY OF CALIFORNIA SANTA BARBARA
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-15 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10430197
• 关键词: Address; Assisted Reproductive Technology; Bar Codes; Biological Process; Biology; Cell division; Cells; Coupled; DNA; DNA Maintenance; DNA Methylation; DNA Modification Methylases; Detection; Development; Disease; Embryo; Embryonic Development; Epiblast; Epigenetic Process; Event; Future; Gene Expression; Genome; Germ Cells; Goals; Heterogeneity; Hybrids; Immunofluorescence Immunologic; Inner Cell Mass; Life Cycle Stages; Liquid substance; Mass Spectrum Analysis; Measurement; Measures; Memory; Messenger RNA; Methods; Methylation; Molecular; Mus; Nucleic Acids; Nucleotides; Parents; Pathway interactions; Pattern; Population; Pre-implantation Embryo Development; Process; Regenerative Medicine; Regulation; Resolution; Robot; Role; System; Technology; Testing; Tissues; Work; base; bisulfite; bisulfite sequencing; blastocyst; cell fate specification; demethylation; embryo stage 2; embryonic stem cell; environmental stressor; epigenome; experimental study; genome-wide; imprint; improved; insight; knock-down; mathematical model; methylome; multiple omics; new technology; next generation sequencing; novel; physical separation; preimplantation; restriction enzyme; single cell sequencing; tumor progression; zygote

PROJECT SUMMARY During mammalian preimplantation development, one of the most dramatic epigenetic events is the global erasure of DNA methylation (5-methylcytosine or 5mC) from the parental genomes. This reprogramming is critical to reset the methylation status of the gametes and restore developmental potency to pluripotent cells in the blastocyst. Elucidating the molecular mechanisms that regulate 5mC reprogramming is central to gaining deeper insights into normal embryonic development as well as to better understand aberrant 5mC patterns and imprinting disorders associated with assisted reproductive technologies (ART). While early studies showed that the paternal genome undergoes ‘active’ demethylation through conversion of 5mC to 5-hydroxymethylcytosine (5hmC) and the maternal genome undergoes ‘passive’ demethylation through a lack of maintenance DNA methyltransferase (Dnmt1) activity during replication, more recent studies have suggested that 5mC erasure from the parental genomes is a combination of these two demethylation pathways. Unraveling the mechanisms that regulate 5mC erasure has been challenging due to our inability to directly distinguish between these pathways. This limitation can be overcome by making genome-wide strand-specific measurements of 5mC in single cells. In addition, this epigenetic reprogramming coincides temporally with the first cell fate specification in the embryo towards the trophectoderm (TE) and inner cell mass (ICM) lineages. However, it remains unclear how 5mC reprogramming influences this cell fate decision. To address these questions, in Specific Aims 1 we propose to develop a novel single-cell sequencing technology to simultaneously quantify 5mC strand-specifically together with mRNA from the same cell. Preliminary experiments in mouse embryonic stem cells and mouse embryos show that we can detect both 5mC and mRNA from the same cell. To test our central hypothesis that the mechanisms regulating the erasure of 5mC are parent- and stage-specific, in Specific Aims 2 we plan to quantify the genome-wide strand-specific distribution of 5mC in hybrid mouse embryos from the 2- to 64-cell stage of embryogenesis. Further, through stochastic mathematical modeling and knockdown experiments, we will elucidate how different molecular factors regulate active and passive demethylation pathways during preimplantation development. Finally, while cell-to-cell variability in a variety of factors have been shown to bias the cell fate potential of early blastomeres towards the TE or ICM lineages, it remains unclear how 5mC reprogramming tunes or reinforces these decisions. To address this question, in Specific Aims 3 we plan to quantify both 5mC and mRNA from the same cell to directly correlate how heterogeneity in genome-wide strand- specific patterns of 5mC influence the decision between symmetric vs. asymmetric cell divisions and the resulting cell fate choices. Thus, through the development of novel single-cell methods we will gain a deeper mechanistic understanding of global demethylation dynamics during preimplantation development that will enable us to better study altered epigenetic reprogramming associated with ART and other environmental stresses in future.

项目摘要 在哺乳动物植入前发育过程中，最引人注目的表观遗传事件之一是全球性的 从亲本基因组中删除DNA甲基化（5-甲基胞嘧啶或5 mC）。这种重新编程是 对于重置配子的甲基化状态和恢复多能细胞的发育潜能至关重要， 囊胚阐明调节5 mC重编程的分子机制是获得 更深入地了解正常的胚胎发育，以及更好地了解异常的5 mC模式， 与辅助生殖技术（ART）相关的印记疾病。虽然早期的研究表明， 父本基因组通过将5 mC转化为5-羟甲基胞嘧啶进行“主动”去甲基化 （5 hmC）和母体基因组通过缺乏维持DNA进行“被动”去甲基化 甲基转移酶（Dnmt 1）的活性，最近的研究表明，5 mC擦除 是这两种去甲基化途径的组合。解开机制 由于我们无法直接区分这些，因此调节5 mC擦除一直具有挑战性 途径。这种局限性可以通过在基因组中进行5 mC的全基因组链特异性测量来克服。 单细胞此外，这种表观遗传重编程与第一个细胞命运规范在时间上一致 在胚胎中向滋养外胚层（TE）和内细胞团（ICM）谱系。但尚不清楚 5 mC重编程是如何影响细胞命运的。为了解决这些问题，在具体目标1中，我们 我建议开发一种新的单细胞测序技术，同时定量5 mC链特异性 以及来自同一细胞的mRNA。小鼠胚胎干细胞和小鼠胚胎干细胞的初步实验 胚胎的研究表明，我们可以从同一个细胞中检测到5 mC和mRNA。为了验证我们的核心假设， 调节5 mC擦除的机制是父代和阶段特异性的，在特定目标2中，我们计划 定量5 mC在2- 64-细胞杂交小鼠胚胎中的全基因组链特异性分布 胚胎发生阶段。此外，通过随机数学建模和击倒实验，我们 将阐明不同的分子因子如何调节主动和被动去甲基化途径， 着床前发育最后，虽然细胞与细胞之间的变异性在各种因素中已被证明会产生偏差， 早期卵裂球向TE或ICM谱系的细胞命运潜力，仍不清楚5 mC 重新编程会调整或强化这些决定。为了解决这个问题，在具体目标3中，我们计划 量化来自同一细胞的5 mC和mRNA，以直接关联全基因组链的异质性- 5 mC的特定模式影响对称与不对称细胞分裂之间的决定， 细胞命运的选择因此，通过开发新的单细胞方法，我们将获得更深层次的机制， 了解植入前发育过程中的整体去甲基化动力学，这将使我们能够更好地 这项研究改变了与ART和未来其他环境压力相关的表观遗传重编程。