Retention of paternal epigenetic memory in the developing teleost germline [alt-splicing]

Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell (PGC) formation. However, it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory, in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage-specificity and that are uncoupled from DNA methylation-mediated regulation. In order to perform alternative splicing analysis, PGC 7 hpf, PGC 24 hpf, Soma 7 hpf and Soma 24 hpf low-input RNA-seq samples have been sequenced on an additional lane of Nova-seq 6000 and analyzed together with the previous RNA-seq run (GSE122480).

哺乳动物胚胎发生（mammalian embryogenesis）过程中存在两轮DNA甲基化重编程（DNA methylation reprogramming）波，分别发生于植入前发育（preimplantation development）阶段与原始生殖细胞（primordial germ cell, PGC）形成阶段。然而目前学界尚未明确这些过程的进化保守性。本研究对四个发育阶段的斑马鱼原始生殖细胞的DNA甲基化组（DNA methylomes）进行了系统表征，揭示了父本表观遗传记忆的保留现象，这与哺乳动物中的相关研究发现形成鲜明对比。对相同发育阶段的斑马鱼原始生殖细胞开展基因表达谱（Gene expression profiling）分析后发现，胚胎生殖系由少量具备显著发育阶段特异性且不受DNA甲基化介导调控的标记基因所定义。为开展可变剪接（alternative splicing）分析，本研究在额外的NovaSeq 6000（Nova-seq 6000）测序泳道上对PGC 7 hpf、PGC 24 hpf、Soma 7 hpf及Soma 24 hpf的低起始量RNA测序（low-input RNA-seq）样本进行了测序，并将其与此前的RNA测序数据集（GSE122480）进行联合分析。