A single-cell map of maternal and zygotic mRNA dynamics during cell-type specification in zebrafish embryos [scSLAM-seq]

During early embryogenesis, embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal-to-zygotic transition requires a tight interplay of mRNA transcription and degradation, but distinguishing their unique contributions remains a challenge. Here, we dissect gene regulation during the zebrafish maternal-to-zygotic transition by combining single-cell RNA-sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single-cell transcriptomes into their new (zygotic) and old (maternal) mRNA components, and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell-type restricted expression arises by zygotic transcription, but distinguish a specific role for maternal transcripts in defining germ-cell and enveloping-layer identity, two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level, and associate a fast replacement with genes that has a restricted zygotic expression in either cell-type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post-transcriptional events that control gene regulation during early embryogenesis. single cell, SLAM-seq, 3 developmental stages, with treated and untreated samples, and biological replicates

在早期胚胎发生过程中，胚胎会经历母源遗传mRNA的大规模降解，并生成新的合子转录本。母源-合子转换（maternal-to-zygotic transition）需要mRNA转录与降解的精密协同调控，但区分二者各自的独特贡献仍为一项挑战。本研究通过将单细胞RNA测序（single-cell RNA-sequencing）与斑马鱼胚胎内的RNA代谢标记及核苷酸转化技术相结合，解析了斑马鱼母源-合子转换过程中的基因调控机制。我们将单细胞转录组拆解为新合成（合子来源）与原有（母源来源）的mRNA组分，并挖掘出基因调控随时间与空间动态展开的关键信息。研究表明，绝大多数细胞类型限制性表达由合子转录产生，但母源转录本在定义生殖细胞与包被层身份——这两种最早特化的细胞身份——中发挥特定功能。我们观测到胚胎基因的母源与合子拷贝间存在整体mRNA水平相对恒定的内在替换现象，并发现快速替换的基因多在特定细胞类型或时间维度上呈现合子限制性表达。本研究为母源与合子转录组的研究提供了宝贵的数据集资源，并揭示了早期胚胎发生过程中调控基因表达的转录后事件。该数据集涵盖单细胞样本、SLAM-seq技术、3个发育阶段，包含处理组与对照组样本，并设置生物学重复。