Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition

Post-transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte-to-embryo transition, which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions, changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified, it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte-to-embryo transition. Here, we focused on the auxiliary 3'-to-5' degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults, yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte-to-embryo transition, transcriptome profiling identified stage-specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type, suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis-regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall, our results provide first insights into the physiological role of vertebrate Ski7 as an important post-transcriptional regulator during the oocyte-to-embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte-to-embryo transition. Every time point from each genotype was performed in triplicates.

转录后调控机制（post-transcriptional mechanisms）对于基因表达调控至关重要。这类机制在快速发育转变过程中尤为关键，例如卵母细胞到胚胎转变（oocyte-to-embryo transition）——该过程的典型特征是发育程序发生剧烈改变，且全程无细胞核转录活动发生。在此类条件下，细胞内RNA含量的变化完全依赖于RNA降解途径。尽管目前已在胚胎发生过程中鉴定出多种促进RNA降解的机制，但仍不明确哪些细胞机制参与了卵母细胞到胚胎转变过程中的母源转录组（maternal transcriptome）重塑。本研究以斑马鱼中的辅助性3'→5' RNA降解因子Ski7为研究对象，因其编码的mRNA在该发育时期的表达量达到峰值。纯合ski7突变体斑马鱼可正常存活并发育为形态无异常的成体，但生育能力有所降低。转录组分析（transcriptome profiling）结果显示，Ski7存在阶段特异性的mRNA靶标，这与“Ski7参与卵母细胞到胚胎转变过程中的转录组重塑”这一假说相符。在ski7突变体中上调的基因，在野生型个体中通常呈低表达状态，提示Ski7可维持该部分基因的低转录本水平。对ski7突变体中异常表达基因进行基因本体（Gene Ontology, GO）富集分析后发现，Ski7参与氧化还原过程的调控。这一结论通过实验得到验证：ski7突变体胚胎对还原应激的抗性显著增强。综上，本研究结果首次揭示了脊椎动物Ski7作为重要转录后调控因子，在卵母细胞到胚胎转变过程中的生理功能。实验设计概述：对卵母细胞到胚胎转变过程中11个时间点的野生型与ski7突变体斑马鱼样本开展转录组分析。每个基因型的每个时间点均设置3次生物学重复。