An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo
An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo
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DOI：
10.1038/s41598-019-49817-3
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发表时间：
2019-09-16
影响因子：
4.6
通讯作者：
Taher, Leila
中科院分区：
文献类型：
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作者：
Israel, Steffen;Ernst, Mathias;Taher, Leila
早期小鼠胚胎具有由细胞质晶格组成的非典型翻译机制，翻译能力差。因此，预计转录组学变化对蛋白质操作水平的影响相对温和。为了研究这一点，我们在从成熟卵母细胞到囊胚的七个发育阶段进行了液相色谱-串联质谱和mRNA测序，并通过免疫荧光和qPCR独立验证了我们的数据。我们检测并定量了6，550种蛋白质和20，535种蛋白质编码转录本。与转录组相比-其中变化发生在早期，主要是在2细胞阶段-我们的数据表明，蛋白质组中最实质性的变化发生在桑椹胚和囊胚之间的后期阶段。我们还发现蛋白质和转录水平的变化之间几乎没有一致性，特别是对于早期阶段，但观察到一致性朝着桑椹胚和囊胚增加，游离核糖体的数量也是如此。这些结果与细胞质晶格到游离核糖体的转变是发育调控的关键介质是一致的。最后，我们展示了这些数据如何用于评估基于mRNA的着床前发育研究的优势和局限性，并扩展了已知的发育标志物。
Early mouse embryos have an atypical translational machinery that consists of cytoplasmic lattices and is poorly competent for translation. Hence, the impact of transcriptomic changes on the operational level of proteins is predicted to be relatively modest. To investigate this, we performed liquid chromatography-tandem mass spectrometry and mRNA sequencing at seven developmental stages, from the mature oocyte to the blastocyst, and independently validated our data by immunofluorescence and qPCR.We detected and quantified 6,550 proteins and 20,535 protein-coding transcripts. In contrast to the transcriptome -where changes occur early, mostly at the 2-cell stage - our data indicate that the most substantial changes in the proteome take place towards later stages, between the morula and blastocyst. We also found little to no concordance between the changes in protein and transcript levels, especially for early stages, but observed that the concordance increased towards the morula and blastocyst, as did the number of free ribosomes. These results are consistent with the cytoplasmic lattice-to-free ribosome transition being a key mediator of developmental regulation. Finally, we show how these data can be used to appraise the strengths and limitations of mRNA-based studies of pre-implantation development and expand on the list of known developmental markers.