Transcription profiling and proteomic of mouse early embryonic brain development

Embryonic mouse brain development involves a sequential differentiation of multipotent progenitor cells into neurons and glia. Using microarrays and large 2-D electrophoresis, we investigated the transcriptome and proteome of mouse brains at embryonic days 9.5, 11.5 and 13.5. During this developmental period, neural progenitor cells shift from proliferation to neuronal differentiation. As expected, we detected numerous expression changes between the time points investigated but interestingly, the rate of alteration was about 10% to 13% of all proteins and mRNAs during every two days of development. Furthermore, up- and downregulation was balanced. This was confirmed for two additional stages of development, embryonic day 16 and 18. We hypothesize that during embryonic development, the rate of protein expression alteration is rather constant due to a limitation of cellular resources such as energy, space and free water. The similar complexity found at the transcriptome and proteome level at all stages suggests, that changes in relative concentration of gene products rather than an increased number of gene products dominate throughout cellular differentiation. We found that metabolism and cell cycle related gene products were downregulated in expression when precursor cells switched from proliferation to neuronal differentiation (day 9.5 to 11.5), whereas neuron specific gene products were upregulated. A detailed analysis revealed their implication in differentiation related processes such as rearrangement of the actin cytoskeleton as well as Notch and Wnt signaling pathways. Experiment Overall Design: 3 embryonic stages: Experiment Overall Design: E9.5: 6 biological replicates Experiment Overall Design: E11.5: 4 biological replicates Experiment Overall Design: E13.5: 6 biological replicates小鼠胚胎脑发育过程中，多能祖细胞会依次分化为神经元与胶质细胞。本研究采用基因芯片（microarray）与大规模二维电泳技术，对胚胎第9.5、11.5及13.5天的小鼠脑组织转录组（transcriptome）与蛋白质组（proteome）进行了分析。在该发育阶段，神经祖细胞会从增殖状态转向神经元分化过程。正如预期，我们在各检测时间点间观测到大量表达变化；但有趣的是，每两日的发育过程中，约有10%至13%的全部蛋白质与信使RNA（mRNA）发生表达改变。此外，基因的上调与下调呈现平衡状态。该结论在另外两个发育阶段——胚胎第16天与第18天——中得到了验证。我们提出假说：在胚胎发育过程中，由于能量、空间与游离水等细胞资源存在限制，蛋白质表达的改变速率相对恒定。各阶段转录组与蛋白质组的复杂程度均相似，这表明在整个细胞分化过程中，占主导地位的是基因产物相对浓度的变化，而非基因产物数量的增加。我们发现，当祖细胞从增殖状态转向神经元分化（第9.5天至第11.5天）时，与代谢及细胞周期相关的基因产物表达量下调，而神经元特异性基因产物的表达量则上调。深入分析显示，这些基因产物参与了肌动蛋白细胞骨架（actin cytoskeleton）重排、Notch与Wnt信号通路等与分化相关的生物学过程。实验整体设计：共涵盖3个胚胎发育阶段： 胚胎第9.5天：6个生物学重复（biological replicates）样本 胚胎第11.5天：4个生物学重复样本 胚胎第13.5天：6个生物学重复样本