Functional Mapping of the Zebrafish Early Embryo Proteome and Transcriptome

Zebrafish is a popular system for
studying vertebrate development
and disease that shows high genetic conservation with humans. Molecular
level studies at different stages of development are essential for
understanding the processes deployed during ontogeny. Here, we performed
comparative analysis of the whole proteome and transcriptome of the
early stage (24 h post-fertilization) zebrafish embryo. We identified
8363 proteins with their approximate cellular abundances (the largest
number of zebrafish embryo proteins quantified thus far), through
a combination of thorough deyolking and extensive fractionation procedures,
before resolving the peptides by mass spectrometry. We performed deep
sequencing of the transcripts and found that the expressed proteome
and transcriptome displayed a moderate correlation for the majority
of cellular processes. Integrative functional mapping of the quantified
genes demonstrated that embryonic developmental systems differentially
exploit transcriptional and post-transcriptional regulatory mechanisms
to modulate protein abundance. Using network mapping of the low-abundance
proteins, we identified various signal transduction pathways important
in embryonic development and also revealed genes that may be regulated
at the post-transcriptional level. Our data set represents a deep
coverage of the functional proteome and transcriptome of the developing
zebrafish, and our findings unveil molecular regulatory mechanisms
that underlie embryonic development.

斑马鱼(Zebrafish)是一种常用于脊椎动物发育与疾病研究的经典模型系统，其与人类具有高度的遗传保守性。对发育不同阶段开展分子层面研究，对于解析个体发生过程中的调控机制至关重要。本研究针对受精后24小时的早期斑马鱼胚胎，开展了全蛋白质组(proteome)与转录组(transcriptome)的比较分析。通过严谨的去卵黄处理与多级分级分离流程，结合质谱解析肽段的实验策略，我们定量鉴定了8363种蛋白质并估算了其大致细胞丰度——这是目前已报道的斑马鱼胚胎蛋白质定量数量之最。我们对转录本进行了深度测序，结果显示，在绝大多数细胞过程中，表达的蛋白质组与转录组呈现中等程度的相关性。对定量基因进行整合功能注释分析表明，胚胎发育系统会差异化利用转录及转录后调控机制，以此调控蛋白质丰度。通过对低丰度蛋白质进行网络图谱分析，我们不仅鉴定出多种在胚胎发育中发挥关键作用的信号转导通路，还揭示了一批可能受转录后水平调控的基因。本数据集实现了发育中斑马鱼功能蛋白质组与转录组的深度覆盖，其研究结果揭示了支撑胚胎发育的分子调控机制。