Conservation of mRNA and protein expression during development of C. elegans. Conservation of mRNA and protein expression during development of C. elegans

Spatiotemporal control of gene expression is crucial for development and subject to evolutionary changes. Although proteins are the final product of most genes, the developmental proteome of an animal has not yet been comprehensively defined, and the correlation between RNA and protein abundance during development is largely unknown. Here, we globally measured and compared protein and mRNA expression changes during the life cycle of the nematodes C. elegans and C. briggsae, separated by ~30 million years of evolution. We observed that developmental mRNA and protein changes were highly conserved, to a surprisingly similar degree, but poorly correlated within a species, suggesting important and widespread post-transcriptional regulation. Post-transcriptional control was particularly well conserved if mRNA fold changes were buffered on the protein level, indicating a predominant repressive function. Finally, among divergently expressed genes, we identified insulin signaling, a pathway involved in life span determination, as a putative target of adaptive evolution. Overall design: Samples of C. elegans and C. briggsae were collected at major developmental stages throughout the nematode life cycle. These stages comprise a population of mixed embryonic stages (E), populations of all four larval stages (L1, L2, L3, L4), late L4 larvae (LL4), young adults (YA), and a reference sample consisting of a mixture of all stages. To obtain synchronized worm populations, embryos were extracted by bleaching gravid adults and synchronized by starvation. Later stages were picked at fixed timepoints after determining the developmental stages by microscopic observation. For all stages, at least a single poly(A)-extracted mRNA library was sequenced on a single lane of an Illumina Genome Analyzer IIx.

基因表达的时空调控对于生物体发育至关重要，且其本身亦会经历演化改变。尽管蛋白质是多数基因的最终表达产物，但目前仍未全面解析任一动物的发育过程蛋白质组（proteome），且发育过程中RNA与蛋白质丰度的相关性在很大程度上仍不明确。本研究对演化分歧时长约3000万年的两种线虫——秀丽隐杆线虫（C. elegans）和布里格斯隐杆线虫（C. briggsae）——的生命周期内蛋白质与mRNA的表达变化进行了全基因组水平的检测与比较。研究发现，两种线虫的发育过程中mRNA与蛋白质的表达变化均呈现高度保守性，且保守程度惊人地一致，但同一物种内的mRNA与蛋白质丰度相关性却极低，这提示存在广泛且关键的转录后调控（post-transcriptional regulation）机制。若mRNA的表达变化倍数在蛋白质水平得到缓冲，则转录后调控的保守性尤为显著，这表明转录后调控主要发挥抑制功能。最后，在表达模式发生演化分歧的基因中，本研究鉴定出胰岛素信号通路（该通路参与寿命调控）为适应性演化的潜在靶点。

实验设计：研究人员在线虫整个生命周期的主要发育阶段采集秀丽隐杆线虫（C. elegans）与布里格斯隐杆线虫（C. briggsae）的样本。所涵盖的发育阶段包括混合胚胎阶段（E）、全部四个幼虫阶段（L1、L2、L3、L4）的种群、晚期L4幼虫（LL4）、年轻成虫（YA），以及由所有阶段样本混合而成的参考样本。为获得同步化的线虫种群，研究人员通过漂白孕成虫获取胚胎，并通过饥饿处理实现种群同步化。后续发育阶段的样本则通过显微镜观察确定发育时期后，在固定时间点采集。针对所有发育阶段，研究人员至少构建了一个poly(A)富集的mRNA文库，并在Illumina基因组分析仪IIx的单个测序通道上完成测序。