The relationship between gene network structure and expression variation among individuals and species

Variation among individuals is a prerequisite of evolution by natural selection. As such, identifying the origins of variation is a fundamental goal of biology. We investigated the link between gene interactions and variation in gene expression among individuals and species, using the mammalian limb as a model system. We first built interaction networks for key genes regulating early (outgrowth; E9.5-11) and late (expansion and elongation; E11-13) limb development in mouse. This resulted in an Early (ESN) and Late (LSN) Stage Network. Computational perturbations of these networks suggest that the ESN is more robust. We then quantified levels of the same key genes among mouse individuals, and found that they vary less at earlier limb stages and that variation in gene expression is heritable. Finally, we quantified variation in gene expression levels among four mammals with divergent limbs (bat, opossum, mouse and pig), and found that levels vary less among species at earlier limb stages. We also found that variation in gene expression levels among individuals and species are correlated for earlier and later limb development. In conclusion, results are consistent with the robustness of the ESN buffering among-individual variation in gene expression levels early in mammalian limb development, and constraining the evolution of early limb development among mammalian species. Bat, mouse, opossum, and pig mRNA profiles at early and late developmental stages on each species fore and hind-limbs . Various replicates of each library were generated by single-end sequencing using Illumina HiSeq 2500. Please note that the de novo transcriptome assembly for bat (Trinity.fasta) was generated from pooled RNA-seq data of fore and hind-limbs at various embryonic developmental stages; Beginning stage (Wanek stage 2: 3 FL and 3 HL samples), early-stage (Wanek stage 3/4: 2 FL and 2 HL samples), and late_stage (Wanek stage 6: 2 FL and 2 HL samples).个体间变异是自然选择驱动进化的先决条件。就此而言，阐明变异的起源是生物学的核心研究目标。本研究以哺乳动物四肢为模型系统，探究基因互作与个体及物种间基因表达变异之间的关联。我们首先构建了调控小鼠早期（肢芽外突；胚胎发育第9.5-11天，E9.5-11）与晚期（肢芽扩增与伸长；E11-13）四肢发育的关键基因的互作网络，分别得到早期阶段网络（Early Stage Network, ESN）与晚期阶段网络（Late Stage Network, LSN）。对上述网络进行计算机扰动分析后发现，早期阶段网络具有更强的鲁棒性。随后，我们量化了小鼠个体间相同关键基因的表达水平，发现早期四肢发育阶段的基因表达变异程度更低，且基因表达变异具有可遗传性。最后，我们对四肢形态分化显著的四种哺乳动物（蝙蝠、负鼠、小鼠与猪）的基因表达变异进行量化，发现物种间的基因表达水平差异在早期四肢发育阶段同样更低。同时我们还发现，无论是早期还是晚期四肢发育，个体间与物种间的基因表达变异程度均呈显著相关。综上，本研究结果支持如下结论：早期阶段网络的鲁棒性可缓冲哺乳动物四肢发育早期的个体间基因表达变异，并限制哺乳动物物种间早期四肢发育的演化。本数据集包含四种哺乳动物（蝙蝠、负鼠、小鼠和猪）在早期和晚期发育阶段的前后肢mRNA表达谱。每个文库均通过Illumina HiSeq 2500平台开展单端测序，并设置了多个重复样本。需特别说明：蝙蝠的从头转录组组装结果（Trinity.fasta）由多个胚胎发育阶段的前后肢RNA-seq混合数据构建而成，具体阶段包括：起始阶段（Wanek 2期：3个前肢样本与3个后肢样本）、早期阶段（Wanek 3/4期：2个前肢样本与2个后肢样本）以及晚期阶段（Wanek 6期：2个前肢样本与2个后肢样本）。