Evolution of microRNA transcriptome at the onset of Drosophila metamorphosis. Evolution of microRNA transcriptome at the onset of Drosophila metamorphosis

MicroRNAs (miRNAs) are endogenous RNA molecules that contribute to the regulation of gene expression post-transcriptionally. Recently, patterns of sequence evolution and evolutionary emergence of miRNAs have been analyzed in detail. However, the extent to which miRNA expression levels vary within and between species, the role of stabilizing selection versus other evolutionary mechanisms in shaping the temporal dynamics of these changes, and how this variation might unveil the interplay between miRNAs and mRNAs remain poorly understood. This is especially true during key developmental transitions involving miRNA regulation. Combining deep-sequencing with multi-species microarrays, we assayed miRNA expression levels immediately before (≥18BPF) and after (PF) the increase in steroid hormone ecdysone that triggers metamorphosis. We did so both at the intra- and interspecific levels in the Drosophila melanogaster species group. In contrast to their sequence conservation, ~25% of the analyzed miRNAs differed significantly in expression levels at ≥18BPF and/or PF across D. melanogaster strains. Additionally, ~33% showed modifications in their pattern of expression bias between developmental timepoints. Relative to the patterns of evolution, changes in miRNA abundance at PF accumulate linearly over evolutionary time while similar changes at ≥18BPF do not. Importantly, expression levels of ≥18BPF-enriched miRNAs are the most variable within and between species and therefore the least likely to evolve under stabilizing selection, especially as compared to non-developmentally enriched miRNAs. Overall, functional attributes such as expression ubiquity are more tightly associated with lower levels of miRNA expression polymorphism at PF than at ≥18BPF. Furthermore, ≥18BPF- and PF-enriched miRNAs showed opposite patterns of covariation in expression with mRNAs, which was found to denote the type of regulatory relationship between miRNA and mRNA. By focusing on the miRNA expression levels at the onset of metamorphosis, our results have unveiled contrasting functional patterns of evolutionary divergence during ontogeny. Overall design: Total 12 samples are included. Please note that the 'description' field in each sample record contains more details for the biological and technical replicate pairs.

微小RNA（MicroRNAs，miRNAs）是一类在转录后水平参与基因表达调控的内源性RNA分子。近年来，学界已针对miRNA的序列演化模式及其演化起源展开了细致的解析。然而，关于miRNA表达水平在物种内部与物种之间的变异程度、稳定选择（stabilizing selection）与其他演化机制在塑造此类变异的时间动态中所发挥的作用，以及这类变异如何揭示miRNA与信使RNA（messenger RNA，mRNAs）之间的相互调控关系，目前仍知之甚少。在涉及miRNA调控的关键发育转变阶段，这一认知空白尤为突出。本研究将深度测序（deep-sequencing）与多物种微阵列（multi-species microarrays）相结合，针对触发果蝇变态发育的蜕皮类固醇激素（ecdysone）升高前后的miRNA表达水平进行了检测，采样时间点分别为激素升高前（≥18BPF）与激素升高后（PF）。实验对象为黑腹果蝇物种群（Drosophila melanogaster species group），且同时在种内与种间两个层面开展检测。与miRNA的序列保守性形成鲜明对比的是，在分析的miRNA中，约25%在≥18BPF和/或PF时间点的表达水平在不同黑腹果蝇品系间存在显著差异。此外，约33%的miRNA在不同发育时间点的表达偏好模式发生了改变。相较于演化模式，PF时间点的miRNA丰度变化随演化时间呈线性累积，而≥18BPF时间点的类似变化则无此规律。值得注意的是，≥18BPF富集型miRNA的表达水平在物种内部与物种之间的变异程度最高，因此相较于非发育富集型miRNA，其在稳定选择作用下发生演化的可能性最低。总体而言，相较于≥18BPF时间点，PF时间点的miRNA表达多态性水平更低，且这一特征与表达普遍性等功能属性的关联更为紧密。此外，≥18BPF富集型与PF富集型miRNA与mRNA的表达共变异模式恰好相反，这一现象可用于区分miRNA与mRNA之间的调控关系类型。本研究聚焦变态发育起始阶段的miRNA表达水平，研究结果揭示了个体发育（ontogeny）过程中演化分化的两类截然不同的功能模式。实验总体设计：本研究共纳入12个样本。请注意，每条样本记录中的“描述”字段包含了生物学重复与技术重复对的更多细节信息。