Buffering exogenous perturbation is crucial to maintain transcriptional homeostasis during development. While miRNAs have been speculated to play a role in stability maintenance, previous studies seeking to check this conjecture focused on measurements of transcript levels at steady state or involved individual miRNA targets. We measured whole-genome expression dynamics by introducing a transient perturbation and establishing a perturbation and recovery system in Drosophila larvae. We inhibited all transcription and assayed transcriptomes at several time points during recovery from inhibition. We performed these experiments in the wild type and miRNA-deficient genetic backgrounds. Consistent with theories about miRNAs’ function in stabilizing the transcriptome, we find that attenuating miRNA expression leads to weak impairment in degradation of targets but strong destabilization of target genes when transcription is re-activated. We further fitted a model that captures the essential aspects of transcription dynamics in our experiments and found that the miRNA target transcripts uniformly overshoot the original steady state as they recover from a general inhibition of transcription if global miRNA levels are reduced. Collectively, our results provide experimental evidence for the idea that miRNAs act cumulatively to stabilize the transcriptional regulatory network. We therefore found a promising approach to assess the effect of these molecules on transcription dynamics.

缓冲外源性扰动对于在发育过程中维持转录稳态至关重要。虽然 miRNA 被推测在稳定性维持中发挥作用，但之前试图验证这一猜想的研究主要集中在稳定状态下转录水平的测量或涉及单个 miRNA 靶点。我们通过在果蝇中引入瞬态扰动并建立扰动和恢复系统来测量全基因组表达动力学幼虫。我们在抑制恢复期间的几个时间点抑制了所有转录并检测了转录组。我们在野生型和 miRNA 缺陷型遗传背景下进行了这些实验。与关于 miRNA 在稳定转录组中的功能的理论一致，我们发现减弱 miRNA 表达会导致靶标降解的弱损伤，但当转录重新激活时靶基因会强烈不稳定。我们进一步拟合了一个模型，该模型在我们的实验中捕获了转录动力学的基本方面，并发现如果全局 miRNA 水平降低，miRNA 目标转录本在从普遍的转录抑制中恢复时会一致地超过原始稳态。总的来说，我们的结果为 miRNA 累积作用以稳定转录调控网络的观点提供了实验证据。因此，我们找到了一种有前途的方法来评估这些分子对转录动力学的影响。