DDX6 decouples translational repression from RNA degradation of miRNA targets [QuantSeq mRNA]

Translation and mRNA degradation are intimately connected, yet the mechanisms that regulate them are not fully understood. Here we examine the regulation of translation and mRNA stability in mouse embryonic stem cells (ESCs) and during differentiation. In contrast to previous reports, we found that transcriptional changes account for most of the molecular changes during ESC differentiation. Within ESCs translation level and mRNA stability are positively correlated. The RNA-binding protein DDX6 has been implicated in processes involving both translational repression and mRNA destabilization; in yeast DDX6 connects codon optimality and mRNA stability and in mammals DDX6 is involved in microRNA-mediated repression. We generated DDX6 KO ESCs and found that while there was minimal connection between codon usage and stability changes, the loss of DDX6 leads to the translational depression of microRNA targets. Surprisingly, the translational derepression of microRNA targets occurs without affecting mRNA stability. Furthermore, DDX6 KO ESCs share overlapping phenotypes and global molecular changes with ESCs that completely lack all microRNAs. Together our results demonstrate that the loss of DDX6 decouples the two forms of microRNA induced repression and emphasize that translational repression by microRNAs is underappreciated. mRNA expression profiling of wild type, DGCR8 KO, and DDX6 KO embryonic stem cells

翻译与mRNA降解紧密关联，但其调控机制尚未完全阐明。本研究对小鼠胚胎干细胞（embryonic stem cells, ESCs）及其分化过程中的翻译与mRNA稳定性调控展开分析。与既往研究报道不同，我们发现ESC分化过程中的多数分子变化可归因于转录水平改变。在ESCs内部，翻译水平与mRNA稳定性呈正相关。RNA结合蛋白DDX6已被证实参与翻译抑制与mRNA降解过程：在酵母中，DDX6关联密码子最优性与mRNA稳定性；在哺乳动物中，DDX6则参与微小RNA（microRNA）介导的基因沉默。我们构建了DDX6敲除（DDX6 KO）的ESCs，研究发现尽管密码子使用偏好与稳定性变化之间几乎无关联，但DDX6的缺失会导致微小RNA靶基因的翻译抑制。令人意外的是，微小RNA靶基因的翻译去抑制现象并不会影响mRNA稳定性。此外，DDX6敲除ESCs与完全缺失所有微小RNA的ESCs具有重叠的表型特征与全局分子变化谱。综上，本研究结果表明，DDX6的缺失使微小RNA介导的两种抑制形式解耦联，并凸显出微小RNA介导的翻译抑制这一过程长期被低估。本研究涵盖野生型、DGCR8敲除（DGCR8 KO）与DDX6敲除（DDX6 KO）胚胎干细胞的mRNA表达谱分析。