Many post-transcriptional mechanisms operate via mRNA 3′UTRs to regulate protein expression, and such controls are crucial for development. We show that homozygous mutations in two zebrafish exon junction complex (EJC) core genes rbm8a and magoh leads to muscle disorganization, neural cell death, and motor neuron outgrowth defects, as well as dysregulation of mRNAs subjected to nonsense-mediated mRNA decay (NMD) due to translation termination ≥ 50 nts upstream of the last exon-exon junction. Intriguingly, we find that EJC-dependent NMD also regulates a subset of transcripts that contain 3′UTR introns (3′UI) < 50 nts downstream of a stop codon. Some transcripts containing such stop codon-proximal 3′UI are also NMD-sensitive in cultured human cells and mouse embryonic stem cells. We identify 167 genes that contain a conserved proximal 3′UI in zebrafish, mouse and humans. foxo3b is one such proximal 3′UI-containing gene that is upregulated in zebrafish EJC mutant embryos, at both mRNA and protein levels, and loss of foxo3b function in EJC mutant embryos significantly rescues motor axon growth defects. These data are consistent with EJC-dependent NMD regulating foxo3b mRNA to control protein expression during zebrafish development. Our work shows that the EJC is critical for normal zebrafish development and suggests that proximal 3′UIs may serve gene regulatory function in vertebrates.

许多转录后机制通过 mRNA 3'UTR 来调节蛋白质表达，此类控制对于发育至关重要。我们发现斑马鱼外显子连接复合体（EJC）两个核心基因rbm8a和magoh的纯合突变会导致肌肉解体、神经细胞死亡和运动神经元生长缺陷，以及无义介导的 mRNA 衰变（NMD）导致 mRNA 失调由于翻译终止于最后一个外显子-外显子连接处上游 ≥ 50 nts。有趣的是，我们发现依赖于 EJC 的 NMD 还调节终止密码子下游包含 3'UTR 内含子 (3'UI) < 50 nts 的转录子子集。一些含有此类终止密码子近端 3'UI 的转录本在培养的人类细胞和小鼠胚胎干细胞中也对 NMD 敏感。我们在斑马鱼、小鼠和人类中鉴定出 167 个含有保守近端 3'UI 的基因。 Foxo3b就是这样一种含有近端 3'UI 的基因，它在斑马鱼 EJC 突变体胚胎中在 mRNA 和蛋白质水平上均上调，并且 EJC 突变体胚胎中Foxo3b功能的丧失可显着挽救运动轴突生长缺陷。这些数据与 EJC 依赖性 NMD 调节Foxo3b mRNA 以控制斑马鱼发育过程中蛋白质表达的情况一致。我们的工作表明，EJC 对于斑马鱼的正常发育至关重要，并表明近端 3'UI 可能在脊椎动物中发挥基因调控功能。