Protein translation rate determines neocortical neuron fate

The mammalian neocortex comprises enormous diversity regarding cell types, morphology, and connectivity. In this work, we discover a unique sensitivity in the development of neurons expressing Satb2, a determinant of upper cortical layers, to translation rates. We find specific upregulation of protein synthesis in the progenitors of later-born neurons and show that translation rates are inherent features of cortical neuron subtypes. In a small molecule screening, we reveal Ire1a as a regulator of Satb2 and global translation rates. In the developing brain, Ire1a coordinates ribosome traffic and the expression of eIF4A1. Furthermore, we demonstrate that the mRNA translation of Satb2 depends on its 5'-untranslated region and requires eIF4A1 helicase activity. Here, we show that cortical neuron diversity is generated by mechanisms operating beyond the gene transcription, with Ire1a-safeguarded proteostasis serving as an essential regulator of brain development factors, and ribosomal proteins. Translation rates distinguish early and late neuronal progenitors and early- and late-born postmitotic neurons, indicative of developmental stage- and differentiation-specific requirements for protein synthesis rates in the formation of upper and deeper cortical layers. We demonstrate that specification and polarization of upper layer neurons is uniquely sensitive to translation rate, in contrast to deep layer neurons. Our data shed light onto the post-transcriptional source of cellular diversity in the developing cortex and unveils stress-independent homeostatic functions of Ire1a. Total RNAseq from P0 Cortices from wild-type and IRE1aEmx1Cre mutant mice as well as RNAseq from purified Polysomes from wild type and IRE1aEmx1Cre mice. 3 batches: Batch 1: Total RNAseq from cortex Batch 2: Total RNAseq from Purified Polysomes Batch 3: Total RNAseq from Purified Light and Heavy Polysomes Analysis scripts can be seen at: https://github.com/qoldt/IRE1aKO_Polysome_RNAseq哺乳动物新皮层在细胞类型、形态及连接性层面展现出极为丰富的多样性。本研究发现，表达Satb2（大脑皮层上层神经元的决定因子）的神经元发育过程，对翻译速率存在独特的敏感性。我们观察到晚出生神经元的祖细胞中蛋白质合成发生特异性上调，并证实翻译速率是皮层神经元亚型的固有特征。在小分子筛选实验中，我们揭示Ire1a是调控Satb2表达与整体翻译速率的关键因子。在发育中的大脑内，Ire1a可协调核糖体运输与eIF4A1的表达。此外，我们证实Satb2的mRNA翻译依赖于其5'非翻译区，且需要eIF4A1的解旋酶活性。本研究表明，皮层神经元的多样性并非仅由基因转录机制所主导，由Ire1a维持的蛋白质稳态可作为脑发育调控因子与核糖体蛋白的关键调节剂，发挥核心作用。翻译速率能够区分早期与晚期神经元祖细胞，以及早出生和晚出生的有丝分裂后神经元，这提示在皮层上层与深层的形成过程中，蛋白质合成速率存在发育阶段特异性与分化特异性的需求。与深层神经元不同，上层神经元的特化与极化过程对翻译速率具有独特的敏感性。本研究结果揭示了发育皮层中细胞多样性的转录后来源，并阐明了Ire1a不依赖于应激的稳态功能。本数据集包含野生型与IRE1aEmx1Cre突变小鼠P0龄皮层的总RNA测序数据，以及野生型和IRE1aEmx1Cre突变小鼠纯化多核糖体的RNA测序数据。实验共分为3个批次：批次1：皮层总RNA测序；批次2：纯化多核糖体总RNA测序；批次3：纯化轻、重多核糖体总RNA测序。分析脚本可参见：https://github.com/qoldt/IRE1aKO_Polysome_RNAseq