Numerical values underlying graphs in S4 Fig.

RNA abundance is controlled by rates of synthesis and degradation. Although mis-regulation of RNA turnover is linked to neurodevelopmental disorders, how it contributes to cortical development is largely unknown. Here, we discover the landscape of RNA stability regulation in the cerebral cortex and demonstrate that intact RNA decay machinery is essential for corticogenesis in vivo. We use SLAM-seq to measure RNA half-lives transcriptome-wide across multiple stages of cortical development. Leveraging these data, we discover cis-acting features associated with RNA stability and probe the relationship between RNA half-life and developmental expression changes. Notably, RNAs that are up-regulated across development tend to be more stable, while down-regulated RNAs are less stable. Using compound mouse genetics, we discover CNOT3, a core component of the CCR4-NOT deadenylase complex linked to neurodevelopmental disease, is essential for cortical development. Conditional knockout of Cnot3 in neural progenitors and their progeny in the developing mouse cortex leads to severe microcephaly due to altered cell fate and p53-dependent apoptosis. Finally, we define the molecular targets of CNOT3, revealing it controls expression of poorly expressed, non-optimal mRNAs in the cortex, including cell cycle-related transcripts. Collectively, our findings demonstrate that fine-tuned control of RNA turnover is crucial for brain development.

RNA丰度由合成与降解速率共同调控。尽管RNA周转失调与神经发育障碍存在关联，但该过程如何参与皮层发育的机制目前仍不明确。本研究首次绘制了大脑皮层中RNA稳定性调控的全景图谱，并证实完整的RNA降解复合体对于体内皮层发生至关重要。我们利用SLAM-seq（SLAM-sequencing）技术，在皮层发育的多个阶段开展全转录组范围的RNA半衰期检测。依托该数据集，我们鉴定出与RNA稳定性相关的顺式作用特征，并探究了RNA半衰期与发育过程中基因表达变化之间的关联。值得注意的是，发育过程中表达上调的RNA往往稳定性更高，而表达下调的RNA稳定性则更低。我们通过复合小鼠遗传学手段，发现CCR4-NOT脱腺苷酸酶复合体（CCR4-NOT deadenylase complex）的核心组分CNOT3——该蛋白与神经发育疾病相关——对于皮层发育不可或缺。在发育中小鼠皮层的神经祖细胞及其子代细胞中条件性敲除Cnot3，会因细胞命运改变及p53依赖的细胞凋亡引发严重小头畸形。最后，我们明确了CNOT3的分子靶标，揭示其可调控皮层中低表达、密码子非最优的mRNA的表达，包括细胞周期相关转录本。综上，本研究证实RNA周转的精细调控对于大脑发育至关重要。