Primers used in this study.

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，但其对皮层发育的具体贡献机制在很大程度上仍未明确。本研究首次绘制了大脑皮层中的RNA稳定性调控全景，并证实完整的RNA降解机器对体内皮层发生过程至关重要。我们采用SLAM测序（SLAM-seq）技术，在皮层发育的多个阶段开展全转录组水平的RNA半衰期检测。依托上述数据，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的关联。值得注意的是，发育进程中表达上调的RNA往往稳定性更高，而表达下调的RNA则稳定性更低。我们通过复合小鼠遗传学手段发现，CNOT3——一种与神经发育疾病相关的CCR4-NOT脱腺苷酶复合物核心组分——对皮层发育不可或缺。在发育中的小鼠皮层内，对神经祖细胞及其子代细胞的Cnot3基因进行条件性敲除，会因细胞命运改变和p53依赖的细胞凋亡引发严重小头畸形。最后，我们明确了CNOT3的分子靶点，揭示其可调控皮层中低表达、密码子偏好性非最优的信使RNA（mRNA）的表达，包括与细胞周期相关的转录本。综上，本研究结果证实，RNA周转的精细调控对大脑发育至关重要。