Chromodomain protein CDYL confers forebrain identity to human cortical organoids by inhibiting neuronatin [RNA-seq]

Epigenetic regulation is essential for the normal development of human cerebral cortex, and its disruptions would lead to diverse neurodevelopmental disorders. The epigenetic co-repressor CDYL exhibits widespread expression across various cell clusters within the human embryonic cortex, yet its roles in this intricate process have remained elusive. Here, we show that CDYL is critical for cortical neurogenesis, and CDYL deficiency led to an augmentation in the generation of GABAergic neurons instead of cortical progenitors and neurons in the cortical organoid model. Combining analysis of bulk RNA-seq and ChIP seq, we identified NNAT as a significant CDYL target by H3K27me3 modification, crucial for the fate determination of neural stem cells within human cortical organoids, distinctly diverging from the murine cortex at a similar developmental stage. Collectively, our study sheds light on the critical function of CDYL in the maintenance of cortical neural stem cell fate commitment during human corticogenesis through the inhibition of NNAT expression. cortical organoids generated from CDYL +/+ and CDYL -/- human ESCs are collected at day 30 and day 80; mouse cortex at E15.5 from control and Emx1-cre-Cdyl-loxp group were collected表观遗传调控（epigenetic regulation）对于人类大脑皮层的正常发育至关重要，其紊乱可引发多种神经发育障碍。表观遗传共抑制因子CDYL在人类胚胎皮层的各类细胞簇中广泛表达，但其在这一复杂过程中的具体功能仍有待阐明。本研究发现，CDYL对皮层神经发生至关重要；在皮层类器官（cortical organoid）模型中，CDYL缺失会导致γ-氨基丁酸能神经元（GABAergic neurons）的生成增多，而非皮层祖细胞与神经元。通过整合批量RNA测序（bulk RNA-seq）与染色质免疫共沉淀测序（ChIP-seq）分析，我们鉴定出NNAT是受CDYL通过组蛋白H3赖氨酸27三甲基化（H3K27me3）修饰调控的关键靶基因，该基因对人类皮层类器官内神经干细胞的命运决定至关重要，这一点与相似发育阶段的小鼠皮层存在显著差异。综上，本研究揭示了CDYL在人类皮层发生过程中，通过抑制NNAT的表达以维持皮层神经干细胞命运决定的关键功能。本研究收集了来自CDYL野生型（CDYL+/+）与CDYL敲除型（CDYL-/-）人类胚胎干细胞（embryonic stem cells, ESCs）的皮层类器官，分别于培养第30天与第80天取样；同时收集了对照组与Emx1-cre-Cdyl-loxp组小鼠胚胎第15.5天（E15.5）的皮层组织。