Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and EedcKO Forebrain Transcriptomes

The histone methyltransferase complex PRC2 is a crucial chromatin modifier and controls key steps in developmental transitions and cell fate choices. Mutations in PRC2 core subunits are found in Weaver syndrome with craniofacial defects, intellectual disabilities, and often macrocephaly, but its pathogenicity and molecular mechanism are unknown. Here, we examined the role of PRC2/Eed in neural stem/progenitor cells (NSPCs) during cortical neurogenesis We found that Eed is highly expressed in embryonic cerebral cortex and specific deletion of Eed in forebrain reduced the number of upper layer neurons but not deeper layer neurons and ultimately contributed to abnormal cortical development. In addition, our results revealed that PRC2/Eed regulated Hedgehog signaling pathway through activation of Gli3 not dependent on H3K27me3 but H3K27ac. What?s more, Increased Gli3 in NSPCs could reduce Gli1 expression and contribute to the defects of cortical neurogenesis caused by Eed deletion. Finally, Hedgehog signaling activation with small molecule SAG or genetic inactivation of Ptch1 could partially rescue the cortical neurogenesis defects in vivo after Eed depletion. In general, we identified a novel PRC2/Eed-Gli3-Gli1 regulatory axis that is critical for normal cortical neurogenesis. Our findings define a critical function for PRC2/Eed in cortical development and shed light on the genetic basis of intellectual disabilities of neural developmental disorders caused by PRC2/Eed mutation. We report the forebrain RNA-seq data of wild type and EedcKO littermate mice at E12.5. We mapped about 30 million sequence reads per sample to the mouse genome (build mm10). By comparing the sequencing data of mice in the wild time group and the EedcKO group, the transcriptome map of Eed deletion can be obtained. These data are useful for the study of Eed in early neurodevelopment. Examination of 2 different group in E12.5 forebrain tissues..组蛋白甲基转移酶复合物PRC2（histone methyltransferase complex PRC2）是一类关键的染色质修饰因子，调控发育转变与细胞命运抉择的核心步骤。PRC2核心亚基的突变可引发韦弗综合征，患者表现为颅面畸形、智力障碍，常伴随巨头畸形，但其致病机制与分子机理尚未明确。本研究针对皮层神经发生过程中PRC2/Eed在神经干细胞/祖细胞（neural stem/progenitor cells，NSPCs）中的作用展开探究。实验发现，Eed在胚胎大脑皮层中高表达；前脑特异性敲除Eed后，上层神经元数量减少而深层神经元数量未受影响，最终导致皮层发育异常。此外，本研究结果揭示，PRC2/Eed可通过激活Gli3调控刺猬信号通路（Hedgehog signaling pathway），该调控过程不依赖H3K27me3，而是依赖H3K27ac。进一步研究显示，NSPCs中Gli3水平升高可下调Gli1的表达，进而加剧Eed缺失引发的皮层神经发生缺陷。最后，通过小分子SAG激活刺猬信号通路，或遗传失活Ptch1，可在体内部分挽救Eed缺失导致的皮层神经发生缺陷。综上，本研究鉴定出一条对正常皮层神经发生至关重要的新型PRC2/Eed-Gli3-Gli1调控轴。本研究明确了PRC2/Eed在皮层发育中的关键功能，为解析PRC2/Eed突变引发的神经发育障碍相关智力障碍的遗传基础提供了新的思路。本研究附带了胚胎第12.5天（E12.5）野生型与Eed条件性敲除（EedcKO）同窝小鼠前脑的RNA测序（RNA-seq）数据：每个样本约获得3000万条序列读段，比对至小鼠基因组（版本mm10）。通过对比野生型组与EedcKO组小鼠的测序数据，可获取Eed缺失后的转录组图谱。该数据集可用于Eed在早期神经发育中的相关研究，共包含E12.5胎龄前脑组织的两组独立样本检测。