TBR1 Regulates Autism Risk Genes in the Developing Neocortex

Exome sequencing studies have identified multiple genes harboring de novo loss-of-function (LoF) variants in individuals with autism spectrum disorders (ASD), including TBR1, a master regulator of cortical development. We performed ChIP-seq for TBR1 during mouse cortical neurogenesis and show that TBR1-bound regions are enriched adjacent to ASD genes. ASD genes were also enriched among genes that are differentially expressed in Tbr1 knockouts, which together with the ChIP-seq data, suggests direct transcriptional regulation. Of the 9 ASD genes examined, 7 were misexpressed in the cortices of Tbr1 knockout mice, including 6 with increased expression in the deep cortical layers. ASD genes with adjacent cortical TBR1 ChIP-seq peaks also showed unusually low levels of LoF mutations in a reference human population and among Icelanders. We then leveraged TBR1 binding to identify an appealing subset of candidate ASD genes. Our findings highlight a TBR1-regulated network of ASD genes in the developing neocortex that are relatively intolerant to LoF mutations, indicating that these genes may play critical roles in normal cortical development. Overall design: ChIP-seq for Tbr1 on mouse whole cortex dissected from embryonic day 15.5 (E15.5) embryos

外显子组测序研究已在自闭症谱系障碍（autism spectrum disorders, ASD）患者中鉴定出多个携带新发功能丧失（loss-of-function, LoF）变异的基因，其中包括皮层发育主调控因子TBR1。本研究针对小鼠皮层神经发生过程中的TBR1开展染色质免疫共沉淀测序（ChIP-seq），结果显示TBR1结合区域在自闭症谱系障碍相关基因附近显著富集。在Tbr1基因敲除小鼠中差异表达的基因中，同样富集了自闭症谱系障碍相关基因，结合染色质免疫共沉淀测序数据提示TBR1对这些基因存在直接转录调控作用。在所检测的9个自闭症谱系障碍相关基因中，有7个在Tbr1敲除小鼠皮层内表达异常，其中6个在皮层深层的表达水平升高。携带邻近皮层TBR1染色质免疫共沉淀测序峰的自闭症谱系障碍相关基因，在参考人类人群及冰岛人群中均呈现出异常低水平的功能丧失变异。本研究进一步借助TBR1结合特征筛选出了一组极具研究价值的候选自闭症谱系障碍基因。本研究结果揭示了发育新皮层中受TBR1调控的自闭症谱系障碍相关基因网络，这类基因对功能丧失变异相对不耐受，表明它们在正常皮层发育过程中可能发挥关键作用。实验整体设计：对胚胎第15.5天（E15.5）小鼠分离获取的全皮层组织开展Tbr1染色质免疫共沉淀测序。