Table_4_Common CHD8 Genomic Targets Contrast With Model-Specific Transcriptional Impacts of CHD8 Haploinsufficiency.xlsx

The packaging of DNA into chromatin determines the transcriptional potential of cells and is central to eukaryotic gene regulation. Case sequencing studies have revealed mutations to proteins that regulate chromatin state, known as chromatin remodeling factors, with causal roles in neurodevelopmental disorders. Chromodomain helicase DNA binding protein 8 (CHD8) encodes a chromatin remodeling factor with among the highest de novo loss-of-function mutation rates in patients with autism spectrum disorder (ASD). However, mechanisms associated with CHD8 pathology have yet to be elucidated. We analyzed published transcriptomic data across CHD8 in vitro and in vivo knockdown and knockout models and CHD8 binding across published ChIP-seq datasets to identify convergent mechanisms of gene regulation by CHD8. Differentially expressed genes (DEGs) across models varied, but overlap was observed between downregulated genes involved in neuronal development and function, cell cycle, chromatin dynamics, and RNA processing, and between upregulated genes involved in metabolism and immune response. Considering the variability in transcriptional changes and the cells and tissues represented across ChIP-seq analysis, we found a surprisingly consistent set of high-affinity CHD8 genomic interactions. CHD8 was enriched near promoters of genes involved in basic cell functions and gene regulation. Overlap between high-affinity CHD8 targets and DEGs shows that reduced dosage of CHD8 directly relates to decreased expression of cell cycle, chromatin organization, and RNA processing genes, but only in a subset of studies. This meta-analysis verifies CHD8 as a master regulator of gene expression and reveals a consistent set of high-affinity CHD8 targets across human, mouse, and rat in vivo and in vitro studies. These conserved regulatory targets include many genes that are also implicated in ASD. Our findings suggest a model where perturbation to dosage-sensitive CHD8 genomic interactions with a highly-conserved set of regulatory targets leads to model-specific downstream transcriptional impacts.

DNA包装为染色质（chromatin）决定了细胞的转录潜能，是真核生物基因调控的核心过程。病例测序研究发现，调控染色质状态的蛋白质——即染色质重塑因子（chromatin remodeling factors）——发生突变与神经发育障碍存在因果关联。染色质域解旋酶DNA结合蛋白8（Chromodomain helicase DNA binding protein 8, CHD8）所编码的染色质重塑因子，在自闭症谱系障碍（autism spectrum disorder, ASD）患者中，其新发功能丧失突变率位居前列。然而，与CHD8致病机制相关的分子通路尚未被阐明。本研究分析了已发表的CHD8体外、体内敲低及敲除模型的转录组数据，以及已发表的染色质免疫沉淀测序（ChIP-seq）数据集的CHD8结合谱，以解析CHD8调控基因的协同机制。不同模型中的差异表达基因（differentially expressed genes, DEGs）存在异质性，但在参与神经元发育与功能、细胞周期、染色质动态及RNA加工的下调基因之间，以及参与代谢与免疫应答的上调基因之间，均观察到基因表达的重叠特征。尽管转录组变化及ChIP-seq分析所涉及的细胞与组织存在异质性，我们仍发现了一组高度保守的高亲和力CHD8基因组结合位点。CHD8在参与基础细胞功能及基因调控的基因的启动子区域呈现富集特征。高亲和力CHD8靶基因与差异表达基因的重叠分析显示，CHD8剂量降低直接与细胞周期、染色质组织及RNA加工相关基因的表达下调相关，但该关联仅在部分研究中被观测到。本荟萃分析证实CHD8是基因表达的主调控因子，并揭示了跨人类、小鼠、大鼠的体内及体外研究中，一组高度一致的高亲和力CHD8靶基因。这些保守的调控靶标包含诸多与ASD相关的致病基因。本研究结果提出了如下模型：剂量敏感型CHD8基因组结合受到扰动，结合一组高度保守的调控靶标，进而引发模型特异性的下游转录组改变。