Table_5_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）的过程决定了细胞的转录潜能，是真核基因调控的核心环节。病例测序研究已揭示，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（CHD8）编码一种染色质重塑因子，在自闭症谱系障碍（ASD）患者中，其功能丧失型新发突变率位居前列。然而，与CHD8致病机制相关的分子通路仍有待阐明。我们对已发表的CHD8体外、体内敲低（knockdown）与敲除（knockout）模型的转录组（transcriptomic）数据，以及已发表的染色质免疫共沉淀测序（ChIP-seq）数据集的CHD8结合图谱进行了整合分析，以明确CHD8调控基因表达的共通机制。不同模型中的差异表达基因（differentially expressed genes, DEGs）存在差异，但在参与神经元发育与功能、细胞周期、染色质动态调控及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，均观察到了基因重叠现象。尽管ChIP-seq分析涉及的转录变化模式、细胞及组织类型存在异质性，我们仍鉴定出一组一致性极高的CHD8高亲和力基因组结合位点。CHD8在参与基础细胞功能及基因调控的基因的启动子区域显著富集。高亲和力CHD8靶基因与DEGs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，但这一关联仅在部分研究中得到验证。本荟萃分析（meta-analysis）证实CHD8是基因表达的主控调控因子，并揭示了跨人类、小鼠、大鼠的体内外研究中一组保守的CHD8高亲和力靶基因。这些保守的调控靶标包含多个已被报道与ASD相关的基因。我们的研究结果提出了一种模型：剂量敏感性的CHD8与一组高度保守的调控靶标的基因组互作发生扰动，会引发模型特异性的下游转录组效应。