Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 955 Main Street, Buffalo, NY 14203, United States.
Hum Mol Genet. 2024 Jun 21;33(13):1176-1185. doi: 10.1093/hmg/ddae058.
Genetic sequencing has identified high-confidence ASD risk genes with loss-of-function mutations. How the haploinsufficiency of distinct ASD risk genes causes ASD remains to be elucidated. In this study, we examined the role of four top-ranking ASD risk genes, ADNP, KDM6B, CHD2, and MED13, in gene expression regulation. ChIP-seq analysis reveals that gene targets with the binding of these ASD risk genes at promoters are enriched in RNA processing and DNA repair. Many of these targets are found in ASD gene database (SFARI), and are involved in transcription regulation and chromatin remodeling. Common gene targets of these ASD risk genes include a network of high confidence ASD genes associated with gene expression regulation, such as CTNNB1 and SMARCA4. We further directly examined the transcriptional impact of the deficiency of these ASD risk genes. Our mRNA profiling with qPCR assays in cells with the knockdown of Adnp, Kdm6b, Chd2 or Med13 has revealed an intricate pattern of their cross-regulation, as well as their influence on the expression of other ASD genes. In addition, some synaptic genes, such as Snap25 and Nrxn1, are strongly regulated by deficiency of the four ASD risk genes, which could be through the direct binding at promoters or indirectly through the targets like Ctnnb1 or Smarca4. The identification of convergent and divergent gene targets that are regulated by multiple ASD risk genes will help to understand the molecular mechanisms underlying common and unique phenotypes associated with haploinsufficiency of ASD-associated genes.
基因测序已经确定了具有功能丧失突变的高可信度 ASD 风险基因。不同的 ASD 风险基因的单倍不足如何导致 ASD 仍然需要阐明。在这项研究中，我们研究了四个排名最高的 ASD 风险基因 ADNP、KDM6B、CHD2 和 MED13 在基因表达调控中的作用。ChIP-seq 分析表明，这些 ASD 风险基因在启动子处结合的基因靶标在 RNA 加工和 DNA 修复中富集。这些靶标中的许多都在 ASD 基因数据库（SFARI）中，并且参与转录调控和染色质重塑。这些 ASD 风险基因的共同基因靶标包括与基因表达调控相关的高可信度 ASD 基因网络，例如 CTNNB1 和 SMARCA4。我们进一步直接检查了这些 ASD 风险基因缺失的转录影响。我们使用 qPCR 测定法在 Adnp、Kdm6b、Chd2 或 Med13 敲低的细胞中进行 mRNA 谱分析，揭示了它们相互调控的复杂模式，以及它们对其他 ASD 基因表达的影响。此外，一些突触基因，如 Snap25 和 Nrxn1，强烈受到这四个 ASD 风险基因缺失的调控，这可能是通过直接结合启动子或间接通过 Ctnnb1 或 Smarca4 等靶标实现的。鉴定受多个 ASD 风险基因调控的趋同和发散的基因靶标将有助于理解与 ASD 相关基因单倍不足相关的常见和独特表型的分子机制。
