Molecular Neuropsychiatry & Development (MiND) Lab, Molecular Brain Science Research Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1RS, Canada.
Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A8, Canada.
Sci Rep. 2023 Nov 21;13(1):20391. doi: 10.1038/s41598-023-46673-0.
Patched domain-containing 1 (PTCHD1) is a well-established susceptibility gene for autism spectrum disorder (ASD) and intellectual disability (ID). Previous studies have suggested that alterations in the dosage of PTCHD1 may contribute to the etiology of both ASD and ID. However, there has not yet been a thorough investigation regarding mechanisms that regulate PTCHD1 expression. We sought to characterize the Ptchd1 promoter in a mouse neuronal model, as well as to identify and validate cis regulatory elements. We defined specific regions of the Ptchd1 promoter essential for robust expression in P19-induced neurons. Evolutionarily-conserved putative transcription factor binding sites within these regions were subsequently identified. Using a pairwise comparison of chromatin accessibility between mouse forebrain and liver tissues, a candidate regulatory region, ~ 9.1 kbp downstream of the Ptchd1 stop codon was defined. This region harbours two ENCODE-predicted enhancer cis-regulatory elements. Further, using DNase footprint analysis, a putative YY1-binding motif was also identified. Genomic deletion of the entire 8 kbp downstream open chromatin region attenuated Ptchd1 transcription by over 60% in our neuronal model, corroborating its predicted regulatory function. This study provides mechanistic insights related to the expression of PTCHD1, and provides important context to interpret genetic and genomic variation at this locus which may influence neurodevelopment.
patched 结构域包含蛋白 1（PTCHD1）是一种公认的自闭症谱系障碍（ASD）和智力障碍（ID）的易感基因。先前的研究表明，PTCHD1 剂量的改变可能导致 ASD 和 ID 的发病机制。然而，目前还没有对调节 PTCHD1 表达的机制进行全面研究。我们试图在小鼠神经元模型中描述 Ptchd1 启动子，并识别和验证顺式调控元件。我们确定了 Ptchd1 启动子中对 P19 诱导神经元中强表达至关重要的特定区域。随后在这些区域内鉴定了具有进化保守性的假定转录因子结合位点。使用鼠标前脑和肝脏组织之间染色质可及性的成对比较，定义了一个候选调控区域，即 Ptchd1 终止密码子下游约 9.1kbp。该区域包含两个 ENCODE 预测的增强子顺式调控元件。此外，通过 DNase 足迹分析，还鉴定了一个假定的 YY1 结合基序。我们的神经元模型中，整个 8kbp 下游开放染色质区域的基因组缺失使 Ptchd1 转录减少了 60%以上，这证实了其预测的调控功能。这项研究提供了与 PTCHD1 表达相关的机制见解，并为解释该基因座可能影响神经发育的遗传和基因组变异提供了重要背景。
