Epigenetics and epitranscriptomics changes in abnormal development of cerebral cortex through mouse microcephaly model [RNA-seq]

The cerebral cortex is a pivotal structure that is integral to advanced brain functions within the mammalian central nervous system. Patterns of DNA methylation and hydroxymethylation play important roles in regulating cerebral cortex development. However, it remains unclear whether abnormal cerebral cortex development, such as microcephaly, could rescale the epigenetic landscape, potentially contributing to dysregulated gene expression during brain development. In this study, we characterize and compare the DNA methylome/hydroxymethylome and transcriptome profiles of the cerebral cortex across several developmental stages in wild-type (WT) mice and Mcph1 knockout (Mcph1-del) mice with severe microcephaly. Intriguingly, we discover a global reduction of 5'- hydroxymethylcytosine (5hmC) level, primarily in TET1-binding regions, in Mcph1-del mice compared to WT mice during juvenile and adult stages. Notably, genes exhibiting diminished 5hmC levels and concurrently decreased expression are essential for neurodevelopment and brain functions. Additionally, genes displaying a delayed accumulation of 5hmC in Mcph1-del mice are significantly associated with the establishment and maintenance of the nervous system during the adult stage. These findings reveal that aberrant cerebral cortex development in early stages can profoundly alter the epigenetic regulation program, which provides new insights into the molecular mechanisms underpinning diseases related to cerebral cortex development.大脑皮层是哺乳动物中枢神经系统中支撑高级脑功能的关键结构。DNA甲基化（DNA methylation）与羟甲基化（hydroxymethylation）模式在大脑皮层发育调控中发挥重要作用。然而，目前尚不清楚诸如小头畸形这类大脑皮层发育异常是否会重塑表观遗传图谱，进而可能导致脑发育过程中基因表达失调。本研究对野生型（WT）小鼠与患有严重小头畸形的Mcph1基因敲除（Mcph1-del）小鼠大脑皮层在多个发育阶段的DNA甲基化组（DNA methylome）、羟甲基化组（hydroxymethylome）及转录组（transcriptome）特征进行了表征与比较。有趣的是，与野生型小鼠相比，Mcph1-del小鼠在幼年及成年阶段的全基因组5'-羟甲基胞嘧啶（5hmC）水平显著降低，且该降低主要发生在TET1结合区域内。值得注意的是，5hmC水平降低且伴随表达量下调的基因，均对神经发育及脑功能至关重要。此外，在Mcph1-del小鼠中表现出5hmC积累延迟的基因，在成年阶段与神经系统的建立及维持显著相关。本研究结果表明，早期大脑皮层发育异常可显著改变表观遗传调控程序，这为阐明大脑皮层发育相关疾病的分子机制提供了新的视角。