Kaan Okay, Juan Ouyang, Katrín Möller, Kasper Daniel Hansen and Hans Tómas Björnsson
The most common phenotype seen in individuals with the Mendelian Disorders of the Epigenetic Machinery (MDEM) is intellectual disability. Previously people have uncovered a DNA methylation (DNAm) signature in the peripheral blood of such patients but it is unclear what happens in a disease relevant cell such as neurons. Here we have analyzed DNAm data from Oxford nanopore technology (ONT) sequencing in neuronal progenitors with EM knockouts (KO). We created 46 EM gene KOs through CRISPR-Cas9 in murine neural progenitor cells (mNPCs). DNA and RNA were isolated in EM-deficient mNPCs followed by ONT sequencing and bulk RNA sequencing to identify shared DNAm and expression abnormalities among EMs, respectively. We identified that the 3’ UTR of Zic4 gene has shared differential methylated region (DMR) among 46 EM KOs and controls. We also showed that expression of Zic4 is downregulated in multiple EM-KO mNPCs and murine neurodevelopment. In general, the changes in global DNAm across EM KOs are subtle, except for Dnmt1 and Dnmt3b, which are part of the DNA methylation machinery. The changes seen in Zic4 expression in the KO mNPCs are similar to those seen in cells further along the normal differentiation trajectory, suggesting that abnormal differentiation rate may be a unifying feature among the MDEM.
