PROSER1 Modulates DNA Demethylation through Dual Mechanisms to Prevent Syndromic Developmental Malformations [ChIP-seq]

The link between DNA methylation and neurodevelopmental disorders is well established. However, how DNA methylation is fine-tuned – ensuring precise gene expression and developmental fidelity – remains poorly understood. PROSER1, a known TET2 interactor, was recently linked to a severe neurodevelopmental disorder. Here, we demonstrate that PROSER1 interacts with all TET enzymes and stabilizes chromatin-bound TET-OGT-PROSER1-DBHS (TOPD) complexes, which regulate DNA demethylation and developmental gene expression. Surprisingly, we find that PROSER1 also sequesters TET enzymes, preventing widespread demethylation and transposable element de-repression. Our findings identify PROSER1 as a key factor which both positively and negatively regulates DNA demethylation essential for mammalian neurodevelopment. Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for endogenous PROSER1 in mESCs using PROSER1 KO as background control, and endogenous TET2 in wildtype and PROSER1 KO mESCs. ChIP-seq in wildtype and PROSER1 KO mESCs for the following histone modifications: H3K27ac, H3K4me1. Enzymatic methyl-seq (EM-seq) in wildtype, PROSER1 KO and PROSER1 KO+Rescue mESCs. RNA sequencing (RNA-seq) in wildtype, PROSER1 KO and PROSER1 KO+Rescue mESCs and wildtype, PROSER1 KO and PROSER1 KO+Rescue mESCs after 2 days differentiation in N2B27 medium ("day2" samples).