SEMINAR: Bayliss Seminar Series: Rebecca Simmons

DNA methylation (5mC) is a gene regulatory mechanism that is associated with repressed transcription through recruitment of methyl binding proteins or by physically blocking transcription factor binding. DNA methylation typically occurs in the CpG dinucleotide context where a methyl group is added to the 5’ position of the cytidine pyrimidine ring. Recently, an atypical form of DNA methylation that occurs in the CH sequence context (where H= A, C, or T) has been shown to accumulate to very high levels in the adult human neuronal genome1. This atypical form of DNA methylation (mCH) has been shown to increase rapidly during the first two years after birth in neurons in humans, corresponding with a period of synaptogenesis and suggesting it may play a critical role in neuronal synapse formation and maturation. The overall goal of this study is to determine whether mCH, or proteins that regulate mCH, are disrupted in neurological pathologies with neurodevelopmental origins. This study will perform whole-genome DNA methylome profiling (MethylC-seq) and transcriptome analysis of neuronal nuclei isolated from human prefrontal cortex tissue affected by neurodevelopmental disorders and determine differences in mCH patterning. Furthermore, studies from our group and others have demonstrated that 5-hydroxymethylcytosine (5-hmC) is very abundant in brain DNA, particularly in neurons1,2. 5-hmC is an intermediate in an active DNA demethylation pathway and is indistinguishable in MethylC-seq from 5mC. Tet-assisted bisulfite sequencing (TAB-seq), a technique that is able to distinguish 5-hmC from 5mC, will be performed on these samples to allow precise identification of cytosines that are hydroxymethylated compared to cytosines that are methylated. Finally, RNA-seq (transcriptome analysis) and assays for transposase-accessible chromatin using sequencing, which defines regulatory regions by looking at the accessibility of chromatin, will be performed on these samples. This multi-layered analysis will be integrated together to yield critical insights into genome regulatory processes that may be disrupted in neurological disorders that have neurodevelopmental origins, and may provide new mechanistic insight into the development of these diseases.