Se. We found that 5hmC enrichment was unique to brain tissues (Fig. 4c, d). This indicates more pronounced DNA demethylation in the brain of hypermethylated C9-BAC mice which is consistent with the highest abundance of the global 5hmC levels occurring in the central nervous system as compared to other tissue types, presumably due to the higher ten-eleven-translocation (TET) enzyme activity [32, 33].We next sought to investigate one possible mechanism of DNA methylation acquisition at the C9ORF72 promoter of ALS patients. By analogy to other repeat expansion disorders, such as Fragile X Syndrome and Freidriech’s Ataxia [21, 34], we hypothesized that DNA-RNA hybrids or R-loops formed by an expanded C9ORF72 transcript lead to epigenetic silencing. In our previous report, we Necrosulfonamide web demonstrated that iPSC lines from a hypermethylated ALS patient can be used as a tool to investigate the acquisition of DNA methylation at the C9ORF72 promoter . In particular, we showed that DNA methylation at the C9ORF72 promoter is erased during iPSC generation and then re-acquired during neuronal differentiation. To determine whether C9ORF72 promoter DNA hypermethylation occurs via DNA-RNA hybrid formation, we created a stable iPSC line from a hypermethylated ALS patient expressing a small hairpin RNA targeting all three C9ORF72 transcript variants (shC9) or a scrambled control (shCTL). We reasoned that disrupting R-loop formation by depleting C9ORF72 mRNAs PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28045099 in iPSCs would prevent DNAEsanov et al. Molecular Neurodegeneration (2017) 12:Page 8 ofFig. 4 DNA demethylation is observed at the expanded C9ORF72 promoter distinctively in the brain. Two CpG dinucleotides located within MspI/ HpaII restriction sites at positions -313 and +104 base pairs from the C9ORF72 transcriptional start site were interrogated by 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) sensitive PCR. The y-axis indicates percent 5hmC (black) and 5mC (grey) from brain cortex samples for a subset of C9-BAC mice (a, b), error bars represent standard deviation, experiments were performed in duplicates (N = 2 from a single biological sample for each age and methylation status). Assessment of 5hmC enrichment at two restriction sites across tissue types of a 30 week old hypermethylated mouse are illustrated in c and d. Student’s t-test was performed to determine significance, indicated by p < 0.05 *hypermethylation upon neuronal differentiation, similar to what was previously shown in Fragile X Syndrome . We generated stable iPSC cell lines expressing either the shC9 or shCTL constructs then differentiated the cells into motor neurons using our previously published protocols . We confirmed efficient depletion of C9ORF72 in shC9 iPSC lines using qPCR (Fig. 5a). We then confirmed efficient disruption of R-loop formation at the C9ORF72 locus in shC9 motor neurons using DNA-RNA immunoprecipitation (DRIP) followed by qPCR with primers to amplify regions upstream and downstream the HRE (Fig. 5b, c). Finally, DNA methylation at the C9ORF72 promoter in motor neurons was assessed across 16 individual CpG dinucleotides using bisulfite pyrosequencing (Fig. 5d). Patient-derived motor neurons from an individual with the Fragile X Syndrome that does not harbor C9ORF72 repeat expansion were used as a negative control. Despite efficient knockdown of C9ORF72 RNAs and disruption of Rloops, we did not observe significant differences in DNA methylation levels at the C9ORF72 promoter between shC9 and shCT.