Loss of non-CpG methylation in inhibitory neurons impairs neural function through a mechanism that partially overlaps with Rett syndrome

Whole striatum were dissected from wild-type, as well as in mice where Dnmt3a or MeCP2 was conditional deleted in inhibitory neurons. Inhibitory neuronal nuclei were also conditionally tagged with GFP in all mice. Tissues were snap-frozen in liquid nitrogen until further analysis. Inhibitory neurons were sorted from whole striatum using anti-GFP-488 and anti-NeuN-647 signals and snap frozen until further analysis. Total DNA was purified from each sample using the DNeasy Blood & Tissue Kit from Qiagen according to manufactures instructions and stored at -20C until library preparation. DNA methylome libraries were generated using a modified snmC-seq method adapted for bulk DNA samples. Paired-end 150 cycle runs was used to sequence the libraries on a Illumina HiSeq 4000 Sequencing System. Overall design: Examination of DNA methylome in Dnmt3a-null and MeCP2-null inhibitory neurons versus wild-type inhibitory neurons.