ChIP assays were performed as a modification of the previously described methods (Dhar et al., 2016; Dhar et al., 2012). In brief, cerebellar (4-month-old) tissues were isolated. DNA was purified from chromatin immunoprecipitates for MLL4 or IgG using the phenol/chloroform extraction. IgG was used as a negative control for ChIP. Then, DNA was amplified by quantitative PCR and normalized to input. To compare H3K4me1, H3K27ac, and H3K4me3 levels between Mll4f/f and Mll4 BSKO cerebellum, ChIP with reference exogenous genome (ChIP-Rx) was carried out as previously described (Li et al., 2016; Orlando et al., 2014). In brief, two biological replicates for Mll4f/f and Mll4 BSKO cerebellum were used for ChIP-Rx experiments. Drosophila melanogaster chromatin and Drosophila-specific H2Av antibody were added to each ChIP assay as a minor fraction. The following components for ChIP-Rx were purchased from Active Motif: the spike-in chromatin (53083), Drosophila-specific H2Av antibody (61686), spike-in ChIP positive control primer set (71037), and negative control primer set (71028). The immunoprecipitated DNAs were sequenced by Next-Generation Sequencing (NGS) (UCI GHTF). ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.