Cerebral cortex was dissected on ice in phosphate buffered saline from 1) MeCP2 knockout and wild-type male litter mates at 7-8 weeks old and 2) MeCP2 overexpression and wild-type male litter mates at 7-10 weeks old. The tissue was flash-frozen in liquid nitrogen and stored at -80°C. ChIP experiments were performed on half a cortex as previously described (Cohen et al., 2011), using an alternative chromatin fragmentation method. Chromatin were fragmented with Covaris E220 sonicator (5% Duty Factory, 140 Peak Incidence Power, 200 cycles per burst, milliTUBE 1mL AFA Fiber). ChIP was performed with H3K27ac (Abcam ab4729), H3K4me3 (Abcam ab1012), H3K36me3 (Active Motif 61101), and MeCP2 (rabbit polyclonal (Chen et al., 2003)). ChIP libraries for H3K27ac, H3K4me3, and H3K36me3 were generated using Ovation Ultralow Library System V2 (NuGEN) and libraries for MeCP2 with Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences). Libraries were pooled to a final concentration of 8-10nM and sequenced using Illumina HiSeq 3000 with GTAC, yielding 15-20 million single-end reads per sample.