About 20 mg brain tissue for each sample and histone mark were lysed by TissueLyser (Qiagen), then cross-linked with 1% formaldehyde in PBS for 10 minutes at room temperature. Cross-linking reactions were quenched with glycine for 5 minutes, followed by washes in cold PBS. The crosslinked tissue was homogenized using a cooled blade homogenizer in homogenization buffer (50 mM Tris-HCl pH 7.5, 1% Nonidet P-40, 0.25% deoxycholic acid, 1 mM EDTA). Then, cells were lysed with Farnham Buffer (5 mM PIPES, pH 8.0, 85 mM KCl, 0.5% Nonidet P-40, 1 mM DTT, 0.1 mM PMSF) and followed by SDS Lysis Buffer (50 mM Tris-HCl pH 7.9, 10 mM EDTA, 1% SDS, 1 mM DTT) to obtain soluble chromatin. Chromatin was sheared using a Covaris M220 Focused-ultrasonicator to generate DNA fragments approximately 200 to 400 bp in size, as verified by gel electrophoresis. The sonicated chromatin was centrifuged at maximum speed in a microcentrifuge for 1 minute at 4°C to remove insoluble debris. The soluble chromatin supernatant was diluted 1:9 with Dilution Buffer (20 mM Tris-HCl pH 7.9, 300 mM NaCl, 2 mM EDTA, 0.5% Triton X-100, 1 mM DTT, 0.2 mM PMSF) supplemented with a protease inhibitor cocktail (Roche). The diluted chromatin was precleared with 20 μL/mL protein A-agarose beads (ThermoFisher Scientific) on a nutator for 1 hour at 4°C. After centrifugation at 1000g for 3 minutes at 4°C, the supernatant was reserved for immunoprecipitation and 24 ng of spike-in chromatin (Active Motif 53083) was added per sample, with 2% set aside as input DNA. For immunoprecipitation, antibodies used included 5 µl H3K9me3 (Abcam; AB8898; 1063771-1), 5 µl H3K4me3 (Active Motif; 39159) or 15 µl H3K27me3 (Cell Signaling; 9733), along with 2 μg of spike-in antibody (Active Motif 61686), which were bound to 50 μl protein G Dynabeads (Invitrogen). The mixture was incubated with precleared supernatant overnight at 4°C with rotation. The Dynabeads were washed sequentially with the following buffers: low-salt wash buffer (10 mM Tris-HCl, pH 8, 2 mM EDTA, 0.1% SDS, 1% Triton X-100, 150 mM NaCl), high-salt wash buffer (10 mM Tris-HCl, pH 8, 2 mM EDTA, 0.1% SDS, 1% Triton X-100, 500 mM NaCl), LiCl wash buffer (10 mM Tris-HCl, pH 8, 1 mM EDTA, 1% NP-40, 1% Na-Deoxycholate, 250 mM LiCl), and a final wash with TE buffer containing 50 mM NaCl. Chromatin was eluted, incubated overnight at 65°C, and treated with RNase A and proteinase K. DNA was purified using the QIAquick PCR Purification Kit (Qiagen). For library preparation, 3 ng of H3K4me3 ChIP DNA, 10 ng of H3K9me3 ChIP DNA, and 10 ng of H3K27me3 ChIP DNA were used with the NEBNext Ultra II DNA Library Preparation Kit for Illumina (New England Biolabs; NEB). Library quality was assessed using a High Sensitivity D5000 ScreenTape on an Agilent 2200 TapeStation and quantified with the Qubit dsDNA HS Assay Kit (Thermo Fisher). Libraries with unique adaptor barcodes were multiplexed and sequenced on an Illumina NextSeq 2000 platform (paired-end, 100 base pair reads), with a sequencing depth of 30 million reads per sample for H3K4me3 ChIP, 50 million reads for H3K9me3 ChIP, and 40 million reads per sample for H3K27me3 ChIP.