KDM2B targets transcriptionally active genes which are mainly repressed by H2AK119ub1. (A) Distribution of ChIP peaks detected in the ChIP-seq analysis of KDM2B using thymocytes overexpressing 3xFLAG-KDM2B. Peaks were called using MACS2 v2.1.1 with a q value <0.05. (B) K-means clustering of 3xFLAG KDM2B, H2AK119ub1, and H3K27me3 ChIP-seq data around TSS (±4 kb) obtained using DP thymocytes overexpressing 3xFLAG KDM2B. (C) Frequency of CGI genes in each cluster; 97.9% of genes in cluster 1 and 49.6% in clusters 2 and 3 were CGI genes. (D) Summary of H2AK119ub1, H3K27me3, and H3K4me3 enrichment around TSS (±2 kb) detected by the ChIP-seq analysis in WT DP thymocytes. The fold enrichment values of ChIP signals calculated against the input signals (ChIP/input, RPKM+0.1) of RefSeq genes. The values in each cluster are shown. WT DP thymocytes were collected 4 weeks after the tamoxifen treatment. (E) RNA expression levels in each cluster obtained by an RNA-seq of WT DP thymocytes. Signal levels of RefSeq genes (FPKM+1 in log2) are shown. WT DP thymocytes were collected 4 weeks after the tamoxifen treatment. **P < .01; ***P < .001 by the Student t test. NA, not available; TTS, transcription termination site; UTR, untranslated region.