Representative genes from 2 classes of EZH2 targets. (A) This figure shows mRNA expression values in NBCs (NB) and centroblasts (CB) (from microarray analyses) and EZH2 binding and H3K27me3 ChIP intensity profiles across probeset-covered regions for 3 genes. In the expression plots (top portion), the y-axis corresponds to log-transformed intensity values from microarray experiments. The x-axis correspond to NB and CB. Expression intensities from 5 CB and 5 NB microarray profiles were used to draw these figures, where both average intensities and standard error (error bars) are shown. In the binding profiles, the x-axis corresponds to genomic position around the transcription start site of the considered genes. RefSeq genes overlapping with the covered regions are shown in blue. CpG islands are shown in green. The y-axis corresponds to smoothed and log-transformed ChIP intensities. The figure shows that CDKN1A/p21, CDKN1B/p27, and BCL2 are not marked by H3K27me3 in NB, and become bound by EZH2 in centroblasts and consequently acquire H3K27me3. Accordingly, these 3 genes are down-regulated at the mRNA expression level in centroblasts compared with NBCs. (B) These 3 genes (together with CDKN2A/p16) are up-regulated at the mRNA level (albeit to a different extent) upon siRNA knockdown of EZH2 in SUDHL4 cells, as measured by Q-PCR. In this figure, mRNA expression levels in siRNA-treated cells are normalized with respect to untreated cells (NTsi). Error bars were drawn using data obtained from 3 replicate experiments. (C) This figure shows average expression levels in NB and CB and binding profiles for CDKN2A/p16. The CDKN2A/p16 promoter is associated with H3K27me3 in NB and expressed at low level; in CB, the same gene is associated with EZH2/H3K27me3 and its expression level does not change.