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...e mark. Gene-specific and limited microarray studies have reported that Lys27 methylation tends to occur at punctate sites near promoters of repressed genes (Cao and Zhang, 2004; Kimura et al., 2004; =-=Kirmizis et al., 2004-=-; Koyanagi et al., 2005). Based on such studies, the distributions of Lys4 and Lys27 methylation have been thought to be nonoverlapping. A notable exception to the punctate pattern of histone modifica...

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...istone H3 lysine-27 (H3K27) methylation, and this enzymatic activity is required for PRC2-mediated gene silencing (Cao et al., 2002; Czermin et al., 2002; Kuzmichev et al., 2002; Muller et al., 2002; =-=Kirmizis et al., 2004-=-). H3K27 methylation is thought to provide a binding surface for PRC1, which facilitates oligomerization, condensation of chromatin structure, and inhibition of chromatin remodeling activity in order ...

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... custom-designed oligonucleotide array from Nimblegen containing an evenly spaced “tiled” set of probes. Custom Nimblegen arrays have been used previously for chIP-chip of human transcription factors =-=(25)-=-, but to our knowledge, this is the first publication describing the use of whole-genome, uniformly tiled arrays. The accuracy and resolution of chIP-chip have been evaluated in a number of previous s...

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...e transcription, we measured methylation of this site across the PABPC1 gene. We failed to detect H3K27me2 or H3K27me3 throughout the PABPC1 gene, with MYT1 serving as a positive control for H3K27me3 =-=(26)-=- (note the different y axes) and CD4 as a positive control for H3K27me2. In contrast, H3K27me1 was detected across the entire PABPC1 locus, with selective depletion in the vicinity of the transcriptio...

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...n the promoter of cyclin D1 was also confirmed by real-time quantitative PCR in which the associations of EZH2 with the promoter of one of its known target genes, myelin transcription factor 1 (MYT1) =-=(19)-=- (positive control), and with -actin (negative control) were validated (Fig. 5C). These experiments strongly suggest that -catenin–EZH2–ER existed in the same protein complex on c-Myc and cyclin D1...

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...e3, H3-K27Me2, and H4K20Me2 to also be positive for gene expression. Based on the H3-K9Me3, H3-K27Me2, and H4-K20Me2 patterns, we speculate that these candidates are regulated by the PcG/TrxG complex =-=(6, 8, 16, 20, 29, 39, 48)-=-. This is supported by evidence that H3-K9Me3 and H3-K27Me2 are linked to PcG controlled silencing (6, 8, 39), although we are aware that other methylations, such as H3-K27Me3, are involved. We also f...

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... than 50% of the genes in the human genome (6). CGI arrays have been used in a number of studies to identify regulatory elements bound directly by transcription factors, including E2F, MYC, and Suz12 =-=(40, 53, 60, 82)-=-. To date, there have been several publications describing global ChIP-based approaches for identifying new p53-regulated genes, but none have used CGI arrays to do so (9, 27, 36, 81). The reasons for...

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...easing interest in the composition of chromatin throughout the human genome (50), and a number of papers have begun to examine the distribution of histone modifications in various chromosomal regions =-=(26,51)-=-. However, such global analyses cannot distinguish between chromatin on homologous chromosomes, as is necessary to examine Figure 4. High-resolution analysis of chromatin in a region of the X chromoso...

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... on ChIP DNA with primers targeting≤65 bp from each ZF-TF target site, as well as primers to a region of H3K27-methylated, closed chromatin in the distal promoter of MYT (Myelin transcription factor) =-=(27)-=-, where the ZF-TFs should not bind. Anti-H3K27me3 selectively pulled downMYT (i.e. at levels greater than non-target regions onOCT4) from all 12 chromatin preps (Supplementary Figure S2B), demonstrati...