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Results: 6

1.
Figure 4

Figure 4. From: A quantitative atlas of histone modification signatures from human cancer cells.

Proteomic analysis of histone H4 PTMs across cell lines. Hierarchical clustering of the 24 lines was performed based on abundances of histone H4 PTMs (shown in right vertical axis). Data are shown as log2 enrichment of histone PTM levels for a given line based on average PTM levels across all 24 lines.

Gary LeRoy, et al. Epigenetics Chromatin. 2013;6:20-20.
2.
Figure 3

Figure 3. From: A quantitative atlas of histone modification signatures from human cancer cells.

Proteomic analysis of histone H3 PTMs across cell lines. Hierarchical clustering of the 24 lines was performed based on abundances of histone H3 PTMs (shown in right vertical axis). Cell line tissue type is shown in the bottom horizontal axis. Data shown as log2 enrichment of histone PTM levels for a given line (biological replicates of 3 to 7) based on average PTM levels across all 24 lines.

Gary LeRoy, et al. Epigenetics Chromatin. 2013;6:20-20.
3.
Figure 1

Figure 1. From: A quantitative atlas of histone modification signatures from human cancer cells.

Gene expression analysis of histone modifying enzymes across cell lines. Hierarchical clustering of the 24 cell lines along the horizontal axis was performed based on transcript abundances of HATs, HDACs, HMTs and HDMs along the vertical axis, where an orthogonal clustering was similarly performed. The insert magnifies two clusters containing the two transcript variants of EZH2 HMT (EZH2.1 and EZH2.2). Data are shown as log2 expression relative to the reference RNA library.

Gary LeRoy, et al. Epigenetics Chromatin. 2013;6:20-20.
4.
Figure 6

Figure 6. From: A quantitative atlas of histone modification signatures from human cancer cells.

EZH2 promotes breast cancer tumorigenesis in vivo. (A) EZH2 was stably knocked down via shRNA in MDA-MB-231 cells. Knockdown efficiency was assessed via quantitative RT-PCR. (B) Control or EZH2-KD MDA-MB-231 cells were xenografted into mammary fat pads of nude mice and tumor burden was quantified over time via weekly bioluminescent imagine (BLI). BLI signals are normalized to the Day 1 signal for each mouse. (C) Images of mice injected with control or EZH2-KD cells are displayed (24 days post-injection). Data are shown as the mean + SD (RT-PCR) or mean + SEM (xenografts). *P <0.05; **P <0.01.

Gary LeRoy, et al. Epigenetics Chromatin. 2013;6:20-20.
5.
Figure 2

Figure 2. From: A quantitative atlas of histone modification signatures from human cancer cells.

Proteomic strategy for histone PTM quantification. Each of the 24 lines was similarly processed to yield the core and linker histones. Histones were derivatized with propionic anhydride to prevent trypsin digestion at the unmodified and monomethylated lysines and, consequently, peptides of uniform length are produced that span the same modified residue (in this example, lysines 9 and 14 of histone H3). Relative quantification is achieved by peak integration of the extracted ion chromatograms of each charge state (the +2 charge state is shown) for each peptide (each colored row, with m/z shown). Note that H3K9acK14un and H3K9unK14ac co-elute in this experiment, thereby requiring tandem MS sequencing to resolve both peptides for separate quantification.

Gary LeRoy, et al. Epigenetics Chromatin. 2013;6:20-20.
6.
Figure 5

Figure 5. From: A quantitative atlas of histone modification signatures from human cancer cells.

Cross-correlation between the genomic and proteomic data. (A) Example of cross-correlation analysis between the gene expression of a given enzyme (in this example, EZH2.2 variant) to the histone PTM log2 abundance (in this example, H3K9me3K14un) across all 24 lines (diamond). (B) Hierarchical clustering of Pearson correlation coefficients for each enzyme and histone H3 PTM cross-correlation analysis. For instance, a positive correlation would indicate that increased enzyme transcript level is associated with increased PTM level. (C) Comparison between enrichment of histone H3 PTMs for MCF7 and MdaMB231 (same data as found in Figure 3) and the correlation between those same H3 PTMs with EZH2 (EZH2.1 and EZH2.2) and MYST1 expression. Note, for instance, the enrichment of a given PTM (for instance, K27me3K36me2) in the two lines is generally accompanied by a positive correlation of EZH2, and a negative correlation of MYST1, for that PTM.

Gary LeRoy, et al. Epigenetics Chromatin. 2013;6:20-20.

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