Gene expression and FAIRE-histone modifications
The gene expression program is tightly controlled by a dynamic chromatin environment, which epigenetic factors, like histone modifications and DNA methylation, play a crucial role in determining. As shown in Fig. 1, we found the linkage of FAIRE regulatory elements with histone modification profiles. To further assess the FAIRE-histone modifications, the gene expression profiles for MCF-7 cells were integrated (Fig. 2). From the overlapped regulatory elements determined by comparison of FARE-H3K4me1 (1,006), FAIRE-H3K4me3 (1,000), and FAIRE-H3K9/14ac (1,264), we selected 229 genes associated with at least 2 of 3 FAIRE-histone modification combinations. Scatter plots were produced to see how the expression level agreed with degree of histone modification (Fig. 2A-2C). The Pearson correlation coefficients between histone modifications and the expression level of genes with FAIRE elements were generally low. The highest coefficient was r = 0.50 for the pair of gene expression and FAIRE-H3K9/14ac (Fig. 2C), and the next was r = 0.4 for gene expression and FAIRE-H3K4me3 (Fig. 2B). However, FAIRE-H3K4me1 showed almost no correlation with gene expression level (r = -0.03) (Fig. 2A). To examine whether breast cancer-related genes were up-regulated in MCF-7 and appeared to have a high level of H3K9/14ac, as found in our previous study [26], we selected 68 genes, the expression levels of which ranked in the top 30% among FAIRE-H3K9/14ac-associated genes, and performed DAVID Functional Annotation analysis. We could isolate 29 functionally significant genes with p < 0.05: ATM, BTG1, CCND1, CDK4, CDKN1B, CRADD, CSDA, CTR9, DDB2, DUSP6, ERBB3, ESPL1, FADD, H2AFX, KRT18, KRT8, MADD, MDM2, MYC, NR4A1, POLA2, RIPK2, RRM2B, SART3, SMARCC2, TSG101, UBE2N, XPOT, and YWHAZ. These genes were associated with the following GO categories: regulation of apoptosis, programmed cell death, nuclear lumen, protein ubiquitination, DNA damage checkpoint, mitotic cell cycle, and small conjugating protein ligase activity (Fig. 2D). Moreover, the KEGG pathway analysis displayed their involvement in the cell cycle, p53 signaling pathway, mitogen-activated protein kinase signaling pathway, and pathways in cancer (Fig. 2E).