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Fig. 3 | BMC Medical Genomics

Fig. 3

From: Integrative epigenomic and genomic filtering for methylation markers in hepatocellular carcinomas

Fig. 3

UCSC genome browser tracks showing histone modifications (H3K4me1, H3K4me3, H3K27me3 and H3K27ac) and DNase I cleavage states around GRASP (a) and TSPYL5 (b) amplicons in HCC HepG2 and seven other cancer cell lines. Shown from top to bottom is the CpG island; layered H3K4Me1 activating mark, H3K4Me3 promoter specific mark in seven other cancer cell lines; H3K4Me3, H3K27me3, H3K4Me1, H3K27Ac activator marks and DNase I hypersensitive sites in HCC HepG2 cells; H3K27Ac activator in 7 other cancer cell lines; and GC percent. a: The genome browser map shows the genomic region around the GRASP (chr12:52,399,000-52,407,500). The bisulfite sequencing data covers 25 CpGs located within the promoter specific the 138th CpG island as shown. Around the GRASP amplicon, no DNase I hypersensitivity peak was observed in HepG2 cells. Histone marks (H3K4me1 and H3K27ac) displayed no signature of active regulation in HepG2 cells, while a silencer of H3K27me3 showed a small hill. Unexpectedly, active histone H3K4me3 also exhibited a peak. The histone modifications for the seven other cancer cell lines displayed high peaks for H3K4me1, H3K4me3 and H3K27ac. b: The genome browser map shows the genomic region around TSPYL5 (chr8:98,287,500-98,292,500). The bisulfite sequencing data covers 57 CpGs located within the promoter specific the 100th CpG island as shown. Consistent with DNA hypermethylation and under-expression of mRNA, there were no active histone marks (H3K4me1, H3K4me3 and H3K27ac), as well as closed chromatin (no peak for DNase I hypersensitive sites) around the TSPYL5 amplicon in HepG2 cells, which is different from the pattern observed in seven other cancer cell lines (showing high peaks for H3K4me1, H3K4me3 and H3K27ac marks). Unexpected, no activation of H3K27me3 was observed around TSPLY5 in HepG2 cells

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