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Fig. 2 | Genome Medicine

Fig. 2

From: DNA methylation-based chromatin compartments and ChIP-seq profiles reveal transcriptional drivers of prostate carcinogenesis

Fig. 2

Genome-wide profiles of chromatin compartmentalization from PRAD and normal prostate tissues. a Genome-wide profiles showing assignment of 100-kb windows to open or closed chromatin compartments in PRADs (top panel) and in normal prostate tissue (bottom panel). Horizontal axis denotes rank of each 100-kb window by genomic coordinate, with each chromosome separated by vertical dashed lines. Vertical axis represents the confidence of assignment of each window to the closed compartment (+ve values) or the open compartment (–ve values). Confidence of assignment is based on the normalized value of the first eigenvector of the DNA methylation correlation matrix from each set of samples. b Scatter-plot showing the relationship between compartment assignment in PRAD tumours and in normal prostate tissue. Horizontal axis gives the closed-ness score (value in first eigenvector of the DNA methylation correlation matrix) for each 100-kb genomic window in the normal prostate tissues. Vertical axis gives the closed-ness score for the same genomic windows in the PRAD tumour tissues. After excluding windows with a low confidence assignment (defined as having a value of less than 0.1 in the first eigenvector of the DNA methylation correlation matrix), windows assigned to the open chromatin compartment in tumours but the closed chromatin compartment in normal tissue are plotted in red, while windows assigned to the closed chromatin compartment in tumours but the open chromatin compartment in normal tissue are plotted in blue. c Genome-wide profile of the differences in compartment assignment between PRAD tumours and normal prostate tissues, as in a but featuring only 100-kb windows with a different compartment assignment in the two tissue types. Genomic windows assigned to the open chromatin compartment in tumours but the closed chromatin compartment in normal tissue are plotted in red, while windows assigned to the closed chromatin compartment in tumours but the open chromatin compartment in normal tissue are plotted in blue. d DNA accessibility in LNCaP prostate cancer cell line, shown for genomic regions classified according to inferred compartment call from normal prostate and PRAD tumour DNA methylation data. Numerical values plotted show the distribution of the average DNAse I sequencing signal across each 100-kb window. e Accessible chromatin histone modification H3K27ac in LNCaP prostate cancer cell line, shown for genomic regions classified according to inferred compartment call from normal prostate and PRAD tumour DNA methylation data. Numerical values plotted show the distribution of the proportion of each 100-kb window that is covered by an H3K27ac ChIP-seq peak

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