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. 2018 Apr 23;8:100. doi: 10.3389/fonc.2018.00100

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Copyright © 2018 Aref-Eshghi, Schenkel, Ainsworth, Lin, Rodenhiser, Cutz and Sadikovic.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Correlation between copy number variation (CNV) status and DNA methylation in prostate cancer: hypermethylation in the promoter of the CLIP4 gene partially correlates with its CNV status. The figure illustrates a segment in the promoter of CLIP4 gene, located in the short arm of chromosome 2. The region is marked with high levels of acetylation of the 27th lysine residue of Histone 3, (H3K27Ac), a maker associated with active promoters. The segment is also recognized as a cytosine-phosphate-guanine (CpG) island (green pane). Panels (A,B) represent 181 base-pairs of this segment, harboring a total of 8 CpG probes, which were identified to concurrently show both hypermethylation and CNV amplification. (A) The color scale of the vertical bars (each probe) represents the log ratios of the copy numbers. The color scale above 0.2 is shown with red and indicates a minimum of one copy amplification for the region. Color scales of white and light blue represent no CNV change (we defined a CNV loss with a log ratio less than −0.3, which is not observed for this region). Samples are sorted from top to bottom. The top 16 samples represent normal tissues and the lower samples indicate the tumors (vertical pane as an indicator: blue and pink). Within this segment, the right five probes show CNV amplification in tumors, but not in the adjacent benign tissues. (B) The methylation status of the same eight probes shows a hypermethylation in tumors (pink) relative to normal adjacent benign tissues (blue). Methylation level of every probe from every sample is presented with a dot, representing a methylation range between 0 and 1 (bottom to top). Lines represent mean, and shadows around the lines indicate 95% confidence intervals of the mean in every group. The region with CNV amplification is significantly hypermethylated; however, this hypermethylation extends beyond the CNV to three probes in the upstream.