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. 2014 Mar 24;9(3):e92815. doi: 10.1371/journal.pone.0092815

Figure 2. DSC3 Promoter is Hypermethylated in Prostate Cancer.

Figure 2

(A) Top panel depicts the UCSC genome browser representation of the genomic organization of DSC3 gene present in human chromosome 18 (28570052-28622781), where exons are indicated by solid boxes and introns by the blue line. The CpG island (CGI) associated with the DSC3 gene promoter is represented as horizontal green solid bar. DNA methylation status of the regions shaded in yellow (+/−3 kb from transcription start site) is presented below. ENCODE Infinium 450K Bead Arrays and Reduced Representation Bisulfite Sequencing datasets (RRBS) showed that DSC3 gene promoter is hypermethylated in LNCaP as compared to the benign cell line PrEC. The CG positions assayed by these methods are represented as vertical bars colored according to their methylation status. ENCODE RRBS, red (100%), yellow (50%), green (0%) are methylated; ENCODE Infinium 450K, orange  =  methylated (score ≥600), bright blue  =  unmethylated (0< score ≤200). LNCaP(1):LNCaP cells treated with androgen; LNCaP(2):LNCaP data from Duke University; LNCaP(3):LNCaP data from University of Washington. (B) Representation of MethylPlex NGS sequencing data (PrEC, LNCaP, prostate normal, benign adjacent, localized PCa and metastatic PCa tissues) for DSC3. Methylated regions observed in the corresponding sample groups are depicted as peaks and numbers in the y-axis denote the peak heights.