Acterized hydroxymethylation and methylation marks by performing whole-genome next-generation sequencing in representative normal and prostate cancer-derived cell lines in order to determine functional pathways and key genes regulated by these epigenomic modifications in cancer. Results: Our cell line model shows disruption of hydroxymethylation distribution in cancer, with global PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28461567 loss and highly specific gain in promoter and CpG island regions. Significantly, we observed locus-specific retention of hydroxymethylation marks in specific intronic and intergenic regions which may play a novel role in the regulation of gene expression in critical functional pathways, such as BARD1 signaling and steroid hormone receptor signaling in cancer. We confirm a modest correlation of hydroxymethylation with expression in intragenic regions in prostate cancer, while identifying an original role for intergenic hydroxymethylation in differentially expressed regulatory pathways in cancer. We also demonstrate a successful strategy for the identification and validation of key candidate genes from differentially regulated biological pathways in prostate cancer. Conclusions: Our results indicate a distinct function for aberrant hydroxymethylation within each genomic feature in cancer, suggesting a specific and complex role for the deregulation of hydroxymethylation in tumorigenesis, similar to methylation. Subsequently, our characterization of key cellular pathways exhibiting dynamic enrichment patterns for methylation and hydroxymethylation marks may allow us to identify differentially epigenetically modified target genes implicated in prostate cancer tumorigenesis. Keywords: 5-Hydroxymethylcytosine, 5-Methylcytosine, Whole-genome, Prostate cancer, Cell lines, Integrative analysis* Correspondence: [email protected] 1 Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada 2 Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada Full list of author information is available at the end of the article?2016 Kamdar et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Kamdar et al. Clinical Epigenetics (2016) 8:Page 2 ofBackground Tumorigenesis is regulated by a cascade of genetic and epigenetic alterations, with aberrant cytosine base methylation (5mC) acting as one of the key defining characteristics of tumor cells. CpG islands (CGIs), characterized by clusters composed of cytosine nucleotides followed by Cynaroside cost guanines, are usually unmethylated in normal conditions. However, in cancer, locus-specific hypermethylation of CGIs, particularly in the promoter regions of tumor suppressor genes, results in their loss of expression [1?]. Simultaneously, genome-wide global hypomethylation of repetitive sequences in tumors results in genomic instability, promoting chromosomal rearrangement and the reactivation of transposable elements [4, 5]. 5-Hydroxymethylated marks (5hmC) were f.