Genome Wide Gene Associated Differential Methylation Pattern in Humans

DNA methylation occurs at the cytosine residue of CG dinucleotides, which are unevenly distributed throughout the mammalian genome. Every cell and tissue type has a unique DNA methylation profile, comprising at least hundreds of tissue specific differentially methylated regions (T-DMRs). As a result, it may be possible to employ differential methylation profiles to identify the type of tissue. The present study aims to identify differentially methylated regions in human body fluids (blood, saliva, semen and vaginal fluid).Our approach involved identification of genes which are differentially expressed in body fluids followed by assignment of surrogate tissues to the body fluids. Public gene expression databases were mined to look for genes specifically overexpressed in surrogate tissues of interest. Transcript identifiers were mapped to EnsEMBL identifiers and gene locations along with associated CpGs were extracted from the EnsEMBL database. Additionally, NGSmethDB whole genome scan data were remapped onto the current genome assembly (GRCh37). Total methylation of CpG islands was calculated using an area under the curve approximation and this was normalized, allowing BED files to be created for viewing against the genome. With the integration of ENCODE and NGSmethDB data, our results presents the largest methylation dataset studied to date. The methylation profile data sets were built according to exon and CpG locations of the genes. For each individual study, the data for every single CG dinucleotide was averaged. Based on the hypermethylation status of the CpG islands associated with our initial gene selection, candidate genes for further studies were chosen.