Differential DNA methylation patterns of homeobox genes in proximal and distal colon epithelial cells

Alan Barnicle, Cathal Seoighe, Aaron Golden, John M Greally, Laurence J Egan

Region and cell-type specific differences in the molecular make up of colon epithelial cells have been reported. Those differences may underlie the region-specific characteristics of common colon epithelial diseases such as colorectal cancer and inflammatory bowel disease. DNA methylation is a cell-type specific epigenetic mark, essential for transcriptional regulation, silencing of repetitive DNA and genomic imprinting. Little is known about any region-specific variations in methylation patterns in human colon epithelial cells. Using purified epithelial cells and whole biopsies (n=19) from human subjects, epigenome-wide DNA methylation data (using the HELP-tagging assay) was generated, comparing the methylation signatures of the proximal and distal colon. A total of 125 differentially methylated sites (DMS) were identified, mapping to transcription start sites of protein-coding genes, most notably several members of the homeobox (HOX) family of genes. Patterns of differential methylation were also validated using MassArray EpiTYPER. DNA methylation was also examined in whole biopsies, applying a computational technique to deconvolve variation in methylation within cell types and variation in cell-type composition across biopsies. Including inferred epithelial proportions as a covariate in differential methylation analysis applied to the whole biopsies resulted in greater overlap with the results obtained from purified epithelial cells compared to when the covariate was not included. Results obtained using both approaches highlight region-specific methylation patterns of HOX genes in colonic epithelium. Regional variation in methylation patterns has implications for the study of diseases that exhibit regional expression patterns in the human colon, such as inflammatory bowel disease and colorectal cancer.