NEW YORK, Nov. 26 (GenomeWeb News) - The Human Epigenome Project, a collaboration between the Wellcome Trust Sanger Institute, Berlin-based biotech Epigenomics, and France's Centre National de Génotypage, has wrapped up a pilot study to profile DNA methylation levels within the major histocompatibility complex -- a region of chromosome 6 that is associated with more diseases than any other region in the human genome.
The MHC pilot, which analyzed 250 regions of 90 genes in 32 tissue samples, is the first sequence-level study of methylation profiles within a multi-megabase region of the human genome, according to the HEP partners. The researchers developed a pipeline for high-throughput methylation analysis using bisulphite DNA sequencing and epigenotyping by MALDI-MS.
According to the authors, a "significant proportion" of the analyzed loci within the MHC show tissue-specific methylation profiles, and inter-individual methylation differences are common. In addition, the study found that epigenetic mechanisms may be involved in the use of alternative transcriptional start sites.
Across the range of tissues tested, high levels of methylation were correlated with low levels of gene activity and high gene activity correlated with low levels of methylation.
Eventually, the HEP plans to assess the methylation profiles for the regulatory regions of all annotated genes in most major cell types and their diseased variants. As a next step, which the authors claim is "well underway," they are analyzing the DNA methylation profiles of more than 5,000 regions associated with around 3,000 genes on human Chromosomes 6, 13, 20, and 22. Samples from more than 40 different individuals representing 20 tissues will be used in this study.