Targeted DNA Methylation & Mitochondrial Heteroplasmy Core

Willard Freeman, Ph.D.

Willard “Bill” Freeman, Ph.D.

Reynolds Oklahoma Center on Aging

Oklahoma Medical Research Foundation

The Targeted DNA Methylation & Mitochondria Heteroplasmy Core (TDMMHC) of the Oklahoma Nathan Shock Center provides researchers with state-of-the-art novel technologies that we have developed to address fundamental questions of how genomes change with age. DNA methylation is a major regulator of gene expression; studies show that DNA methylation patterns change with aging, and these changes can be caused by a wide variety of environmental stimuli at any point in the lifespan.  On the other hand, increases in mutations and deletions in the mitochondrial genome (mtDNA) with age have been known for some time, but the field has struggled because assays have lacked coverage across the entire mitochondrial genome and have limited quantitative accuracy. This Core will provide Geroscience researchers with unique assays of DNA methylation and mtDNA heteroplasmy not present in individual laboratories.

Quantitatively-accurate DNA methylation analyses:

  • Bisulfite Oligonucleotide Capture Sequencing (BOCS):
    The BOCS assay gives investigators a genome-wide analysis of 5mC levels. This approach uses thousands of oligonucleotide probes designed to capture/target all gene promoters and all of the non-repeat region CpG islands, shores, and shelves of the genome sequencing analysis. We have probe sets for the human, mouse, and rat genomes and can design probes for any annotated genome. Currently, only the probe set for humans is commercially available. Our capture probe sets for rats are a resource unavailable elsewhere. Cost $2,500/sample.
  • Bisulfite Amplicon Sequencing (BSAS):
    For more directed hypothesie (e.g., does the promoter regions of a specific set of genes change with age) or to orthogonally confirm BOCS findings, we have developed BSAS (Masser et al., 2013) that allows one to measure the site specific levels of 5mC in specific regions (a few hundred bases to a few kilobases) of the genome. Cost: $85/sample.

Mitochondrial genome heteroplasmy and copy number: