Enrichment HELP

Credit: Courtesy of John Greally, Albert Einstein College of Medicine, and PLoS ONE" /> Credit: Courtesy of John Greally, Albert Einstein College of Medicine, and PLoS ONE Researcher: John Greally, associate professor of Molecular Genetics, Albert Einstein College of Medicine, NY Project: Comparing ep

Jeffrey M. Perkel
Aug 1, 2008
<figcaption> Credit: Courtesy of John Greally, Albert Einstein College of Medicine, and PLoS ONE</figcaption>
Credit: Courtesy of John Greally, Albert Einstein College of Medicine, and PLoS ONE

Researcher:

John Greally, associate professor of Molecular Genetics, Albert Einstein College of Medicine, NY

Project:

Comparing epigenetic marks in different human leukemias.

Problem:

Bisulfite sequencing traditionally reveals methylation at specific individual locations. Greally wanted to measure promoter methylation on a genome-wide scale.

Solution:

Greally and his collaborators used a PCR-based technique called HELP (HpaII tiny fragment enrichment by ligation-mediated PCR) to map methylation patterns at about 26,000 promoter regions across the genome.

"It's a very simple technique," says Greally. "It enriches unmethylated DNA from the genome [by] using restriction enzymes." Genomic DNA is split into two fractions, one of which is digested with the methylation-insensitive enzyme, MspI, the other with its methylation-sensitive isoschizomer, HpaII. Ligation-mediated PCR is used to select for fragments...