John Greally, associate professor of Molecular Genetics, Albert Einstein College of Medicine, NY
Comparing epigenetic marks in different human leukemias.
Bisulfite sequencing traditionally reveals methylation at specific individual locations. Greally wanted to measure promoter methylation on a genome-wide scale.
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...