Methylation Profiling for Determining Gene Activity

Researchers working with the plant Arabidopsis have used a powerful new microarray-based methylation profiling technology to study the role of epigenetic information in determining gene activity.

In their study, the investigators at Cold Spring Harbor Laboratory (NY, USA) utilized the MethylScope technology of Orion Genomics (Saint Louis, MO, USA). MethylScope employs a microarray analysis technique to assess to what extent genes in a genome are methylated. The technology relies on proprietary methods to divide genomic DNA into two fractions: methylated and unmethylated.

Each fraction is labeled with a different color of fluorescent dye (e.g., unmethylated DNA is green and methylated DNA is red and is then hybridized to a microarray. If an array feature corresponding to a single gene in the genome glows red, then that gene was methylated in the tissue from which the DNA was prepared. If, however, an array feature glows green, then that gene was unmethylated. Observing the red-green ratio for each feature on an array allows investigators to quantitatively determine the degree to which a gene may be methylated.


The investigators reported in the August 6, 2004, issue of Nature that the DNA sequences at the sites of transposon activity correspond to small interfering RNAs (siRNAs). They also showed that transposable elements could regulate genes epigenetically, but only when inserted within or very close to them.

"Our research concerns the mechanism by which methylated DNA and other epigenetic information determines gene activity,” said senior author Dr. Rob Martienssen, a professor at Cold Spring Harbor Laboratory and co-founder of Orion Genomics. "Because of this ‘second code,' epigenetic changes are emerging as important defects in childhood diseases as well as in cancer. The profiling technology described in this paper will help to uncover these epigenetic defects, providing biomarkers and leads for potential therapy.”





Related Links:
Cold Springs Harbor Laboratory
Orion Genomics