Just because two people live on the same street doesn’t necessarily mean they live that close to each other or in the same house, yet that’s what you often have to assume when using ChIP to detect epigenetic modifications. Either that, or you have to use tons of sample and/or a labor-intensive method to figure that out more definitively. Now, a team reports that they can tell where multiple epigenetic marks are located simultaneously, quantitatively, and quickly.
We’ve been keeping an eye on this method, called Single Chromatin molecule Analysis in Nanochannels (SCAN). We first told you about it way back in 2009 when Paul Soloway of Cornell University told us about his plan to do something similar to flow cytometry to detect epigenetic modifications on single chromatin molecules in nanochannels.
The next year, he and colleagues at Cornell, including collaborator Harold Craighead, reported that they’d actually demonstrated it could work, and that they could detect DNA methylation with it. We also interviewed Soloway last year to get his take on the pluses and minuses of chromatin analysis approaches in play today.
Now, they’ve gone a step further, showing they can detect DNA methylation and histone modifications all at the same time in a quantitative way. They used a fluorescent antibody against one modification and a differently labeled antibody against another mod.
The whole thing, chromatin and antibodies, goes through a nanochannel, and they detect the fluorescence. Here’s what they found out:
- H3K9me3 and methylated cytosines (mC) were often on the same molecule of mouse embryonic stem cell (ESC) chromatin. 60% of the H3K9me3 depends on mC for their placement.
- H3K27me3 and mC, however, “antagonize” each other and are rarely seen together in ESC and primary cells. But in cancer cells, H3K27me3 needs mC. They say this could be a fundamental step in cancer progression.
“We are exploring new technologies for practical single molecule analysis, in this case directed toward obtaining information on epigenetic modifications to chromosomes that is not easily obtained by existing approaches,” says Craighead, Charles W. Lake, Jr. Professor of Engineering and Professor of Applied and Engineering Physics at Cornell. “Our experiments address the possibility for obtaining information on combinations of epigenetic marks that may be of importance in understanding or diagnosing diseases such as cancer.”
Discover what SCAN can do for you at PNAS, April, 2013.