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New labeling method expands ability to read DNA modification
Date:12/13/2010

methods did not allow them to distinguish between 5-mC and 5-hmC.

Seeking to fill this gap, a team at the University of Chicago led by Chuan He, PhD, professor of chemistry, exploited the properties of an enzyme from a bacterial phage, which can attach a chemically modified sugar tag to 5-hmC. They collaborated with Jin, postdoc Keith Szulwach and colleagues to map where 5-hmC appears in the genome and in various cell types.

While the chemical labeling method allows the separation of DNA containing 5-hmC from other DNA, it does not yet provide the ability to see 5-mhC when DNA is read letter-by-letter. He, Jin and their colleagues are working on a higher resolution method for finer analysis.

Mouse embryonic stem cell DNA contains 5-hmC at a level of 500 parts per million, the researchers found. In a mouse's cerebellum, the level rises from 1000 to 4000 parts per million as the mouse becomes an adult and that part of the brain matures. In contrast to 5-mC, which is generally found on genes that are turned off, 5-hmC is enriched on active genes, the researchers found.

"This specific gene enrichment suggests that it is not just an intermediate step when cells need to get rid of DNA methylation, but it may have a unique function in gene regulation," Jin says.

Mutations in the enzymes responsible for converting 5-mC to 5-hmC have also been linked to a form of leukemia, he notes.

The team looked to see which genes tend to acquire 5-hmC as the brain ages, and found an enrichment for genes involved with neurodegeneration, the cell's response to low oxygen and growth of new blood vessels.

"Because the enzymes that convert 5-mC into 5-hmC require oxygen, this may be another way that cells sense and respond to oxygen levels and oxidative stress," Jin says.


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Contact: Holly Korschun
hkorsch@emory.edu
404-727-3990
Emory University
Source:Eurekalert

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