Detecting An Elusive Modified DNA Base

A newly developed tool will allow scientists to study the function of the modified DNA base 5-hydroxymethylcytosine (5-hmC). The technique, which selectively detects and maps 5-hmC in genomic DNA, could make it possible to determine the role of the variant base in health and disease.

5-hmC represents up to 0.5% of the total nucleotides in some mammalian cells, such as brain and stem cells, where it is believed to play a role in gene expression, development, and disease. But sequencing techniques have not been able to distinguish 5-hmC from 5-methylcytosine, making it difficult to study 5-hmC’s effects.

Now, researchers have devised a method to analyze 5-hmC selectively (Nat. Biotechnol., DOI: 10.1038/nbt.1732). They label 5-hmC in genomic DNA with a glucose azide, attach biotin to each azide, and use affinity purification and sequencing to map the biotin-tagged 5-hmC bases. The technique was developed by chemists Chuan He and Chun-Xiao Song of the University of Chicago, in collaboration with geneticist Peng Jin of Emory University School of Medicine and coworkers.

The scientists used the method on mouse cerebellar DNA to obtain the first genome-wide distribution map of 5-hmC. They found that 5-hmC content is greater in highly expressed genes, suggesting the base might promote gene expression. They also observed 5-hmC enrichment in genes linked to hypoxia and angiogenesis and an association of 5-hmC with genes implicated in neurodegenerative disorders.

The researchers have not yet done live-cell labeling, but “we are working on it,” He says. The University of Chicago has patented the technique and plans to license it for commercialization of research reagents and disease diagnostics.

The work could lead to “new insights into the distribution and physiological significance of 5-hmC,” says Carolyn R. Bertozzi, a chemistry professor at the University of California, Berkeley. “It allows selective detection and enrichment of gene fragments rich in this mysterious modification, which will enable mapping of its prevalence on a genome-wide scale, as well as its dynamics during processes such as aging and disease.”

Chemical & Engineering News

ISSN 0009-2347

Copyright © 2011 American Chemical Society