New Efficient Method for Sequencing Epigenetic Modifications

Researchers at the University of Pennsylvania’s School of Medicine have developed a new method for sequencing chemical groups attached to the surface of DNA. These chemical groups are modifications of the DNA bases that convey important information relating to the patterns of gene expression. These modifications have been studied for the past two decades and are now known to be involved in the development of a variety of diseases, including cancer, making the identification of these modifications a promising tool for diagnostic and prognostic purposes.

Traditional methods for deciphering this epigenetic code have utilized bisulfite because of its advantageous selective chemical reactivity, however the use of bisulfite has many limitations. One of the main issues with using bisulfite-based methods is that it can destroy much of the sample during experimentation. This makes the investigation of specific cell types or rare cell populations much more challenging. To address this issue, the method proposed by the group at the University of Pennsylvania, instead makes use of a class of immune-defense enzymes called APOBEC DNA deaminases. These deaminase enzymes can achieve the same effect as bisulfite without degrading the sample. In their paper published in Nature Biotechnology detailing their method, the team demonstrated that they required a DNA sample 1,000 times smaller in their method than in bisulfite-based methods to determine the epigenetic code of one type of neuron.

The team members hope that their new method will provide opportunities to study the epigenetic code of DNA from small and rare populations of cells and yield further insight into the mechanisms underlying the involvement of these cells in disease. “This technological advance paves the way to better understand complex biological processes such as how the nervous system develops or how a tumor progresses,” said co-senior author Hao Wu, PhD. Future work will be required to develop other schemes integrating APOBEC to further advance its identification capabilities.

Study in Nature Biotechnology: Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase…

Via: Penn Medicine…