When someone tells you that they can save you time, money and sample, the magic trifecta for most scientists, your first thought is probably: “Bull&@%!”…your second thought might be: “Where do I sign up?” A new Nature Methods article from researchers at Broad, MIT, Harvard, and the Max Planck Institute promises to do just that with their recently spruced up RRBS (Reduced Representation Bisulfite Sequencing_ method for genome-scale methylation analysis.
With the RRBS method, only a subset of the genome is analyzed—that’s why the researchers describe it as “genome-scale” instead of “genome-wide”. First, they digest the DNA in a sample with a methylation-insensitive restriction enzyme (MspI), to remove much of the unmethylated regions of the genome. Next they bisulfite sequence only the fragments of a specified length, which consist of mostly methylated DNA.
RRBS was originally developed for mouse samples, so the researchers did four things to optimize it for human specimens and make this method really powerful:
- Reduced the required sample DNA input from 1 μg to 30 ng. That’s a big help, allowing technicians to study rare or precious samples.
- Optimized the method to work on FFPE (formalin-fixed, paraffin-embedded) specimens, so that even old samples stored away in archival collections can now be analyzed.
- Improved the bisulfite treatment protocol so that the conversion of unmethylated cytosines was optimized while DNA loss due to bisulfite-induced degradation was minimized.
- Added a bioinformatics pipeline to sensitively detect differences between cases and controls.
See if this new method might be right for your next methylation study. Get the full story at Nature Methods January 10 2010.