By Bio-IT World staff
June 19, 2012 | Pacific Biosciences has taken a step towards an important technological advance in studying gene regulation with the release of new software to detect epigenetic modifications in DNA.
Epigenetics refers to the plethora of chemical modifications to the chromatin that can dramatically impact gene activity in health and disease. Current methods for detecting these chemical modifications, such as bisulphite sequencing, are indirect and relatively cumbersome. But PacBio believes that its single-molecule next-generation sequencing technology could provide an important breakthrough in the direct measurement of chemical modifications.
“Modifications such as methylation have been shown to be critical in influencing disease onset and severity, the pathogenicity of bacteria, and gene regulation,” says Eric Schadt, director of the Institute for Genomics and Multiscale Biology at Mt. Sinai Hospital and chief science officer at PacBio.
“The work we have done using SMRT sequencing to resolve the German E. coli outbreak strain, for example, points to a crucial role for base modification in the regulation of a gene associated with the strain’s severity. If we aren’t looking at base modifications, we aren’t seeing the whole picture in the biology of pathogens.”
The PacBio RS sequencing instrument, released two years ago, ‘eavesdrops’ on single molecules of DNA as they are synthesized in real time in tiny wells, or zero-mode waveguides. Since the publication of the first single-molecule reads in 2009, it has been clear that there is a wide variation in the interval between each incorporated base, representing the time that each incoming nucleotide spends in the grasp of the DNA polymerase before it is stitched into the growing DNA strand.
While the cause of some of these timing differences are presumably stochastic in nature, PacBio scientists have long insisted that they also provide a measure of the inherent chemical differences between different bases.
The new analysis software for the PacBio RS enables users to detect and visualize these DNA modifications by measuring the rate of DNA base incorporation during sequencing. The result is a sort of heat map of incorporation times at each position along the DNA strand.
The SMRT Analysis software upgrade is available to scientists through a free download from PacBio’s DevNet portal: http://www.smrtcommunity.com/ The analysis tool works on any data generated by the PacBio RS with its latest chemistry, enabling researchers to re-analyze existing data to detect methylation and other base modifications.
“We are pleased to provide the first and only tool that offers researchers worldwide the ability to detect base modifications as an integral part of the sequencing workflow,” says Kevin Corcoran, senior VP market Development at PacBio. “This is a major milestone for Pacific Biosciences and a valuable new tool for the scientific community.”
The new software release enables detection of modification events in native genomic DNA through a user-friendly visualization interface. Guidelines on studying the methylomes of bacteria are available on the company’s website at www.pacb.com/basemod.
Schadt presented further details of the new software during a talk at the annual American Society for Microbiology’s conference in San Francisco, in which he discussed the characterization of methyladenine residues in pathogenic strains of bacteria. However, a PacBio spokesperson says it will be a little while before external researchers can gain familiarity and provide feedback on the effectiveness of the new software.