Since the first PacBio instrument was released in 2011, methylation detection has been one of the advantages of SMRT Sequencing. The kinetics of nucleotide incorporation change as the DNA polymerase moves across a methylated position on the DNA template strand, producing distinctive perturbation patterns (Figure 1) that can be recognized by methylation-calling software. Figure 1: The arrows indicate the methylated positions on a 199 bp circular template. Bars indicate the ratio of the average intra-pulse distance (IPD) on the methylated template to that of the control template. Each methylation type produces a unique fingerprint. With the advent of a simple…
A recent publication from scientists at the University of Florida and the University of Missouri used SMRT Sequencing to analyze epigenomic changes that occur when free-living bacteria associate with a host and become symbiotic instead. Published in the Frontiers in Microbiology journal, “Integrating DNA Methylation and Gene Expression Data in the Development of the Soybean-Bradyrhizobium N2-Fixing Symbiosis” comes from a team of collaborators including lead author Austin Davis-Richardson and senior author Eric Triplett. The scientists aimed to assess the role of epigenetics in bacterial evolution from free-living to symbiont and chose SMRT Sequencing because it generates base-specific modification information as it…
A new publication from scientists at Lawrence Berkeley National Laboratory, the Joint Genome Institute, and other organizations reports a landmark study of genome-wide methylation in prokaryotes. The analyses of 230 bacteria and archaea species revealed both more methylation than expected and novel epigenetic mechanisms. “The Epigenomic Landscape of Prokaryotes” from lead author Matthew Blow, senior author Richard Roberts, and collaborators was recently published in PLoS Genetics. The team used SMRT Sequencing to detect 6-methyladenosine (m6A), 4-methylcytosine (m4C), and 5-methylcytosine (5mC) across the 230 genomes. “Bisulfite sequencing has enabled genome-wide surveys of 5mC methylation, but a historic absence of tools for…