Guest Blog: Rich Roberts Urges Scientists to ‘Think Methylation’ in Microbial Sequencing

Richard Roberts, Nobel Laureate and Chief Scientific Officer of New England Biolabs, offers his thoughts on the utility of methylation data for understanding prokaryotes. In his words:
“Please run SMRT Analysis to detect methylation in your prokaryotic PacBio data.
Most bacteria and archaea encode DNA methylases, many of which are known components of restriction-modification systems. Usually, these are quite specific in terms of the sequences they recognize; the restriction component becomes a key defense mechanism preventing phages, plasmids, and other DNA elements from infecting the cell.
Until recently, it was quite difficult to determine the recognition sequences of these methylases. For most organisms, we had no idea whether the genes we could detect in the genome were active or not. Now, thanks to the properties of the DNA polymerase used during SMRT Sequencing, we can accurately locate the positions of m6A and m4C along the genome and sometimes can deduce the position of m5C. By analyzing the sequence context of these modified bases, we can deduce motifs that are the recognition sequences for the various methylases encoded in the genomes. Increasingly, we can then accurately match the genes with the motifs they produce to enable precise, experimentally-determined annotation for those genes.
Further progress in this area will depend on our ability to gather as much experimental data as we can; to improve the algorithms for calling the motifs accurately from the raw PacBio reads; and to improve our ability to match the DNA methylase genes in a genome with the PacBio motifs that are found experimentally. The public availability of motif data produced by running SMRT Analysis after each PacBio run can be enormously beneficial. Even better, if the raw sequence reads are also available, then this can help the development of better algorithms for data interpretation.
There is another terrific use of the methylation data for anyone interested in trying to transform these strains: While the presence of methylated motifs — and hence methylase genes — does not mean that an active restriction system is present, very often it does, offering some information about how one might protect DNA to be used for transformation before it is introduced into the cell.
I encourage everyone to think ‘methylation’ when using PacBio systems to sequence bacterial and archaeal genomes. The current results of such methylation analysis can be found in REBASE by clicking on the blue PacBio icon. This also has a link through which you can submit your methylation motifs to REBASE.”