Thursday, April 26, 2012

Nice use of PacBio sequencing to characterize methyltransferase specificity

Figure 1.

Rich Roberts just pointed me to this cool paper on which he is a co-author: Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing.  The paper was published in Nucleic Acids Research and is from Robert's group at New England Biolabs and Jonas Korlach's and others at Pacific Biosciences. What is cool is that they used the timing of the real time DNA sequencing to identify bases in particular DNA fragments that were methylated.  And this then allowed them to determine the specificity of particular methyltransferases (first tested on ones with known activity and then on ones with unknown activity).  This highlights one of the unique features of PacBio sequencing - because the method watches DNA replication in real time - if something alters the timing of the replication process - this can possibly be leveraged to detect alterations in DNA chemistry (e.g., methylation, DNA damage, etc).  Folks at PacBio have been promoting the methylation detection capabilities of their system for some time but I guess I did not get that interested in it because I viewed it is analogous to many other tools to quantify methylation.  But with this paper I now realize that the PacBio approach (and perhaps those of other methylation detection systems) are not just about quantifying methylation status on average across a set of DNA pieces, but can also be very specific as to exactly which bases are methylated.  And this in turn can be used to define specificity for a variety of unknown methyltransferases. Clark, T., Murray, I., Morgan, R., Kislyuk, A., Spittle, K., Boitano, M., Fomenkov, A., Roberts, R., & Korlach, J. (2011). Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing Nucleic Acids Research, 40 (4) DOI: 10.1093/nar/gkr1146


  1. Methylation specific or useful study.

  2. The "other methylation detection systems" win out here. PacBio has too low a throughput to stack up against standard MethylC-seq/BS-seq (Lister et al. 2008 and Cokus et al. 2008, respectively), which use any short read platform. A similar strategy was just developed to detect another variant of methylation, 5 hydroxymethylcytosine, at single base resolution ( ($)). However, detecting nucleotide modifications via incorporation kinetics is a cool application of PacBio.

    1. Thanks Matt - as I said I have been kind of ignoring the methylation detection stuff (too many things to do ...).

    2. You certainly can't be an expert on everything! Just figured I'd throw in my two cents since it's what I study. Thanks for all the great posts.


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