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Prevalent Methylation in Prokaryotic Genomes Suggests Regulatory Functions

Thursday, March 3, 2016

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 studying m6A and m4C modifications that predominate in prokaryotic DNA has precluded more comprehensive studies,” the authors write, noting that the unique ability of SMRT Sequencing to capture all of these methylation states made a much more comprehensive study possible for the first time.

The authors reported widespread methylation in these genomes, with 93% of organisms harboring at least some methylated DNA. The scientists went on to identify methylated motifs, finding more than 800 distinct patterns, and also annotated the binding specificities of the 600+ methyltransferases detected. Of particular interest were the evolutionarily conserved orphan methyltransferases — or Type II methyltransferases with no obvious restriction enzyme — found in nearly half of all prokaryotes analyzed. Overall, these findings suggest that methylation has an important role in genome regulation for these organisms in addition to the well-established function of genome protection.

The team sequenced prokaryotes to an average 130X coverage, generating a total of 105 Gb of sequence data across all organisms. They report an average of three methylated motifs per organism, with m6A methylation accounting for 75% of all base modifications observed. “SMRT sequencing offers a powerful approach to determine the recognition specificities of several Types of [restriction-modification] systems that have previously been very difficult to decipher,” Blow et al. write. “Type I RM systems cleave DNA at large distances from their binding site, while both Type IIG and Type III systems sometimes have difficulties in producing complete cleavage patterns. This can make them difficult to study using traditional approaches that rely on analysis of patterns of restriction digestion.”

Novel restriction-modification systems as well as new forms of existing systems, including Type IIG systems, were discovered throughout the data set, suggesting alternative functions including genome regulation. The scientists also found evidence of methylation pattern conservation. “Given the extensive amount of methylation present in the majority of the genomes we have examined, it is tempting to believe that methylation is a very important modification of bacterial and archaeal DNA perhaps providing regulatory functions that we have yet to fully appreciate,” the team reports. “Additionally, it is reasonable to assume that the evolution of DNA methylation was an early event that was important for the viability of primitive organisms.”

If you like JGI studies as much as we do, don’t miss the institute’s user meeting starting on March 21st.

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