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The methylomes of six bacteria
Iain A Murray1, Tyson A Clark, Richard D Morgan
1New England Biolabs, 240 County Road, Ipswich, MA 01938, USA.
Nucleic Acids Research
|October 5, 2012
Summary
Single-molecule, real-time (SMRT) sequencing revealed novel N(6)-methyladenine and N(4)-methylcytosine patterns in six bacterial genomes. This advanced method identified active DNA methyltransferases and their recognition sequences, enhancing genome analysis.
Area of Science:
- Genomics
- Epigenetics
- Microbiology
Background:
- Bacterial methylomes contain crucial information about DNA regulation and function.
- Previous genome sequencing platforms lacked the resolution to fully characterize DNA methylation patterns.
Purpose of the Study:
- To re-sequence six bacterial genomes using SMRT sequencing to analyze their methylomes.
- To identify novel N(6)-methyladenine ((m6)A) and N(4)-methylcytosine ((m4)C) methylation patterns.
- To assign responsible DNA methyltransferases (MTases) and their recognition sequences.
Main Methods:
- Re-sequencing of six bacterial genomes (G. metallireducens, C. salexigens, V. breoganii, B. cereus, C. jejuni) using SMRT sequencing.
- Analysis of methylomes to identify (m6)A and (m4)C methylation patterns.
- Sub-cloning of specific MTase genes to confirm activity and recognition sequences.
Main Results:
- Discovery of new (m6)A and (m4)C methylation patterns in all six genomes.
- Successful assignment of responsible MTase genes for most patterns.
- Identification of 15 MTase genes with their recognition sequences without sub-cloning.
- Confirmation of activity for two previously unexpressed MTase genes after sub-cloning.
Conclusions:
- SMRT sequencing provides comprehensive functional genomic information beyond traditional methods.
- This approach accurately detects active (m6)A and (m4)C methyltransferases and their recognition sites.
- SMRT sequencing significantly enhances the understanding of bacterial epigenomes.
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