Journal Name: Nature Methods
Title of the Article: Discovering multiple types of DNA methylation from individual bacteria and microbiome using nanopore sequencing
Corresponding Author: Gang Fang, PhD
Results: In this work, we developed a new method that enables nanopore sequencing for broadly applicable methylation discovery. We applied it to individual bacteria and the gut microbiome for reliable methylation discovery. In addition, we demonstrated the use of DNA methylation for high resolution microbiome analysis, mapping mobile genetic elements with their host genomes directly from microbiome samples.
Why the Research Is Interesting:
How: By examining three types of DNA methylation in a large diversity of sequence contexts, we observed that nanopore sequencing signal displays complex heterogeneity across methylation events of the same type. To capture this complexity and enable nanopore sequencing for broadly applicable methylation discovery, we generated a training dataset from an assortment of bacterial species and developed a novel method that couples the identification and fine mapping of the three forms of DNA methylation into a multi-label classification design. We evaluated the method and then applied it to individual bacteria and mouse gut microbiome for reliable methylation discovery. In addition, we demonstrated in the microbiome analysis the use of DNA methylation for binning metagenomic contigs, associating mobile genetic elements with their host genomes, and for the first time, identifying misassembled metagenomic contigs.
Said Mount Sinai's Gang Fang of the work:
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