Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing.

ABSTRACT: Bacterial DNA methylation occurs at diverse sequence contexts and plays important functional roles in cellular defense and gene regulation. Existing methods for detecting DNA modification from nanopore sequencing data do not effectively support de novo study of unknown bacterial methylomes. In this work, we observed that a nanopore sequencing signal displays complex heterogeneity across methylation events of the same type. To enable nanopore sequencing for broadly applicable methylation discovery, we generated a training dataset from an assortment of bacterial species and developed a method, named nanodisco ( https://github.com/fanglab/nanodisco ), that couples the identification and fine mapping of the three forms of methylation into a multi-label classification framework. We applied it t

SUBMITTER: Tourancheau A 

PROVIDER: S-EPMC8107137 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature