Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications.

ABSTRACT: DNA modifications in bacteria present diverse types and distributions, playing crucial functional roles. Current methods for detecting bacterial DNA modifications via nanopore sequencing typically involve comparing raw current signals to a methylation-free control. In this study, we found that bacterial DNA modification induces errors in nanopore reads. And these errors are found only in one strand but not the other, showing a strand-specific bias. Leveraging this discovery, we developed Hammerhead, a pioneering pipeline designed for de novo methylation discovery that circumvents the necessity of raw signal inference and a methylation-free control. The majority (14 out of 16) of the identified motifs can be validated by raw signal comparison methods or by identifying corresponding methyltr

SUBMITTER: Liu X 

PROVIDER: S-EPMC11610603 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature