Included in methylation, nanopore themes

Research area: bioinformatics

De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing

Created on 19th December 2016

Marcus H Stoiber; Joshua Quick; Rob Egan; Ji Eun Lee; Susan E Celniker; Robert Neely; Nicholas Loman; Len Pennacchio; James B Brown;

Advances in single molecule sequencing technology have enabled the investigation of the full catalogue of covalent DNA modifications. We present an assay, Modified DNA sequencing (MoD-seq), that leverages raw nanopore data processing, visualization and statistical testing to directly survey DNA modifications without the need for a large prior training dataset. We present case studies applying MoD-seq to identify three distinct marks, 4mC, 5mC, and 6mA, and demonstrate quantitative reproducibility across biological replicates processed in different labs. In a ground-truth dataset created via in vitro treatment of synthetic DNA with selected methylases, we show that modifications can be detected in a variety of distinct sequence contexts. We recapitulated known methylation patterns and frequencies in E. coli, and propose a pipeline for the comprehensive discovery of DNA modifications in a genome without a priori knowledge of their chemical identities.

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