Continuing with the Human genome sequencing and analysis Nanopore Learning course, tonight I watched the video on “Methylation Detection: Sample to Answer Workflow Overview.” Dilrini De Silva from the Technical Services Team at Oxford Nanopore started by defining epigenetics as the study of gene activity caused by chemical modification of nucleic acids, both DNA and RNA. Methylation was described as the addition of methyl groups to DNA. The most common is 5 methyl cytosine (5mC). Oxford Nanopore is the only current system able to detect methylation directly. Signals are captured that can be used to identify modified bases using specific base calling models. For example, there is a 5mC model. Other models, De Silva indicated, already exist or are in production. PCR is not needed for library prep for methylation detection with Oxford Nanopore Technologies. De Silva recommends using Remora models for detecting 5mC and 5hmC via MinKNOW. Modbam2BED can produce per genomic position modification frequencies. There is a human variation workflow in EPI2ME that can be used for phasing and methylation analyses. The detection of modified bases is a feature of Oxford Nanopore Technologies that is available with the Direct RNA Sequencing kits. We are interested in investigating RNA modification in bacteria.
