Abstract
DNA N6-methyladenine (6mA) modification has been discovered as the most prevalent DNA modification in prokaryotes and eukaryotes, involving gene expression, DNA replication and repair, and host-pathogen interactions. Single-molecule real-time sequencing (SMRT-seq) can detect 6mA events in prokaryotic and eukaryotic genomes at the single-nucleotide level. However, there are no strict and economical quality control methods for high false-positive 6mA events in eukaryotic genomes. Therefore, by analyzing the distribution of 6mA in eukaryotic and prokaryotes, we proposed a method named MASQC (MeDIP-seq assists SMRT-seq for quality control in 6mA identification), which can identify 6mA events without doing the whole genome amplification (WGA) sequencing. The proposed MASQC method was assessed on two eukaryotic genomes and six bacterial genomes, our results demonstrate that MASQC performs well in quality control of false positive 6mA identification for both eukaryotic and prokaryotic genomes.
Highlights
Epigenetics is a study based on changes in gene expression levels caused by non-gene sequence changes
Other types of DNA modifications (DNA damage, 5mC and derivatives produced during demethylation) in adjacent bases may interfere with the inter-pulse duration (IPD) ratio of adenine sites, leading to high false positive rate (FPR) in the 6mA events detection
Take full advantage of the peak regions from methylated DNA immunoprecipitation (MeDIP)-seq datasets, we identified the 6mA events detected by Single-molecule real-time (SMRT) sequencing and calculated a threshold of IPD ratio directly to filter out a large number of false positive events
Summary
Epigenetics is a study based on changes in gene expression levels caused by non-gene sequence changes. It is well known that C5-methylcytosine (5mC) and N6-methyldeoxyadenosine (6mA) are the most abundant and predominant DNA methylation modifications and play a crucial role in both eukaryotic and prokaryotic life processes (Ratel et al, 2006; Liu et al, 2016). The 5mC modification has been well-studied in prokaryotes and eukaryotes which regulates diverse biological functions and life processes. The development of specific antibodies and Generation Sequencing technology brought a glimmer of light to this problem, which could detect the conservative regions 6mA events occur in. Based on these techniques, previous researches have been reported the detection of 6mA events in C. elegans
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