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Simultaneous Detection of DNA Adenine and Cytosine Methylation using NT-seq

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Escherichia coli Oxytricha trifallax mixed culture metagenome Helicobacter pylori

PROVIDER: GSE184374 | GEO | 2022/05/12

REPOSITORIES: GEO

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Simultaneous Detection of DNA Adenine and Cytosine Methylation using NT-seq [series1: no enrichment]

Project description:DNA methylation plays important roles in foreign DNA defense, mismatch repair, and gene regulation in prokaryotic genomes. Existing methods for DNA methylation detection using next-generation sequencing (NGS) are incapable of simultaneously detecting multiple types of DNA methylation. Here, we present nitrite treatment followed by sequencing (NT-seq), a sequencing method to simultaneously detect adenine and cytosine methylation. We demonstrated that NT-seq reliably detects three types of methylation motifs in E. coli and H. pylori genomes. We further applied NT-seq to a microbial community standard for de novo methylation motif discovery. Finally, by coupling methyl DNA immunoprecipitation and NT-seq (DIP-NT-seq), we showed that 6mA could be accurately mapped at single-base resolution in the bacterial and eukaryotic genomes. NT-seq thus provides a simple and reliable solution for detecting multiple types of DNA methylations.

2022-05-12 | GSE184372 | GEO

Simultaneous Detection of DNA Adenine and Cytosine Methylation using NT-seq [series2: 6mA DIP enrichment]

2022-05-12 | GSE184373 | GEO

Simultaneous Detection of DNA Adenine and Cytosine Methylation using NT-seq

Project description:Simultaneous Detection of DNA Adenine and Cytosine Methylation using NT-seq

| PRJNA764231 | ENA

Simultaneous Detection of DNA Adenine and Cytosine Methylation using NT-seq [series1: no enrichment]

Project description:Simultaneous Detection of DNA Adenine and Cytosine Methylation using NT-seq [series1: no enrichment]

| PRJNA764234 | ENA

Simultaneous Detection of DNA Adenine and Cytosine Methylation using NT-seq [series2: 6mA DIP enrichment]

Project description:Simultaneous Detection of DNA Adenine and Cytosine Methylation using NT-seq [series2: 6mA DIP enrichment]

| PRJNA764233 | ENA

Graphene Oxide Nanoribbons in Chitosan for Simultaneous Electrochemical Detection of Guanine, Adenine, Thymine and Cytosine.

Project description:Herein, graphene oxide nanoribbons (GONRs) were obtained from the oxidative unzipping of multi-walled carbon nanotubes. Covalent coupling reaction of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) and N-hydroxy succinimide (NHS) with amine functional groups (-NH2) of the chitosan natural polymer (CH) was used for entrapping GONRs on the activated glassy carbon electrode (GCE/GONRs-CH). The nanocomposite was characterized by high-resolution transmission electron microscopy (HRTEM), and field-emission scanning electron microscopy (FESEM). In addition, the modification steps were monitored using FTIR. The nanocomposite-modified electrode was used for the simultaneous electrochemical determination of four DNA bases; guanine (G), adenine (A), thymine (T) and cytosine (C). The nanocomposite-modified GCE displayed a strong, stable and continuous four oxidation peaks during electrochemistry detection at potentials 0.63, 0.89, 1.13 and 1.27 V for G, A, T and C, respectively. The calibration curves were linear up to 256, 172, 855 and 342 ?M with detection limits of 0.002, 0.023, 1.330 and 0.641 ?M for G, A, T and C, respectively. The analytical performance of the GCE/GONRs-CH has been used for the determination of G, A, T and C in real samples and obtained a recovery percentage from 91.1%-104.7%. Our preliminary results demonstrated that GCE/GONRs-CH provided a promising platform to detect all four DNA bases for future studies on DNA damage and mutations.

| S-EPMC7236021 | biostudies-literature

DNA methylation on C5-Cytosine and N6-Adenine in the Bursaphelenchus xylophilus genome.

Project description:BackgroundThe pinewood nematode is the causal agent of the pine wilt disease, which causes severe ecological and economic losses in coniferous forests. The invasion of pine wood nematode has undergone various rapid adaptations to a wide range of temperatures and to new hosts and vector insects. DNA methylation may play crucial roles in the rapid adaptation of PWN during invasion. However, whether the PWN genome contins functional DNA modifications remains elusive.ResultsHere, we detected the extensive presence of 5-methylcytosine (5mC) and N6-methyladenine (6mA) in the B. xylophilus genome, with low methylation levels at most positions. Cytosines were methylated in the CpG, CHG. and CHH sequence contexts, with the lowest methylation levels at CpG sites. The methylation levels of CpG and 6mA in gene regions showed opposite trends. The changes in the abundance of 5mC and 6mA showed the same trends in response to temperature change, but opposite trends during development. Sequence and phylogenetic analyses showed that the proteins BxDAMT and BxNMAD have typical characteristics of a methylase and demethylase, respectively, and are conserved among species.ConclusionsThese findings shed light on the epigenetic modifications present in the genome of PWN, and will improve our understanding of its invasiveness and evolution.

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Simultaneous detection of chromatin accessibility and DNA methylation in cell cycle

Project description:The goal of this study is to comprehensively assess chromatin accessibility and DNA methylation dynamic in different cell cycle phases, we found DNA methylation is stable in different phases wherase chromatin accessibility underwent enormous changes, but local structure at NDR and NSR are well preserved to maintain cellular identity.

2017-11-09 | GSE89708 | GEO

Detection of Cytosine methylation in ancient DNA from five native american populations using bisulfite sequencing.

Project description:While cytosine methylation has been widely studied in extant populations, relatively few studies have analyzed methylation in ancient DNA. Most existing studies of epigenetic marks in ancient DNA have inferred patterns of methylation in highly degraded samples using post-mortem damage to cytosines as a proxy for cytosine methylation levels. However, this approach limits the inference of methylation compared with direct bisulfite sequencing, the current gold standard for analyzing cytosine methylation at single nucleotide resolution. In this study, we used direct bisulfite sequencing to assess cytosine methylation in ancient DNA from the skeletal remains of 30 Native Americans ranging in age from approximately 230 to 4500 years before present. Unmethylated cytosines were converted to uracils by treatment with sodium bisulfite, bisulfite products of a CpG-rich retrotransposon were pyrosequenced, and C-to-T ratios were quantified for a single CpG position. We found that cytosine methylation is readily recoverable from most samples, given adequate preservation of endogenous nuclear DNA. In addition, our results indicate that the precision of cytosine methylation estimates is inversely correlated with aDNA preservation, such that samples of low DNA concentration show higher variability in measures of percent methylation than samples of high DNA concentration. In particular, samples in this study with a DNA concentration above 0.015 ng/?L generated the most consistent measures of cytosine methylation. This study presents evidence of cytosine methylation in a large collection of ancient human remains, and indicates that it is possible to analyze epigenetic patterns in ancient populations using direct bisulfite sequencing approaches.

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N6-adenine DNA methylation in Tetrahymena

Project description:In this study, we provided the first genome-wide, base pair-resolution map of 6mA in Tetrahymena by applying single-molecule real-time (SMRT) sequencing.

2017-10-11 | GSE96521 | GEO

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