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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): Oxytricha trifallax Escherichia coli 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]

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

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

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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]

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

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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.

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DNA N6-adenine methylation in Arabidopsis thaliana (methylation)

Project description:DNA methylation on N6-adenine (6mA), the most prevalent DNA modification in prokaryotes, has recently been found as a potentially new epigenetic mark in several unicellular and multicellular eukaryotes. However, the distribution patterns and potential functions of 6mA in land plants, which are primary producers for most ecosystems, remain completely unknown. Here we report global profiling of 6mA sites at single-nucleotide resolution in the genomes of Arabidopsis thaliana Columbia-0 (Col), using single-molecule real-time sequencing. DNA methylome analysis shows that 6mA sites are widely distributed across the Col genomes and enriched over the pericentromeric heterochromatin regions. Nearly 30% of 6mA sites are present in gene bodies with a trend of enrichment around the transcriptional start site. In addition to a common consensus 6mA site found in other eukaryotes, novel 6mA sites were found, indicating that 6mA could evolve new functions in land plants. Further analysis of 6mA methylome and RNA-sequencing data demonstrates that 6mA positively correlates with the gene expression level in Col plants. Consistently, DNA affinity chromatography coupled with mass spectrometry reveals that histone variants associated with actively expressed genes interact with 6mA DNA. Our results uncover 6mA as a DNA mark associated with actively expressed genes in Arabidopsis, indicating that 6mA could serve as a potentially novel epigenetic mark in land plants.

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