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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): mixed culture metagenome Escherichia coli Oxytricha trifallax 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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Graphene Oxide Nanoribbons in Chitosan for Simultaneous Electrochemical Detection of Guanine, Adenine, Thymine and Cytosine.

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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.

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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.

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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.

2018-04-16 | GSE81596 | GEO

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