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

ABSTRACT: 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.

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

PROVIDER: GSE184372 | GEO | 2022/05/12

REPOSITORIES: GEO

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

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

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Unique cell-type specific patterns of DNA methylation in the root meristem (RNA-seq)

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Project description:DNA methylation is an epigenetic modification that differs between plant organs and tissues, but the extent of variation between cell types is not known. Here, we report single-base resolution whole genome DNA methylomes, mRNA transcriptomes, and small RNA transcriptomes for six cell populations covering the major cell types of the Arabidopsis root meristem. We identify widespread cell type specific patterns of DNA methylation, especially in the CHH sequence context. The genome of the columella root cap is the most highly methylated Arabidopsis cell characterized to date. It is hypermethylated within transposable elements, accompanied by increased abundance of transcripts encoding RNA-directed DNA methylation (RdDM) pathway components and 24 nt small RNAs. Absence of the nucleosome remodeler DECREASED DNA METHYLATION 1, required for maintenance of DNA methylation, and low abundance of histone transcripts involved in heterochromatin formation suggests a loss of heterochromatin may occur in the columella, thus allowing access of RdDM factors to the whole genome, and producing excess 24 nt small RNAs in this tissue. Together, these maps provide new insights into the epigenomic diversity that exists between distinct plant somatic cell types. MethylC-seq from six cell populations covering the major cell types of the Arabidopsis root meristem.

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