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High-precision mapping reveals rare N6-deoxyadenosine methylation in the mammalian genome

ABSTRACT: High-precision mapping reveals rare N6-deoxyadenosine methylation in the mammalian genome

PROVIDER: PRJNA720613 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14182532_1.fastq.gz	Fastqsanger.gz
	SRR14182532_2.fastq.gz	Fastqsanger.gz
	SRR14182533_1.fastq.gz	Fastqsanger.gz
	SRR14182533_2.fastq.gz	Fastqsanger.gz
	SRR14182534_1.fastq.gz	Fastqsanger.gz

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High-precision mapping reveals rare N6-deoxyadenosine methylation in the mammalian genome

Project description:DNA modification has been characterized as a critical epigenetic regulator in gene expression. N6-deoxyadenosine methylation (6mA) is the most widespread type in prokaryotes and some unicellular eukaryotes. Nevertheless, the lack of a precise and comprehensive mapping method greatly hinders studying the presence and biological significance of 6mA in mammals. Here, we develop a new method MM-seq (Modification-induced Mismatch Sequencing) for genome-wide 6mA mapping in single-base resolution. This method balances accuracy and sensitivity based on a novel detection principle. We find modified DNA bases are likely to flip out of the DNA duplex, forming a mismatch-like structure that an antibody can capture. The mismatch-like structure can be recognized by endonuclease or exonuclease, which marks the exact modified site for readout via sequencing. Using this method, we examine the genomic positions of 6mA in bacteria, green algae, and mammalian cells. We find that human and mouse genomes contain rare and randomly distributed 6mA sites, with almost no overlap between different cell types. After knock-out of the RNA m6A methyltransferase Mettl3, limited 6mA sites in gDNA are diminished. Our results support the perspective that rare 6mA in the mammalian genome is caused by the misincorporation of N6-methyladenine via the nucleotide-salvage pathway.

2023-01-11 | GSE171698 | GEO

Sequencing of N6-methyl-deoxyadenosine at single-base resolution across the mammalian genome

Project description:Sequencing of N6-methyl-deoxyadenosine at single-base resolution across the mammalian genome

| PRJNA882844 | ENA

Identification and Characterization of the Mammalian Nuclear RNA N6-Adenosine Methyltransferase Core Complex

Project description:N6-methyladenosine (m6A) is the most prevalent internal modification found in mammalian messenger and non-coding RNAs. The discoveries of functionally significant demethylases that reverse this methylation as well as the recently revealed m6A distributions in mammalian transcriptomes strongly indicate regulatory functions of this modification. Here we report the identification and characterization of the mammalian nuclear RNA N6-adenosine methyltransferase core (RNMTC) complex. Besides METTL3, a methyltransferase which was the only known component of RNMTC in the past, we discovered that a previously uncharacterized methyltransferase, METTL14, exhibits a N6-adenosine methyltransferase activity higher than METTL3. Together with WTAP, the third component that dramatically affects the cellular m6A level, these three proteins form the core complex that orchestrates m6A deposition on mammalian nuclear RNA. Biochemistry assays, imaging experiments, as well as transcriptome-wide analyses of the binding sites and their effects on m6A methylation support methylation function and reveal new insights of RNMTC. PAR-CLIP and m6A-seq in HeLa cells

2013-11-29 | E-GEOD-46705 | biostudies-arrayexpress

Sequencing of N6-methyl-deoxyadenosine at single-base resolution across the mammalian genome

Project description:While DNA N6-methyl-deoxyadenosine (6mA) is abundant in bacteria and protists, its presence and function in mammalian genomes have been less clear. We present Direct-Read 6mA sequencing (DR-6mA-seq), an antibody-independent method to measure 6mA at base-resolution with high sensitivity. DR-6mA-seq employs a unique mutation-based strategy to reveal 6mA sites as misincorporation signatures without any chemical or enzymatic modulation of 6mA. We validated DR-6mA-seq through successful mapping of the well-characterized G(6mA)TC motif in the E. coli DNA and identified 6mA sites in the mammalian mitochondrial DNA. As expected, when applying DR-6mA-seq to mammalian systems, we found that genomic DNA (gDNA) 6mA abundance is in general low in most mammalian tissues and cells; however, we did observe distinct gDNA 6mA sites in mouse testis and glioblastoma cells. DR-6mA-seq provides an enabling tool to detect 6mA at single-base resolution with high sensitivity for a comprehensive understanding of DNA 6mA in eukaryotes.

2023-12-28 | GSE213876 | GEO

CSER: Exploring Precision Cancer Medicine for Sarcoma and Rare Cancers

Project description:CSER: Exploring Precision Cancer Medicine for Sarcoma and Rare Cancers

| PRJNA223419 | ENA

Identification and Characterization of the Mammalian Nuclear RNA N6-Adenosine Methyltransferase Core Complex

2013-11-29 | GSE46705 | GEO

Prevalent N6-methyldeoxyadenosine methylation in mammalian mitochondrial DNA

Project description:N6-methyldeoxyadenosine (6mA or m6dA), a well-known prokaryotic DNA modification has recently been shown to exist and play regulatory roles in eukaryotic genomic DNA. However, biological functions of 6mA in mammals remain to be explored largely due to its low abundance in most mammalian genomes. Here, we report a significant enrichment of 6mA in mammalian mitochondrial DNA (mtDNA), and identify METTL4 as a methyltransferase that installs 6mA. The level of 6mA in mtDNA is elevated up to over 0.02% of the total deoxyadenosines under hypoxia, representing ~7,00-fold enrichment over 6mA in the genomic DNA (gDNA) under normal growth conditions. The presence of 6mA negatively regulates mitochondrial transcription and balances mitochondrial function for cellular adaption to hypoxic stress. While DNA 5-methylcytosine (5mC) is a well-established, prevalent epigenetic mark in mammalian genomic DNA, our study reveals for the first time DNA 6mA methylation as a regulatory mark in mammalian mtDNA.

2020-03-24 | GSE102670 | GEO

High-precision mapping reveals rare N<sup>6</sup>-deoxyadenosine methylation in the mammalian genome.

Project description:N6-deoxyadenosine methylation (6mA) is the most widespread type of DNA modification in prokaryotes and is also abundantly distributed in some unicellular eukaryotes. However, 6mA levels are remarkably low in mammals. The lack of a precise and comprehensive mapping method has hindered more advanced investigations of 6mA. Here, we report a new method MM-seq (modification-induced mismatch sequencing) for genome-wide 6mA mapping based on a novel detection principle. We found that modified DNA bases are prone to form a local open region that allows capture by antibody, for example, via a DNA breathing or base-flipping mechanism. Specified endonuclease or exonuclease can recognize the antibody-stabilized mismatch-like structure and mark the exact modified sites for sequencing readout. Using this method, we examined the genomic positions of 6mA in bacteria (E. coli), green algae (C. reinhardtii), and mammalian cells (HEK239T, Huh7, and HeLa cells). In contrast to bacteria and green algae, human cells possess a very limited number of 6mA sites which are sporadically distributed across the genome of different cell types. After knocking out the RNA m6A methyltransferase METTL3 in mouse ES cells, 6mA becomes mostly diminished. Our results imply that rare 6mA in the mammalian genome is introduced by RNA m6A machinery via a non-targeted mechanism.

| S-EPMC9794812 | biostudies-literature

single-nucleotide resolution sequencing of N6-methyladenine in E. coli genomes and mammalian mitochondrial DNA

Project description:N6-methyladenine (6mA) is a natural DNA modification and functions primarily in restriction-modification (R-M) systems in prokaryotes. Recent studies uncovered the existence and revealed the genome-wide distribution of 6mA in eukaryotes. Specifically, it was reported that 6mA was mainly enriched in mammalian mitochondrial DNA (mtDNA) and could regulate mitochondrial activity. we achieved the genome-wide mapping of 6mA in E. coli genome and mammalian mtDNA at single-nucleotide resolution.

2022-01-26 | GSE194212 | GEO

Flavobacterium sp. N6 strain:N6

Project description:Flavobacterium sp. N6 strain:N6 Genome sequencing

| PRJNA1088267 | ENA