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Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution

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

ORGANISM(S): Mus musculus Saccharomyces cerevisiae Homo sapiens

PROVIDER: GSE122961 | GEO | 2019/07/01

REPOSITORIES: GEO

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Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution [III]

Project description:N6-methyladenosine (m6A) is the most abundant modification on mRNA, and is implicated in critical roles in development, physiology and disease. A major challenge in the field has been the inability to quantify m6A stoichiometry and the lack of antibody-independent methodologies for interrogating m6A. Here, we develop MASTER-seq for systematic quantitative profiling of m6A at single nucleotide resolution, building on differential cleavage by an RNAse at methylated sites. MASTER-seq permitted validation and de novo discovery of m6A sites, calibration of the performance of antibody based approaches, and quantitative tracking of m6A dynamics in yeast gametogenesis and mammalian differentiation. We discover that m6A stoichiometry is ‘hard-coded’ in cis via a simple and predictable code. This code accounts for ~50% of the variability in methylation levels and allows accurate prediction of m6A loss/acquisition events across evolution. MASTER-seq will allow quantitative investigation of m6A regulation in diverse cell types and disease states.

2019-07-01 | GSE129842 | GEO

Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution [II]

2019-07-01 | GSE122956 | GEO

Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution [I]

2019-07-01 | GSE122955 | GEO

Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution

Project description:Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution

| PRJNA506999 | ENA

Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution [III]

Project description:Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution [III]

| PRJNA532933 | ENA

Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution [I]

Project description:Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution [I]

| PRJNA507003 | ENA

Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution [II]

Project description:Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution [II]

| PRJNA507002 | ENA

Quantitative and whole-transcriptome N6-Methyladenosine profiling at single-nucleotide resolution

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-01-19 | GSE162357 | GEO

Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome.

Project description:N(6)-methyladenosine (m6A) is the most abundant modified base in eukaryotic mRNA and has been linked to diverse effects on mRNA fate. Current mapping approaches localize m6A residues to transcript regions 100-200 nt long but cannot identify precise m6A positions on a transcriptome-wide level. Here we developed m6A individual-nucleotide-resolution cross-linking and immunoprecipitation (miCLIP) and used it to demonstrate that antibodies to m6A can induce specific mutational signatures at m6A residues after ultraviolet light-induced antibody-RNA cross-linking and reverse transcription. We found that these antibodies similarly induced mutational signatures at N(6),2'-O-dimethyladenosine (m6Am), a modification found at the first nucleotide of certain mRNAs. Using these signatures, we mapped m6A and m6Am at single-nucleotide resolution in human and mouse mRNA and identified small nucleolar RNAs (snoRNAs) as a new class of m6A-containing non-coding RNAs (ncRNAs).

| S-EPMC4487409 | biostudies-literature

Single-nucleotide resolution mapping of m6A and m6Am throughout the transcriptome

Project description:N6-methyladenosine (m6A) is the most abundant modified base in eukaryotic mRNA and has been linked to diverse effects on mRNA fate and function. Current m6A mapping approaches rely on immunoprecipitation of m6A-containing RNA fragments to identify regions of transcripts that contain m6A. This approach localizes m6A residues to 100-200 nt-long regions of transcripts. The precise position of m6A in mRNAs cannot be identified on a transcriptome-wide level because there are no chemical methods to distinguish between m6A and adenosine. Here we show that anti-m6A antibodies can induce specific mutational signatures at m6A residues after ultraviolet light-induced antibody-RNA crosslinking and reverse transcription. Similarly, we find these antibodies induce mutational signatures at N6, 2’-O-dimethyladenosine (m6Am), a nucleotide found at the first encoded position of certain mRNAs. Using these mutational signatures, we map m6A and m6Am at single-nucleotide resolution in human and mouse mRNA and identify snoRNAs as a novel class of m6A-containing ncRNAs. UV-crosslinking and immunoprecipitation with m6A-specific antibodies was used to map m6A and m6Am in cellular RNA with single nucleotide resolution.

2015-06-29 | E-GEOD-63753 | biostudies-arrayexpress

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