Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome
Open accessAbstract
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).
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The m6A modification occurs in all types of RNA, although it has the lowest abundance in tRNA.
“The m6A modification occurs in all types of RNA, although it has the lowest abundant in tRNA (Linder et al., 2015; Flamand et al., 2023).”
From β-amyloid accumulation enhances microtubule associated protein tau pathology in an APPNL-G-F/MAPTP301S mouse model of Alzheimer’s disease (2024) · cites this paper as Linder et al., 2015
The Results sections on crosslinking sites and snoRNAs identify m6A in rRNA and snoRNAs, and the Abstract reports it in mRNA. Our copy does not establish that m6A occurs in all RNA types or that its abundance is lowest in tRNA; a search for tRNA abundance found no supporting passage. Page numbers were not available in the indexed copy. (LLM, conf=0.87)
Experimental — accuracy not yet measuredAntibodies against m6A also recognize demethylated adenosine, m6Am.
“Antibodies against m6A also recognize demethylated adenosine, m6Am.”
From β-amyloid accumulation enhances microtubule associated protein tau pathology in an APPNL-G-F/MAPTP301S mouse model of Alzheimer’s disease (2024) · cites this paper as Linder et al., 2015
The Abstract reports that anti-m6A antibodies also produce mutational signatures at m6Am, supporting the claim that they recognize it. But it identifies m6Am as N6,2′-O-dimethyladenosine, not demethylated adenosine. (LLM, conf=0.91)
Experimental — accuracy not yet measuredm6Am non-enzymatically converts to m6A.
“Interestingly, m6Am also non-enzymatically converts to m6A, so the biological impact of m6Am is currently ambiguous (Linder et al., 2015; Flamand et al., 2023).”
From β-amyloid accumulation enhances microtubule associated protein tau pathology in an APPNL-G-F/MAPTP301S mouse model of Alzheimer’s disease (2024) · cites this paper as Linder et al., 2015
The Results section, “CITS miCLIP identifies m6Am at the TSS” (page unavailable), says the function of m6Am is poorly understood, but does not say it converts to m6A. Searches for non-enzymatic conversion, demethylation, and loss of the 2′-O-methyl group found no passage addressing the claimed conversion. (LLM, conf=0.72)
Experimental — accuracy not yet measuredm6Am constitutes 2-10% of total m6A detected in tissues, with brain being on the lower end of the abundance.
“This modification constitutes 2–10% of total m6A detected in tissues, with brain being on the lower end of the abundance (Linder et al., 2015).”
From β-amyloid accumulation enhances microtubule associated protein tau pathology in an APPNL-G-F/MAPTP301S mouse model of Alzheimer’s disease (2024) · cites this paper as Linder et al., 2015
The Results section, “CITS miCLIP identifies m6Am at the TSS” (page unavailable), reports mapping m6Am in mRNAs but gives no 2–10% abundance estimate or tissue comparison. Searches for that percentage, relative abundance, and brain found no passage supporting the claim; the Methods describe HEK293 cells and mouse liver, not brain tissue. (LLM, conf=0.75)
Experimental — accuracy not yet measured
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- Authors
- Linder, B., Grozhik, A. V., Olarerin-George, A. O., Meydan, C., Mason, C. E., & Jaffrey, S. R.
- Affiliations
- Cornell University (US)
- Corresponding author
- Jaffrey, Samie R
- Venue
- Nature Methods
- Published
- 2015-06-29
- Volume
- 12
- Issue
- 8
- Pages
- 767-772
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC4487409
- OpenAlex
- W776567260
- Cited by
- 1,569
- References
- 5
- Citations by year
- 2026: 111 · 2025: 156 · 2024: 203 · 2023: 179 · 2022: 174 · 2021: 211 · 2020: 173 · 2019: 132 · 2018: 100 · 2017: 77 · 2016: 46 · 2015: 7
- FWCI
- 33.31
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute on Drug Abuse (R01DA037150, DA037150)
- National Cancer Institute (T32CA062948)
- National Institute of Neurological Disorders and Stroke (NS076465, R01NS076465)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (T32HD060600)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- N6-methyladenosine, mRNA methylation, UV crosslinking, small nucleolar RNA
- MeSH terms
- Adenosine, Animals, Antibodies, Cross-Linking Reagents, DNA Mutational Analysis, Humans, Methylation, Mutation, Nucleotide Mapping, RNA, Messenger, Transcription, Genetic, Ultraviolet Rays, Sequence Analysis, DNA, RNA, Small Nucleolar, Mice, HEK293 Cells, Transcriptome
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