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

By Bastian Linder, Anya V. Grozhik, Anthony O. Olarerin-George, Cem Meydan, Christopher E. Mason, Samie R. Jaffrey. Nature Methods, 2015

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N6-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 N6,2′-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).

Subfields: Electrical and Electronic Engineering, Molecular Biology, Oncology

View Paper: https://www.semanticscholar.org/paper/c1293d4b6b4e5636e78e12e51710162bb94809ad

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Citations in the corpus

Advances and Trends in Omics Technology Development (2022, methodology): “Other approaches such as PA-m6A-seq (146), miCLIP-seq (147), m1A-MAP (148), and m7G-MeRIP-seq (149) have been established to enhance the resolution to a single base level taking advantages of nucleotide mismatches or truncation signatures induced to the modiﬁed nucleotides before reverse…”
A Unified Model for the Function of YTHDF Proteins in Regulating m6A-Modified mRNA (2020, methodology): “The rank-order of the prevalence of the submotifs recognized by the DF paralogs was similar to the overall prevalence of each m6A submotif in the transcriptome (Linder et al., 2015) (Figure 1B).”
Systematic allelic analysis defines the interplay of key pathways in X chromosome inactivation (2018, background): “Accordingly, several studies have identi ﬁ ed sites of m6A deposition in Xist RNA 19 – 22 .”
RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data (2017, background): “To locate the m6A modification sites in a genome, we predicted the exact m6A positions from the m6A-seq or MeRIP-Seq peaks by searching for consensus RRACH motifs (where R denotes A or G and H denotes A, C or U) (18,30) among the 13 species.”
The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal and leukemia cells (2017, positive): “As in other cell types 15 , m 6 A was most commonly found in the canonical m 6 A motif DRACH (D = A, G, U; R = G, A; H = A, C, U), with GGACU being the most frequent sequence context.”
Gene2vec: gene subsequence embedding for prediction of mammalian N6-methyladenosine sites from mRNA (2018, methodology): “Recently, Zhou et al. established an m 6 A data set from published single-nucleotide-resolution maps of human and mouse m 6 A sites (Ke et al. 2015; Linder et al. 2015).”
Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism (2018, background): “Unlike m(5)C that can be directly quantified by C-to-T transition after bisufite treatment, m(6)A modification can only be quantified so far as the enrichment score by IP/input(51,52) or detected as mutation or truncation products following a UV cross-linking procedure.(119,141,142) The real methyla”