The initial concept of the epitranscriptome was born with the transcriptome-wide mapping of thousands of internally located modified nucleotide N 6-methyladenosine (m 6A) residues in the transcriptome 1, 2. These results demonstrate that high-stoichiometry m 1A sites are exceedingly rare in mRNAs and that previous mappings of m 1A to 5’UTRs were the result of antibody cross-reactivity to the 5’ cap. A different m 1A antibody that lacks cap-binding cross-reactivity does not show enriched binding in 5’UTRs. However, further analysis revealed that these were false-positives caused by binding of the antibody to the m 7G-cap. Using this approach, we detected appreciable levels of m 1A only in one mRNA: the mitochondrial MT-ND5 transcript. As an alternative approach, we also developed an antibody-based m 1A-mapping approach to detect m 1A at single-nucleotide resolution, and confirmed that the commonly used m 1A antibody maps sites to the transcription-start site in mRNA 5’UTRs. We developed a bioinformatic approach to discover m 1A and other modifications in mRNA throughout the transcriptome by analyzing preexisting ultra-deep RNA-Seq data for modification-induced misincorporations. N 1-methyladenosine (m 1A) was proposed to be a highly prevalent modification in mRNA 5’UTRs based on mapping studies using an m 1A-binding antibody.

Cross reactivity antibody