Nucleotide sequences at the N6-methyladenosine sites of HeLa cell messenger ribonucleic acid

Borate gel chromatography was used to separate internal oligonucleotides containing N6-methyladenosine (m6A) from methylated 5'-terminal oligonucleotides of HeLa cell polyadenylylated mRNA. N6-Methyladenosine occurs primarily in two sequences, -G-m6A-C (70%) and -A-m6A-C-(30%). The nucleoside immediately following cytidine may be uridine, cytidine, or adenosine, while guanosine as well as other nucleosides occupy subsequent positions. Each of the four positions preceding the -(G or A)-m6A-C- sequence may be occupied by a pyrimidine or a purine ribonucleoside. Since on a random basis all possible sequences containing -(G or A)-A-C-(U or C or A)- could occur once per 43 nucleotides whereas there is only one m6A residue per thousand nucleotides, then either (1) not all potential sites are methylated, (2) there are multiple unique sequences perhaps methylated by several different enzymes, or (3) there are other unrecognized discriminating factors. The possibility that methylation of adenosine occurs exclusively in the region close to the 5' terminus of the mRNA was considered. However, such a localization was excluded since the majority of m6A residues were not found in 4 to 6S 5'-terminal fragments isolated by borate gel chromatography.