What do you do when you to try to thread a needle? You straighten out the thread. This is exactly what a newly discovered RNA modification (1 methyl adenosine) is doing. If you look at the of adenine pairing with thymine in the following link, the hydrogen sitting between the adenine and thymine is replaced with a much bulkier methyl group in 1 methyl adenosine. Watson-Crick base pairing is impossible.
Not much 1 methyl adenosine is found in a given mRNA (usually one or less). The authors note that it is usually found near a transcription start site (and in a highly structured region — based on the PARS score — whatever that is). In particular it is found at alternative initiation sites in the second or third exon of a gene. Unsurprisingly, when it is present more protein is expressed from the mRNA.
The work is described in Nature vol. 530 pp. 422 – 423, 441 – 446 ’16. The authors wonder how many mRNA modifications are out there waiting to be discovered. Let’s hope they look. Other mRNA modifications are known (pseudouridine, 6 methyl adenine and 5 methyl cytosine). The modification is dynamic, the amount changing with cellular conditions. This isn’t a flash in the pan as 1/3 of the same sites are methylated in mouse mRNA.