Like DNA, which can be modified after synthesis by C-methylation (which generally leads to transcriptional repression through methyl CpG-binding proteins; see page 404), pre-mRNAs, mRNAs, and lncRNAs can undergo base modifications following their transcription. The functions of the most frequent post-transcriptional base modification of mRNA, methylation of the N⁶ position of adenine (m⁶A), are currently intense areas of investigation. In mammalian cells, about one in every 2000 bases in mRNAs and long noncoding RNAs (lncRNAs) are m⁶As, amounting to 3–5 m⁶As per mRNA, on average. Sites of m⁶A are found in all rRNAs, in all snRNAs, and in the TΨCG loop of all tRNAs (see Figure 5-20). In contrast, among mRNAs and lncRNAs, only a fraction of all molecules contain m⁶A, ranging from 10 to 70 percent for the few mRNAs and lncRNAs thus far analyzed. But m⁶A has been detected in transcripts of over 7000 human protein-coding genes and some 300 lncRNAs. It has also been detected in introns, indicating that it can be added to pre-mRNAs co-transcriptionally. In mRNAs, a high percentage of m⁶As are located near stop codons, in 3′ untranslated regions, and in unusually long internal exons.

As for DNA, specific enzymes add methyl groups from S-adenosylmethionine (a common donor of methyl groups in many biochemical reactions) to specific sites, and enzymes have been identified that can remove RNA methyl groups. These observations raise the possibility that m⁶A modification of a particular RNA molecule may be dynamically regulated. However, these enzymes are primarily nuclear, so once an mRNA is modified with m⁶A, it is probably not demethylated in the cytoplasm. Importantly, proteins have been identified that bind m⁶A-modified RNAs preferentially over RNAs lacking m⁶A. By analogy with DNA C-methylation, this class of proteins may carry out the function(s) of m⁶A modification.

Recent research indicates that m⁶A may affect many aspects of the “life cycle” of specific mRNAs, including RNA splicing, nuclear export, translation, and degradation. In Drosophila and the plant A. thaliana, there is a single mRNA m⁶A methyl transferase, and knockouts of these genes are embryonic lethal in both organisms, attesting to the functional importance of m⁶A modification. RNA molecules containing m⁶A are less stable than the same unmethylated RNAs. In this regard, m⁶A-binding proteins have been reported to induce association of m⁶A-containing mRNAs with P bodies, potentially accounting for how this base modification affects mRNA translation and stability. In addition to m⁶A, more than a hundred other modifications of the four bases have been characterized in RNAs. Obviously, much remains to be learned about the functions of these base modifications.