Reversible RNA adenosine methylation in biological regulation

Abstract

N(6)-methyladenosine (m(6)A) is a ubiquitous modification in mRNA and other RNAs across most eukaryotes. For many years, however, the exact functions of m(6)A were not clearly understood. The discovery that the fat mass and obesity-associated protein (FTO) is an m(6)A demethylase indicates that this modification is reversible and dynamically regulated, suggesting that it has regulatory roles. In addition, it has been shown that m(6)A affects cell fate decisions in yeast and plant development. Recent affinity-based m(6)A profiling in mouse and human cells further showed that this modification is a widespread mark in coding and noncoding RNA (ncRNA) transcripts and is likely dynamically regulated throughout developmental processes. Therefore, reversible RNA methylation, analogous to reversible DNA and histone modifications, may affect gene expression and cell fate decisions by modulating multiple RNA-related cellular pathways, which potentially provides rapid responses to various cellular and environmental signals, including energy and nutrient availability in mammals.

Figure 1. Modifications in eukaryote mRNA

The structure and localization of RNA modifications in mRNA are shown. m⁷G is at the 5′ terminus of the cap structure, m⁶A_m at the first position of the 5′ terminus and internal positions, 2′-O-methylated N_m on the first two starting positions of the 5′ terminus and internal sequence, and m⁵C and m⁶A are internal mRNA modifications (green ball indicates the modifications located at the cap, pink ball indicates internal modifications).

Figure 2

The history of the research on m⁶A in mRNA.

Figure 3. The reversible adenosine methylation reaction in mRNA and non-coding RNA

(a) The reversible m⁶A methylation catalyzed by N⁶-adenosine methyltransferase and demethylases (FTO and ALKBH5). (b) The proposed S_N2 methylation reaction of N⁶-adenosine and the oxidative demethylation through a proposed N⁶-hydroxymethyladenosine intermediate. SAM: S-adenosylmethionine, SAH: S-adenosyl-L-homocysteine.

Figure 4. Proposed functions of reversible m⁶A methylation

(a) The intermediate modification created by FTO could be recognized by a specific RNA-binding protein to impact RNA metabolism. If this interaction occurred in the nuclear speckle, where FTO is localized, it might protect the modification until it was exported from the nuclear speckle (b) The m⁶A methylation may be recognized by specific m⁶A-binding proteins, or preclude the binding by certain RNA-binding proteins that preferably bind to unmethylated RNA. The presence of m⁶A can therefore impact various aspects of RNA metabolism such as pre-mRNA splicing, mRNA transport from nuclear to cytoplasm, translation, mRNA turnover, mRNA stability or sub-cellular localization. In addition, the presence of m⁶A in the 3′UTR of mRNA might weaken or enhance mRNA association with miRNA (yellow box) via modulation of protein-RNA recognitions.