m6 A RNA methylation: from mechanisms to therapeutic potential

Abstract

RNA carries a diverse array of chemical modifications that play important roles in the regulation of gene expression. N⁶ -methyladenosine (m⁶ A), installed onto mRNA by the METTL3/METTL14 methyltransferase complex, is the most prevalent mRNA modification. m⁶ A methylation regulates gene expression by influencing numerous aspects of mRNA metabolism, including pre-mRNA processing, nuclear export, decay, and translation. The importance of m⁶ A methylation as a mode of post-transcriptional gene expression regulation is evident in the crucial roles m⁶ A-mediated gene regulation plays in numerous physiological and pathophysiological processes. Here, we review current knowledge on the mechanisms by which m⁶ A exerts its functions and discuss recent advances that underscore the multifaceted role of m⁶ A in the regulation of gene expression. We highlight advances in our understanding of the regulation of m⁶ A deposition on mRNA and its context-dependent effects on mRNA decay and translation, the role of m⁶ A methylation of non-coding chromosomal-associated RNA species in regulating transcription, and the activities of the RNA demethylase FTO on diverse substrates. We also discuss emerging evidence for the therapeutic potential of targeting m⁶ A regulators in disease.

Keywords: RNA modifications; epitranscriptome; gene expression; m6A methylation; mRNA.

Figure 1. m⁶A is a multifaceted regulator of gene expression

m⁶A (red circle) regulates transcription, alternative splicing, alternative polyadenylation, nuclear export, cap‐dependent and cap‐independent translation, mRNA degradation, and mRNA stabilization. A diverse set of reader proteins that selectively bind m⁶A, either directly or indirectly, mediate these multifaceted effects on gene expression. Note that for clarity, nuclear processes are shown to occur after release of RNA from the polymerase, but some of the depicted nuclear processes may also occur co‐transcriptionally.

Figure 2. Specificity of the m⁶A epitranscriptome

(A) Schematic representing the distribution of m⁶A in the mammalian transcriptome. A subset of transcripts contain one or more m⁶A sites, while another subset are not methylated. m⁶A is enriched in unusually long internal exons and near stop codons/start of last exons. (B) Deposition is regulated by intrinsic factors, such as the preference of the METTL3/METTL14 methyltransferase for specific RNA sequences. m⁶A deposition is also regulated by external factors; transcription factors, RNA‐binding proteins, RNA polymerase II, and the H3K36me3 histone modification have been reported to recruit the METTL3/METTL14 methyltransferase to mRNAs to promote methylation. m⁶A demethylases FTO and ALKBH5 can also tune m⁶A levels at a subset of sites following their initial deposition by METTL3/METTL14.

Figure 3. Theoretical model for how changes in cellular state may impact m⁶A regulation

m⁶A regulatory factors can act at multiple levels to enable differential gene expression regulation. Upon a change in cell state, m⁶A sites that are extensively regulated by extrinsic determinants (e.g., RNA‐binding proteins that recruit METTL3/METTL14 to the site) may vary in their methylation level if the levels or activities of these factors change. In contrast, m⁶A sites that are primarily controlled by intrinsic determinants may exhibit stable methylation. Additionally, levels or activities of m⁶A readers may vary upon a change in cell state. This may result in differential reader binding to m⁶A sites. Given the diverse activities of various m⁶A readers, the effect of a particular m⁶A site on mRNA metabolism may change even if methylation levels remain stable.

Figure 4. m⁶A on chromosome‐associated regulatory RNA regulates chromatin state and transcription

m⁶A methylation of non‐coding eRNA, paRNA, and LINE element RNA promotes their decay, leading to reduction in active histone marks such as H3K27ac and H3K4me3 and downregulation of transcription (top). In Mettl3 KO cells, these non‐coding transcripts are stabilized resulting in increased deposition of H3K27ac and H3K4me3 and upregulated transcription of associated mRNAs (bottom).