RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation

Abstract

N(6)-methyladenosine (m(6)A) is the most prevalent and internal modification that occurs in the messenger RNAs (mRNA) of most eukaryotes, although its functional relevance remained a mystery for decades. This modification is installed by the m(6)A methylation "writers" and can be reversed by demethylases that serve as "erasers." In this review, we mainly summarize recent progress in the study of the m(6)A mRNA methylation machineries across eukaryotes and discuss their newly uncovered biological functions. The broad roles of m(6)A in regulating cell fates and embryonic development highlight the existence of another layer of epigenetic regulation at the RNA level, where mRNA is subjected to chemical modifications that affect protein expression.

Keywords: METTL3–METTL14; N6-methyladenosine; RNA demethylase; m6A methyltransferase; mRNA methylation; post-transcriptional regulation.

Figure 1.

Illustration of the cellular pathways of m⁶A in nuclear RNAs. The m⁶A methyltransferases and demethylases dynamically control the m⁶A methylation landscape within the nucleus. The m⁶A reader proteins preferentially bind to the methylated RNA and mediate specific functions. In the nucleus, m⁶A may affect alternative splicing of pre-mRNA and mature mRNA storage and export. After mature RNAs are exported to the cytoplasm, cytoplasmic m⁶A reader YTHDF2 can bind to the m⁶A-containing mRNAs to mediate mRNA decay. Other cytoplasmic readers could modulate mRNA translation and storage.

Figure 2.

The normalized distribution (density) of m⁶A peaks along the mRNA transcripts in HeLa cells (top panel) and Arabidopsis thaliana (bottom panel), where each mRNA transcript is divided into the 5′ UTR, coding sequences (CDS), and the 3′ UTR.

Figure 3.

Simplified phylogenetic analysis of the MT-A70 (METTL3) superfamily. Each subfamily is marked with different colors; its corresponding conserved signature motif at the catalytic site is listed for comparison.

Figure 4.

Methyltransferases set m⁶A marks on mRNAs to balance the expression levels of pluripotency genes and lineage commitment genes in naïve and primed states of the ESCs. In the naïve state, the expression level of the pluripotency genes is dominant over that of lineage commitment genes, while in the primed state, the trend exhibits the opposite. The m⁶A methyltransferase depletion in naïve pluripotent cells further up-regulates already highly abundant naïve pluripotency genes, while the lineage commitment genes remain at very low residual levels. As a result, cells stay in a “hypernaïve” pluripotent state and fail to progress into the primed state. If the methyltransferase depletion occurs in the primed state, the expression level of the differentiation priming markers is further boosted, which pushes cells above the critical threshold toward differentiation, leading to fast differentiation and/or cell death.