m6A in the Signal Transduction Network

Abstract

In response to environmental changes, signaling pathways rewire gene expression programs through transcription factors. Epigenetic modification of the transcribed RNA can be another layer of gene expression regulation. N⁶-adenosine methylation (m⁶A) is one of the most common modifications on mRNA. It is a reversible chemical mark catalyzed by the enzymes that deposit and remove methyl groups. m⁶A recruits effector proteins that determine the fate of mRNAs through changes in splicing, cellular localization, stability, and translation efficiency. Emerging evidence shows that key signal transduction pathways including TGFβ (transforming growth factor-β), ERK (extracellular signal-regulated kinase), and mTORC1 (mechanistic target of rapamycin complex 1) regulate downstream gene expression through m⁶A processing. Conversely, m⁶A can modulate the activity of signal transduction networks via m⁶A modification of signaling pathway genes or by acting as a ligand for receptors. In this review, we discuss the current understanding of the crosstalk between m⁶A and signaling pathways and its implication for biological systems.

Keywords: ERK; N⁶-methyladenosine; RNA modifi­cation; TGFβ; mTOR; signaling.

Fig. 1. Key players of the m6A RNA modification process.

The deposition of m⁶A on mRNA is mediated by the writer complex which consists of m⁶A-METTL complex (MAC) and scaffolding MAC-associated complex (MACOM). MAC includes METTL3, a catalytic core protein, and METTL14, a scaffolding protein, which methylates adenosine in the consensus motif (DRACH, D = A, G, or U; R = A or G; A = m⁶A-modified A; H = A, C, or U). MACOM consists of adaptor proteins including Wilms’ tumor 1-associated protein (WTAP), VIRMA (vir-like m⁶A methyltransferase associated), RBM15 (RNA-binding motif protein 15), HAKAI, and ZC3H13 (zinc finger CCCH domain-containing protein 13). FTO and ALKBH5 demethylate m⁶A (erasers). The m⁶A binding proteins (readers) include YT521-B homology (YTH) and insulin-like growth factor-2 mRNA binding protein (IGF2BP) family proteins, which determine the fate of m⁶A-methylated mRNA such as splicing, nuclear export, stability, and translation. The chemical structure of m⁶A is shown in the circle.

Fig. 2. TGFβ controls gene expression through m6A modification.

Upon TGFβ stimulation, SMAD2/3 interact with METTL3, METTL14, and WTAP, to induce m⁶A methylation and degradation of pluripotency genes for differentiation of embryonic stem cells. On the other hand, in cancer cells, TGFβ induces SNAIL mRNA methylation during EMT. The methylated SNAIL mRNA binds with YTHDF1, which induces SNAIL translation through interaction with a translation elongation factor eEF-2 (eukaryotic elongation factor-2).

Fig. 3. Dynamic regulation of m6A enzymes by ERK.

METTL3 phosphorylation by ERK inhibits its degradation by recruiting ubiquitin-specific protease 5 (USP5). ERK-mediated METTL3 phosphorylation also enhances the interaction between METTL3 and WTAP (bottom panel). ERK stabilizes YTHDF2 through phosphorylation (right panel). ALKBH5 phosphorylation by ERK sustains its sumoylation and induces disassociation of ALKBH5 from m⁶A-modified mRNA (left panel).

Fig. 4. mTORC1 activates the activity of m6A writer complex.

mTORC1 activates the m⁶A writer complex in three ways. mTORC1-mediated activation of chaperonin protein, chaperonin containing tailless complex polypeptide 1 (CCT) complex, stabilize METTL3 and METTL14 (middle panel). mTORC1 induces WTAP expression through eukaryotic initiation factor 4A (eIF4A)/4B-dependent translation (right panel). mTORC1 also stimulates S-adenosylmethionine (SAM) synthesis through cMyc-mediated upregulation of MAT2A (methionine adenosyl transferase 2A) (left panel).

Fig. 5. Regulation of signal transduction by m6A.

(A) m⁶A modification suppresses Akt signaling by destabilizing mRNAs of Akt activators mTOR, proline rich protein 5 (PRR5), and PRR5-like (PRR5L) (top panel), while increasing translational efficiency of Akt suppressors phosphatase and tensin homolog (PTEN) and PH domain leucine rich repeat protein phosphatase 2 (PHLPP2) (bottom panel). (B) Upon cytotoxic stress, m⁶A is generated by RNA degradation and binds to the G-protein coupled receptor, adenosine receptor, which in turn activates ERK signaling.