Post-transcriptional gene regulation by mRNA modifications

Abstract

The recent discovery of reversible mRNA methylation has opened a new realm of post-transcriptional gene regulation in eukaryotes. The identification and functional characterization of proteins that specifically recognize RNA N⁶-methyladenosine (m⁶A) unveiled it as a modification that cells utilize to accelerate mRNA metabolism and translation. N⁶-adenosine methylation directs mRNAs to distinct fates by grouping them for differential processing, translation and decay in processes such as cell differentiation, embryonic development and stress responses. Other mRNA modifications, including N¹-methyladenosine (m¹A), 5-methylcytosine (m⁵C) and pseudouridine, together with m⁶A form the epitranscriptome and collectively code a new layer of information that controls protein synthesis.

Figure 1. The writer, eraser and reader proteins of m⁶A

The deposition, removal and recognition of N⁶-methyladenosine (m⁶A) are carried out by cognate factors termed writers, erasers and readers, respectively. Mammalian m⁶A writers function as a protein complex with four identified components so far: methyltransferase-like 3 (METTL3), METTL14, Wilms tumour 1-associated protein (WTAP) and KIAA1429. Two m⁶A erasers have been reported: fat mass and obesity-associated protein (FTO) and alkB homologue 5 (ALKBH5). The function of m⁶A is mediated partly by reader proteins, which have been identified in members of the YT521-B homology (YTH) domain-containing protein and the heterogeneous nuclear ribonucleoprotein (HNRNP) protein families.

Figure 2. m⁶A-dependent mRNA processing promotes translation and decay, and affects splicing

a| After being deposited by the methyltransferase core catalytic components methyltransferase-like 3 (METTL3) and METTL14, N⁶-methyladenosine (m⁶A) is recognized by various reader proteins. In the nucleus, heterogeneous nuclear ribonucleoprotein C (HNRNPC) functions as an indirect m⁶A reader by binding unstructured m⁶A switch regions and regulating splicing, whereas YT521-B homology (YTH) domain-containing 1 (YTHDC1) regulates alternative splicing by binding m⁶A directly and recruiting the splicing factors serine and arginine-rich splicing factor 3 (SRSF3) while blocking binding by SRSF10. HNRNPA2B1 also mediates alternative splicing in a manner similar to YTHDC1. In the cytoplasm, YTHDF1 mediates translation initiation of m⁶A-containing transcripts by binding directly to m⁶A and recruiting eukaryotic initiation factor 3 (eIF3), thereby facilitating the loading of the eukaryotic small ribosomal subunit (40S). YTHDF2 promotes mRNA decay by binding to CCR4–NOT transcription complex subunit 1 (CNOT1), thereby facilitating the recruitment of the CCR4–NOT complex and inducing accelerated deadenylation. b | Methylated transcripts may be sorted by reader proteins into a fast track (right) for processing, translation and decay. This fast-tracking effectively groups transcripts with otherwise markedly different properties to ensure their timely and coordinated translation and degradation, possibly generating a sharp ‘pulse’ of gene expression to satisfy a need for translational bursts and subsequent clearance of these transcripts.

Figure 3. m⁶A affects mouse embryonic stem cell differentiation

The N⁶-methyl-adenosine (m⁶A) methyltransferase METTL3 (methyltransferase-like 3) is required for the transition of mouse embryonic stem cells (mouse ES cells) from a naive to the more differentiated primed state. During this process, the key pluripotency factor transcripts POU domain, class 5, transcription factor 1(Pou5f1), Krueppel-like factor 4 (Klf4) and Sox2 must be cleared. In mouse ES cells lacking Mettl3, this clearance is defective because non-methylated mRNAs are less subjected to decay, which prevents the establishment of a differentiated transcriptome required to achieve a primed mouse ES cell state.

Figure 4. m⁶A and other mRNA post-transcriptional modifications

a| Qualitative distribution profiles of N¹-methyladenosine (m¹A; purple) and N⁶-methyladenosine (m⁶A; red) in mRNA. m¹A is found primarily near translation start codons and first splice sites, whereas m⁶A is primarily found in long exons and within 3′ untranslated regions (3′ UTRs). b | In addition to m⁶A and m¹A, other chemical modifications found on eukaryotic mRNA with emerging regulatory functions include 5-methylcytosine (m⁵C), pseudouridine (ψ) and 2′-O-methylation (2′OMe). CDS, coding DNA sequence.

Figure 5. m⁶A synchronizes mRNA processing in response to various internal and external stimuli

The activities of N⁶-methyladenosine (m⁶A) writers, erasers and readers may be regulated by the same signalling pathways and stimuli that tune transcription and translation, potentially through various post-translational modifications (not shown) on writers, erasers and readers. This process could constitute an additional mechanism to post-transcriptionally coordinate the expression of large groups of genes in response to internal and external stimuli, which may affect many physiological processes that require rapid responses involving multiple genes. ALKBH5, alkB homologue 5; CCR4–NOT, carbon catabolite repression 4–negative on TATA-less; eIF3, eukaryotic initiation factor 3; FTO, fat mass and obesity-associated protein; METTL, methyltransferase-like; Pol II, RNA polymerase II; WTAP, Wilms tumour 1-associated protein; YTHDF2, YT521-B homology domain-containing family protein 2.