Chemical Modifications in the Life of an mRNA Transcript

Abstract

Investigations over the past eight years of chemical modifications on messenger RNA (mRNA) have revealed a new level of posttranscriptional gene regulation in eukaryotes. Rapid progress in our understanding of these modifications, particularly, N⁶-methyladenosine (m⁶A), has revealed their roles throughout the life cycle of an mRNA transcript. m⁶A methylation provides a rapid mechanism for coordinated transcriptome processing and turnover that is important in embryonic development and cell differentiation. In response to cellular signals, m⁶A can also regulate the translation of specific pools of transcripts. These mechanisms can be hijacked in human diseases, including numerous cancers and viral infection. Beyond m⁶A, many other mRNA modifications have been mapped in the transcriptome, but much less is known about their biological functions. As methods continue to be developed, we will be able to study these modifications both more broadly and in greater depth, which will likely reveal a wealth of new RNA biology.

Keywords: N6-methyladenosine; RNA metabolism; epitranscriptome; ribonucleotide modifications.

Figure 1

Messenger RNA (mRNA) modifications and mRNA processing. ❶ mRNA transcripts are transcribed from their genomic locus by RNA Polymerase II (Pol II). As transcription proceeds, nascent transcripts are ❷ capped, ❸ spliced, and ❹ polyadenylated so they can be ❺ efficiently exported for protein translation. Though the canonical mRNA cap contains m⁷G, m⁶A_m at the cap-adjacent nucleotide can render transcripts resistant to decapping by DCP2. m⁶A has been implicated in many aspects of mRNA processing, ❻ translation, and ❼ decay. m⁵C may mediate mRNA export through ALYREF, whereas Ψ and 2′OMe may influence protein translation by altering codon-anticodon interactions.

Figure 2

Mechanisms of m⁶A-mediated regulation. m⁶A installation and removal are regulated by the nuclear METTL3/METTL14 methyltransferase complex and the demethylases FTO and ALKBH5, respectively. In the nucleus, HNRNPC and YTHDC1 likely regulate m⁶A-mediated splicing, processing, and export. In the cytoplasm, YTHDF1 enhances cap-dependent translation, eIF3 induces cap-independent translation through m⁶A binding, and YTHDF2 regulates m⁶A-dependent mRNA decay. YTHDC2 appears to affect both decay and translation. YTHDF3 may be involved in some of these processes, in particular, m⁶A-mediated translational regulation. Abbreviations: 40S, small ribosomal subunit; eIF3, eukaryotic initiation factor 3; FTO, fat mass- and obesity-associated protein; pre-mRNA, precursor mRNA.

Figure 3

Mechanisms of m⁶A-mediated transcriptome turnover and translation. (a) m⁶A marks transcripts required for maintaining a pluripotent state in numerous stem cell types. For differentiation to proceed, these transcripts must be degraded, presumably to minimize continued production of pluripotency factors. Cell type–specific factors must then be transcribed and translated to guide cells to the proper cell fate. In stem cell populations, loss of m⁶A often manifests as a block in differentiation, as pluripotency factors remain expressed at high levels. In cancer, loss of m⁶A can result in elevated levels of oncogenic factors to drive cancer progression, but this is not a general mechanism in all cases. (b) m⁶A can regulate translation of specific pools of transcripts under stress conditions. Under normal conditions, cap-dependent translation is heavily relied on to produce protein in the cell, and m⁶A-binding proteins such as YTHDF1 may contribute in some cases. Under heat shock stress, however, cap-dependent translation is compromised, yet the cell needs to efficiently translate specific factors such as HSP70. By recruiting eIF3, m⁶A can facilitate cap-independent translation of key transcripts in the heat shock response. Abbreviations: 40S, small ribosomal subunit; DF1, YTHDF1; eIF3, eukaryotic initiation factor 3; M3/M14, METTL3/METTL14; PABP, poly(A) binding protein; Pol II, Polymerase II.