mRNA Regulation by RNA Modifications

Abstract

Chemical modifications on mRNA represent a critical layer of gene expression regulation. Research in this area has continued to accelerate over the last decade, as more modifications are being characterized with increasing depth and breadth. mRNA modifications have been demonstrated to influence nearly every step from the early phases of transcript synthesis in the nucleus through to their decay in the cytoplasm, but in many cases, the molecular mechanisms involved in these processes remain mysterious. Here, we highlight recent work that has elucidated the roles of mRNA modifications throughout the mRNA life cycle, describe gaps in our understanding and remaining open questions, and offer some forward-looking perspective on future directions in the field.

Keywords: RNA metabolism; RNA modifications; epitranscriptome; posttranscriptional regulation.

Figure 1

Chemical structures of the modifications described in this review, as well as known enzymes that install and remove these modifications specifically on mRNA. Abbreviations: Ψ, pseudouridine; ac⁴C, N⁴-acetylcytidine; ALKBH, alkB homolog; D, dihydrouridine; DCP2, decapping mRNA 2; DUS, dihydrouridine synthase; DXO, decapping exoribonuclease; FTO, alpha-ketoglutarate dependent dioxygenase; GTase, guanylyl transferase; m¹A, N¹-methyladenosine; m⁵C, N⁵-methylcytidine; m⁶A, N⁶-methyladenosine; METTL, methyltransferase like; MTase, methyltransferase; NAD⁺ppA, NAD⁺ cap structure with 2′-O-methylated adenosine; NAT10, nuclear acetyltransferase 10; NSUN2, NOP2/Sun RNA methyltransferase 2; PCIF1, phosphorylated CTD interacting factor 1; PUS, pseudouridine synthase; RPUS, RNA pseudouridine synthase; TPase, RNA triphosphatase; TRMT, tRNA methyltransferase; TRUB, TruB pseudouridine synthase family.

Figure 2

Chemical structures of A:U and G:C base pairs, showing how the chemical modifications m¹A, m⁶A, Ψ, D, m⁵C, and ac⁴C impact base pairing. Arrows indicate increased (blue) or decreased (red) base pair stability as a result of the indicated modification. Abbreviations: Ψ, pseudouridine; ac⁴C, N⁴-acetylcytidine; D, dihydrouridine; m¹A, N¹-methyladenosine; m⁵C, N⁵-methylcytidine; m⁶A, N⁶-methyladenosine.

Figure 3

mRNA modifications can be installed cotranscriptionally and regulate multiple steps in nuclear processing and export. (a) Some modifications are installed cotranscriptionally via direct recruitment of modification enzymes to RNA Pol II as it synthesizes nascent transcripts. (b) mRNA capping involves multiple modifications of the 5′ end of transcripts, which can directly modulate mRNA stability by altering susceptibility to decapping and degradation enzymes. (c) Splicing also often occurs cotranscriptionally and has been shown to be regulated by multiple modifications that can alter mRNA–snRNA interactions, recruit proteins that regulate exon inclusion, or mark improperly spliced transcripts. (d) Less is known about how mRNA modifications influence polyadenylation, but both m⁶A and Ψ may play important roles. (e) RNA modifications likely also influence the nuclear export of properly processed transcripts through both the NXF1- and CRM1-dependent pathways. Abbreviations: Ψ, pseudouridine; ALY, Aly/REF export factor; CRM1, exportin 1; DCP2, decapping mRNA 2; DXO, decapping exoribonuclease; FMRP, fragile X messenger ribonucleoprotein; m⁵C, N⁵-methylcytidine; m⁶A, N⁶-methyladenosine; m⁶A_m, N⁶-2′-O-dimethyladenosine; m⁷G, N⁷-methylguanosine; NAD⁺, nicotinamide-adenine dinucleotide; NXF1, nuclear RNA export factor 1; PCIF1, phosphorylated CTD interacting factor 1; RNA Pol II, RNA polymerase II; snRNA, small nuclear RNA; SRSF3, serine and arginine rich splicing factor 3; THO, THO nuclear export complex; UAP56, DExD-box helicase 39B; XRN1, 5′–3′ exoribonuclease 1; YTHDC1, YTH domain containing protein 1.

Figure 4

mRNA modifications can regulate translation via multiple mechanisms. Installation of different chemical groups can stabilize or destabilize structured 5′ untranslated regions, which in turn influences the efficiency with which the ribosome can scan those regions. Modifications at canonical (AUG) or near-cognate (CUG) translation initiation sites can also directly impact codon–anticodon interactions. Abbreviations: Ψ, pseudouridine; ac⁴C, N⁴-acetylcytidine; D, dihydrouridine; m¹A, N¹-methyladenosine; m⁷G, N⁷-methylguanosine.

Figure 5

m⁶A and m⁵C can act as opposing regulatory marks during biological processes, such as the maternal-to-zygotic transition. While m⁶A destabilizes maternal mRNAs via recruitment of mRNA decay machinery, m⁵C protects a subset of maternal transcripts from premature degradation by recruiting YBX1 and PABPC1. Abbreviations: m⁵C, N⁵-methylcytidine; m⁶A, N⁶-methyladenosine.