Molecular Mechanisms Driving mRNA Degradation by m6A Modification

N6-Methyladenosine (m6A) as an mRNA modification plays multiple roles in various steps/characteristics of mRNA processing and metabolism, such as splicing, export, translation, and stability.YTHDF2 preferentially recognizes m6A and recruits RNA-degrading enzymes or adaptor proteins to trigger rapid degradation of the m6A-containing mRNA.Depending on the presence of HRSP12-binding sites in m6A-containing mRNAs, YTHDF2 elicits one of two RNA decay pathways: deadenylation by the YTHDF2–CCR4/NOT deadenylase complex or endoribonucleolytic cleavage via the YTHDF2–HRSP12–RNase P/MRP complex.The stability of m6A-containing mRNAs is regulated by the dynamic crosstalk between m6A and other cellular factors, such as RNA-binding proteins, RNA structures, and/or other types of modification. N6-Methyladenosine (m6A), the most prevalent internal modification associated with eukaryotic mRNAs, influences many steps of mRNA metabolism, including splicing, export, and translation, as well as stability. Recent studies have revealed that m6A-containing mRNAs undergo one of two distinct pathways of rapid degradation: deadenylation via the YT521-B homology (YTH) domain-containing family protein 2 (YTHDF2; an m6A reader protein)–CCR4/NOT (deadenylase) complex or endoribonucleolytic cleavage by the YTHDF2–HRSP12–ribonuclease (RNase) P/mitochondrial RNA-processing (MRP) (endoribonuclease) complex. Some m6A-containing circular RNAs (circRNAs) are also subject to endoribonucleolytic cleavage by YTHDF2–HRSP12–RNase P/MRP. Here, we highlight recent progress on the molecular mechanisms underlying rapid mRNA degradation via m6A and describe our current understanding of the dynamic regulation of m6A-mediated mRNA decay through the crosstalk between m6A (or YTHDF2) and other cellular factors. N6-Methyladenosine (m6A), the most prevalent internal modification associated with eukaryotic mRNAs, influences many steps of mRNA metabolism, including splicing, export, and translation, as well as stability. Recent studies have revealed that m6A-containing mRNAs undergo one of two distinct pathways of rapid degradation: deadenylation via the YT521-B homology (YTH) domain-containing family protein 2 (YTHDF2; an m6A reader protein)–CCR4/NOT (deadenylase) complex or endoribonucleolytic cleavage by the YTHDF2–HRSP12–ribonuclease (RNase) P/mitochondrial RNA-processing (MRP) (endoribonuclease) complex. Some m6A-containing circular RNAs (circRNAs) are also subject to endoribonucleolytic cleavage by YTHDF2–HRSP12–RNase P/MRP. Here, we highlight recent progress on the molecular mechanisms underlying rapid mRNA degradation via m6A and describe our current understanding of the dynamic regulation of m6A-mediated mRNA decay through the crosstalk between m6A (or YTHDF2) and other cellular factors. Many recent studies point to the role of RNA modification as a mode of post-transcriptional gene regulation and this field has been termed ‘epitranscriptomics’ [1.Roundtree I.A. et al.Dynamic RNA modifications in gene expression regulation.Cell. 2017; 169: 1187-1200Abstract Full Text Full Text PDF PubMed Scopus (836) Google Scholar, 2.Kadumuri R.V. Janga S.C. Epitranscriptomic code and its alterations in human disease.Trends Mol. Med. 2018; 24: 886-903Abstract Full Text Full Text PDF PubMed Scopus (49) Google Scholar, 3.Esteller M. Pandolfi P.P. 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Genet. 2018; 52: 349-372Crossref PubMed Scopus (66) Google Scholar]. In this review, we summarize recent reports on m6A deposition and function. In particular, we discuss recent findings regarding how m6A contributes to mRNA stability at the molecular level. Although first discovered in the 1970s, m6A modification recently returned to the spotlight with the development of RNA-seq techniques and the characterization of the proteins involved in the m6A modification [4.Meyer K.D. et al.Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons.Cell. 2012; 149: 1635-1646Abstract Full Text Full Text PDF PubMed Scopus (1634) Google Scholar,8.Dominissini D. et al.Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.Nature. 2012; 485: 201-206Crossref PubMed Scopus (1829) Google Scholar]. This modification is found in mRNA expressed in various mammalian cell types including blood, muscle, liver, intestinal, and neuronal cells. At the molecular level, the m6A modification functions at almost all stages of the mRNA life cycle, including splicing, export, and translation, and regulates mRNA stability (Figure 1). The m6A modification has also been implicated in a variety of cellular and physiological events including spermatogenesis [9.Lin Z. et al.Mettl3-/Mettl14-mediated mRNA N6-methyladenosine modulates murine spermatogenesis.Cell Res. 2017; 27: 1216-1230Crossref PubMed Scopus (119) Google Scholar], embryogenesis [10.Wang Y. et al.N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications.Nat. 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As the most prevalent internal mRNA modification, approximately 25% of cellular mRNAs harbor one or more m6A bases [4.Meyer K.D. et al.Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons.Cell. 2012; 149: 1635-1646Abstract Full Text Full Text PDF PubMed Scopus (1634) Google Scholar,8.Dominissini D. et al.Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.Nature. 2012; 485: 201-206Crossref PubMed Scopus (1829) Google Scholar]. In general, the m6A modification is enriched around translation stop codons and in the 3′ untranslated region (UTR) [4.Meyer K.D. et al.Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons.Cell. 2012; 149: 1635-1646Abstract Full Text Full Text PDF PubMed Scopus (1634) Google Scholar,8.Dominissini D. et al.Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.Nature. 2012; 485: 201-206Crossref PubMed Scopus (1829) Google Scholar,15.Linder B. et al.Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome.Nat. Methods. 2015; 12: 767-772Crossref PubMed Scopus (590) Google Scholar], although this varies among different mRNAs. Accumulating evidence indicates that the m6A RNA modification is a dynamic and reversible event (Figure 1). The coordinated action of methyltransferases (m6A writers) and demethylases (m6A erasers) contributes to the deposition and depletion of this modification. Methyltransferase-like protein 3 (METTL3) (see Glossary), also known as MT-A70, and METTL14 function as a catalytic core complex known as the m6A–METTL complex (MAC). This complex recognizes the DRACH motif (where D = A, G, or U; R = purine; and H = A, C, or U) and introduces m6A into nascent transcripts [4.Meyer K.D. et al.Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons.Cell. 2012; 149: 1635-1646Abstract Full Text Full Text PDF PubMed Scopus (1634) Google Scholar,8.Dominissini D. et al.Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.Nature. 2012; 485: 201-206Crossref PubMed Scopus (1829) Google Scholar,15.Linder B. et al.Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome.Nat. Methods. 2015; 12: 767-772Crossref PubMed Scopus (590) Google Scholar]. Notably, METTL3 has catalytic activity, whereas METTL14 forms a heterodimer with METTL3 and contributes to the binding of the complex to target RNA [16.Scholler E. et al.Interactions, localization, and phosphorylation of the m6A generating METTL3–METTL14–WTAP complex.RNA. 2018; 24: 499-512Crossref PubMed Scopus (118) Google Scholar, 17.Sledz P. Jinek M. Structural insights into the molecular mechanism of the m6A writer complex.eLife. 2016; 5e18434Crossref PubMed Scopus (195) Google Scholar, 18.Wang P. et al.Structural basis for cooperative function of Mettl3 and Mettl14 methyltransferases.Mol. Cell. 2016; 63: 306-317Abstract Full Text Full Text PDF PubMed Scopus (341) Google Scholar]. The methylation activity of MAC functions in conjunction with a regulatory protein complex – the m6A–METTL-associated complex (MACOM) – comprising Wilms tumor 1-associated protein (WTAP) (also known as female-lethal[2]d), RNA-binding motif 15 (RBM15), Vir-like m6A methyltransferase-associated (VIRMA) (also known as Virilizer or KIAA1429), Cbl proto-oncogene-like protein 1 (CBLL1) (also known as Hakai), and zinc-finger CCCH-type-containing 13 (ZC3H13) [19.Lence T. et al.Mechanistic insights into m6A RNA enzymes.Biochim. Biophys. Acta. 2019; 1862: 222-229Crossref Scopus (37) Google Scholar]. Although the MACOM itself lacks methyltransferase activity, the coordinated interaction of its components with the MAC promotes the localization of the MAC to specific RNA sites for m6A modification. RBM15 and its paralog RBM15B interact with METTL3 in a WTAP-dependent manner and preferentially bind to U-rich sequences near m6A sites [20.Patil D.P. et al.m6A RNA methylation promotes XIST-mediated transcriptional repression.Nature. 2016; 537: 369-373Crossref PubMed Scopus (572) Google Scholar,21.Knuckles P. et al.Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d.Genes Dev. 2018; 32: 415-429Crossref PubMed Scopus (170) Google Scholar]. As a result, RBM15 and/or RBM15B recruit the MAC–WTAP complex to sites proximal to m6A consensus motifs. It has been suggested that VIRMA preferentially mediates the m6A modification near stop codons and participates in alternative polyadenylation through its association with the polyadenylation cleavage factor CFIm (a tetramer complex of CPSF5 and CPSF6) in an RNA-dependent manner [22.Yue Y. et al.VIRMA mediates preferential m6A mRNA methylation in 3′UTR and near stop codon and associates with alternative polyadenylation.Cell Discov. 2018; 4: 10Crossref PubMed Scopus (223) Google Scholar]. Depletion of VIRMA or METTL3 induces 3′UTR lengthening, with a reduced amount of m6A modification. By contrast, depletion of CPSF5 leads to shortening of the 3′UTR, with an increased abundance of the m6A modification in the 3′UTR, near stop codons. Considering that stop codons are defined in the cytoplasm, whereas 3′UTR lengthening occurs in the nucleus, the molecular details underlying the VIRMA-mediated m6A modification near stop codons should be investigated in future studies. ZC3H13 is required for the nuclear localization of the ZC3H13–WTAP–VIRMA–CBLL1 complex in mouse embryonic stem cells [23.Wen J. et al.Zc3h13 regulates nuclear RNA m6A methylation and mouse embryonic stem cell self-renewal.Mol. Cell. 2018; 69: 1028-1038.e1026Abstract Full Text Full Text PDF PubMed Scopus (242) Google Scholar]. ZC3H13 also serves as an adapter protein between WTAP and RBM15, to enable efficient methylation [21.Knuckles P. et al.Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d.Genes Dev. 2018; 32: 415-429Crossref PubMed Scopus (170) Google Scholar]. It is now well established that m6A is installed cotranscriptionally on nascent transcripts [12.Barbieri I. et al.Promoter-bound METTL3 maintains myeloid leukaemia by m6A-dependent translation control.Nature. 2017; 552: 126-131Crossref PubMed Scopus (366) Google Scholar,24.Knuckles P. et al.RNA fate determination through cotranscriptional adenosine methylation and microprocessor binding.Nat. Struct. Mol. Biol. 2017; 24: 561-569Crossref PubMed Scopus (72) Google Scholar, 25.Ke S. et al.m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover.Genes Dev. 2017; 31: 990-1006Crossref PubMed Scopus (221) Google Scholar, 26.Slobodin B. et al.Transcription impacts the efficiency of mRNA translation via co-transcriptional N6-adenosine methylation.Cell. 2017; 169: 326-337.e312Abstract Full Text Full Text PDF PubMed Scopus (182) Google Scholar]. CCAAT/enhancer-binding protein zeta (CEBPZ) binds to a transcription start site and recruits METTL3 to the promoter region independent of METTL14, thereby inducing the m6A modification in the protein-coding region of the associated transcripts [12.Barbieri I. et al.Promoter-bound METTL3 maintains myeloid leukaemia by m6A-dependent translation control.Nature. 2017; 552: 126-131Crossref PubMed Scopus (366) Google Scholar]. It is also known that METTL3 is recruited to chromatin in a transcription-dependent manner and cotranscriptionally methylates nascent transcripts [24.Knuckles P. et al.RNA fate determination through cotranscriptional adenosine methylation and microprocessor binding.Nat. Struct. Mol. Biol. 2017; 24: 561-569Crossref PubMed Scopus (72) Google Scholar]. In particular, a recent report showed that the cotranscriptional conversion of A bases into m6As depends on the activity of RNA polymerase II. A low rate of transcriptional elongation leads to a greater number of m6A bases throughout the nascent transcript [26.Slobodin B. et al.Transcription impacts the efficiency of mRNA translation via co-transcriptional N6-adenosine methylation.Cell. 2017; 169: 326-337.e312Abstract Full Text Full Text PDF PubMed Scopus (182) Google Scholar]. Furthermore, it is known that the majority of m6As are formed in exon sequences in chromatin-associated nascent transcripts during transcription [25.Ke S. et al.m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover.Genes Dev. 2017; 31: 990-1006Crossref PubMed Scopus (221) Google Scholar]. The possible reversibility of the m6A mRNA modification was demonstrated by the identification of two mammalian m6A demethylases: the α-ketoglutarate-dependent dioxygenase alk B homolog 5 (ALKBH5) protein and fat mass and obesity-associated protein (FTO) [27.Jia G. et al.N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO.Nat. Chem. Biol. 2011; 7: 885-887Crossref PubMed Scopus (1512) Google Scholar,28.Zheng G. et al.ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility.Mol. Cell. 2013; 49: 18-29Abstract Full Text Full Text PDF PubMed Scopus (1256) Google Scholar]. ALKBH5 preferentially demethylates m6A in a consensus DRACH motif-dependent manner, whereas FTO demethylates a broad spectrum of substrates including m6A [28.Zheng G. et al.ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility.Mol. Cell. 2013; 49: 18-29Abstract Full Text Full Text PDF PubMed Scopus (1256) Google Scholar]. Therefore, it is plausible that ALKBH5 is more involved than FTO in global m6A demethylation. FTO was originally implicated in overweight and obesity in humans [29.Dina C. et al.Variation in FTO contributes to childhood obesity and severe adult obesity.Nat. Genet. 2007; 39: 724-726Crossref PubMed Scopus (1129) Google Scholar,30.Frayling T.M. et al.A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity.Science. 2007; 316: 889-894Crossref PubMed Scopus (2997) Google Scholar]. Later, FTO was shown to demethylate m6A in polyadenylated RNAs [27.Jia G. et al.N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO.Nat. Chem. Biol. 2011; 7: 885-887Crossref PubMed Scopus (1512) Google Scholar,31.Fu Y. et al.FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA.Nat. Commun. 2013; 4: 1798Crossref PubMed Scopus (208) Google Scholar]. Although several studies have provided evidence that FTO depletion results in the upregulation of total m6A [27.Jia G. et al.N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO.Nat. Chem. Biol. 2011; 7: 885-887Crossref PubMed Scopus (1512) Google Scholar,32.Zhao X. et al.FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis.Cell Res. 2014; 24: 1403-1419Crossref PubMed Scopus (459) Google Scholar], several recent reports suggest that FTO participates more in the demethylation of N6,2′-O-dimethyladenosine (m6Am), which is found adjacent to the 7-methylguanosine cap on mRNA and affects mRNA stability [33.Mauer J. et al.Reversible methylation of m6Am in the 5′ cap controls mRNA stability.Nature. 2017; 541: 371-375Crossref PubMed Scopus (425) Google Scholar]. More recently, FTO was also found to demethylate N1-methyladenosine (m1A) in tRNAs [34.Wei J. et al.Differential m6A, m6Am, and m1A demethylation mediated by FTO in the cell nucleus and cytoplasm.Mol. Cell. 2018; 71: 973-985.e975Abstract Full Text Full Text PDF PubMed Scopus (193) Google Scholar]. A variety of gene-regulatory pathways and biological effects mediated by the m6A modification have been summarized in several recent review papers [35.Shi H. et al.Where, when, and how: context-dependent functions of RNA methylation writers, readers, and erasers.Mol. Cell. 2019; 74: 640-650Abstract Full Text Full Text PDF PubMed Scopus (284) Google Scholar,36.Delaunay S. Frye M. RNA modifications regulating cell fate in cancer.Nat. Cell Biol. 2019; 21: 552-559Crossref PubMed Scopus (93) Google Scholar]. It should be noted that these molecular and biological functions involving m6A are mostly mediated by m6A-recognizing RNA-binding proteins (RBPs) (m6A reader proteins), such as YTH domain-containing proteins (YTHDF1, YTHDF2, YTHDF3, YTHDC1, and YTHDC2), eukaryotic translation initiation factor 3, heterogeneous nuclear ribonucleoprotein (hnRNP) C, hnRNP G, and hnRNPA2B1. Here, we highlight recent progress in our understanding of the molecular details of m6A-mediated mRNA decay. The destabilization of m6A-containing mRNAs was first identified in studies that uncovered an increase in the half-life of mRNAs after m6A writer protein (METTL3 or WTAP) downregulation in both human and mouse cells [37.Batista P.J. et al.m6A RNA modification controls cell fate transition in mammalian embryonic stem cells.Cell Stem Cell. 2014; 15: 707-719Abstract Full Text Full Text PDF PubMed Scopus (549) Google Scholar, 38.Schwartz S. et al.Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5′ sites.Cell Rep. 2014; 8: 284-296Abstract Full Text Full Text PDF PubMed Scopus (558) Google Scholar, 39.Liu J. et al.A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation.Nat. Chem. Biol. 2014; 10: 93-95Crossref PubMed Scopus (1090) Google Scholar]. Then, after the discovery of m6A-specific YTH reader proteins and structural studies that showed they are conserved across various species [40.Li F. et al.Structure of the YTH domain of human YTHDF2 in complex with an m6A mononucleotide reveals an aromatic cage for m6A recognition.Cell Res. 2014; 24: 1490-1492Crossref PubMed Scopus (109) Google Scholar,41.Zhu T. et al.Crystal structure of the YTH domain of YTHDF2 reveals mechanism for recognition of N6-methyladenosine.Cell Res. 2014; 24: 1493-1496Crossref PubMed Scopus (131) Google Scholar], it became possible to characterize the details of RNA destabilization by m6A (Figure 2, Key Figure). Thus far, it seems that all three YTHDF proteins (YTHDF1, 2, and 3) can work together to destabilize the same subset of transcripts [42.Lu W. et al.N6-Methyladenosine-binding proteins suppress HIV-1 infectivity and viral production.J. Biol. Chem. 2018; 293: 12992-13005Crossref PubMed Scopus (37) Google Scholar, 43.Shi H. et al.YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA.Cell Res. 2017; 27: 315-328Crossref PubMed Scopus (500) Google Scholar, 44.Tirumuru N. et al.N6-Methyladenosine of HIV-1 RNA regulates viral infection and HIV-1 Gag protein expression.eLife. 2016; 5e15528Crossref PubMed Scopus (138) Google Scholar]. Nonetheless, recent reports outlining the mechanism behind the decay of m6A-containing mRNAs seem to consistently indicate that YTHDF2 is the major decay-inducing reader protein [45.Du H. et al.YTHDF2 destabilizes m6A-containing RNA through direct recruitment of the CCR4–NOT deadenylase complex.Nat. Commun. 2016; 7: 12626Crossref PubMed Scopus (407) Google Scholar,46.Park O.H. et al.Endoribonucleolytic cleavage of m6A-containing RNAs by RNase P/MRP complex.Mol. Cell. 2019; 74: 494-507.e498Abstract Full Text Full Text PDF PubMed Scopus (126) Google Scholar]. Growing evidence shows that YTHDF2 is responsible for localizing transcripts from translating pools to processing bodies (P bodies) [47.Wang X. et al.N6-Methyladenosine-dependent regulation of messenger RNA stability.Nature. 2014; 505: 117-120Crossref PubMed Scopus (1457) Google Scholar,48.Ries R.J. et al.m6A enhances the phase separation potential of mRNA.Nature. 2019; 571: 424-428Crossref PubMed Scopus (171) Google Scholar], where cellular proteins participating in mRNA degradation are enriched [49.Luo Y. et al.P-bodies: composition, properties, and functions.Biochemistry. 2018; 57: 2424-2431Crossref PubMed Scopus (120) Google Scholar,50.Sheth U. Parker R. Decapping and decay of messenger RNA occur in cytoplasmic processing bodies.Science. 2003; 300: 805-808Crossref PubMed Scopus (914) Google Scholar]. A recent study revealed that, under stress conditions, the complex of an m6A-containing mRNA and YTHDF proteins partitions into intracellular phase-separated compartments, such as P bodies, stress granules, or neuronal RNA granules [48.Ries R.J. et al.m6A enhances the phase separation potential of mRNA.Nature. 2019; 571: 424-428Crossref PubMed Scopus (171) Google Scholar]. However, another research group reported that YTHDF2 directly recruits the CCR4/NOT deadenylase complex to m6A-containing mRNA independently of the association between YTHDF2 and P body components, thereby triggering deadenylation of m6A-containing RNAs [45.Du H. et al.YTHDF2 destabilizes m6A-containing RNA through direct recruitment of the CCR4–NOT deadenylase complex.Nat. Commun. 2016; 7: 12626Crossref PubMed Scopus (407) Google Scholar]. It is known that deadenylation of an mRNA precedes the formation of P bodies [51.Zheng D. et al.Deadenylation is prerequisite for P-body formation and mRNA decay in mammalian cells.J. Cell Biol. 2008; 182: 89-101Crossref PubMed Scopus (138) Google Scholar] and that the exosome (3′-to-5′ exoribonuclease complex), which is engaged in rapid mRNA degradation after deadenylation, is not enriched in P bodies [49.Luo Y. et al.P-bodies: composition, properties, and functions.Biochemistry. 2018; 57: 2424-2431Crossref PubMed Scopus (120) Google Scholar, 50.Sheth U. Parker R. Decapping and decay of messenger RNA occur in cytoplasmic processing bodies.Science. 2003; 300: 805-808Crossref PubMed Scopus (914) Google Scholar, 51.Zheng D. et al.Deadenylation is prerequisite for P-body formation and mRNA decay in mammalian cells.J. Cell Biol. 2008; 182: 89-101Crossref PubMed Scopus (138) Google Scholar]. Therefore, it is plausible that CCR4/NOT-mediated deadenylation and subsequent exosome-mediated 3′-to-5′ exoribonucleolytic decay may initiate the degradation of an m6A-containing mRNA outside of P bodies. The remaining mRNA intermediate may then be subject to decapping, followed by 5′-to-3′ exoribonucleolytic cleavage in P bodies, where the decapping complex and 5′-to-3′ exoribonuclease (XRN1) are enriched [49.Luo Y. et al.P-bodies: composition, properties, and functions.Biochemistry. 2018; 57: 2424-2431Crossref PubMed Scopus (120) Google Scholar,50.Sheth U. Parker R. Decapping and decay of messenger RNA occur in cytoplasmic processing bodies.Science. 2003; 300: 805-808Crossref PubMed Scopus (914) Google Scholar]. An additional route for YTHDF2-mediated mRNA decay was reported recently [46.Park O.H. et al.Endoribonucleolytic cleavage of m6A-containing RNAs by RNase P/MRP complex.Mol. Cell. 2019; 74: 494-507.e498Abstract Full Text Full Text PDF PubMed Scopus (126) Google Scholar]. m6A-containing mRNAs bound by YTHDF2 associate with RNase P/MRP, an endoribonuclease (Box 1). The association between YTHDF2 and RNase P/MRP is bridged by an adaptor protein: heat-responsive protein 12 (HRSP12) (also known as reactive intermediate imine deaminase A homolog, UK114 antigen homolog, or 14.5 kDa translational inhibitor protein). Experiments based on crosslinking immunoprecipitation followed by next-generation sequencing have characterized HRSP12 as a new RBP with a binding preference for the sequence GGUUC. Of note, this sequence is located in the 5′ half of a potential palindromic sequence, suggesting that HRSP12 may recognize an RNA stem–loop structure as well as primary sequences. Besides serving as an adaptor, HRSP12 facilitates the binding of YTHDF2 to mRNA. Moreover, YTHDF2 promotes the binding of HRSP12 to target mRNAs. With the help of this cooperative binding, RNase P/MRP is eventually recruited to an m6A-containing mRNA and performs endoribonucleolytic cleavage [46.Park O.H. et al.Endoribonucleolytic cleavage of m6A-containing RNAs by RNase P/MRP complex.Mol. Cell. 2019; 74: 494-507.e498Abstract Full Text Full Text PDF PubMed Scopus (126) Google Scholar]. Currently, it remains unknown whether this endoribonucleolytic-cleavage event is associated with P bodies.Box 1Molecular Properties of RNase P/MRPRNase P and RNase MRP are both RNP complexes that are conserved across a variety of species including humans, yeast, mice, and flies [86.Jarrous N. Roles of RNase P and its subunits.Trends Genet. 2017; 33: 594-603Abstract Full Text Full Text PDF PubMed Scopus (27) Google Scholar]. RNase P was first identified as an endonuclease that cleaves the 5′ leader sequence of a precursor form of tRNAs. The protein subunits of RNase P can interact with various cellular proteins and this combinatorial assembly can give rise to myriad RNP complexes. RNase MRP was first found to cleave mitochondrial RNA in mouse cells (hence the name), but subsequent research has revealed that RNase MRP is not associated with mitochondria and is now widely known as a nuclease for 5.8S rRNA processing. Notably, in humans, RNase P and RNase MRP share at least seven protein components (POP1, POP5, RPP20, RPP25, RPP30, RPP38, and RPP40) and have similar secondary and tertiary structures. Other than several protein components, RNase P and RNase MRP are distinguished by their unique ncRNA components: RPPH1 and RMRP RNA, respectively.Targets of RNase P/MRP are not limited to tRNA, but also include long ncRNAs and mRNAs. As for mRNAs, RNase MRP has been reported to accumulate at a particular cytoplasmic location and destabilize CLB2 mRNA to promote cell cycle progression. In addition, viperin mRNA has been shown to be directly cleaved by RNase P/MRP in human cells. Furthermore, a recent study by Park et al. indicates that RNase P/MRP directly binds to m6A-containing mRNAs in the cytoplasm and internally cleaves them [46.Park O.H. et al.Endoribonucleolytic cleavage of m6A-containing RNAs by RNase P/MRP complex.Mol. Cell. 2019; 74: 494-507.e498Abstract Full Text Full Text PDF PubMed Scopus (126) Google Scholar]. RNase P and RNase MRP are both RNP complexes that are conserved across a variety of species including humans, yeast, mice, and flies [86.Jarrous N. Roles of RNase P and its subunits.Trends Genet. 2017; 33: 594-603Abstract Full Text Full Text PDF PubMed Scopus (27) Google Scholar]. RNase P was first identified as an endonuclease that cleaves the 5′ leader sequence of a precursor form of tRNAs. The protein subunits of RNase P can interact with various cellular proteins and this combinatorial assembly can give rise to myriad RNP complexes. RNase MRP was first found to cleave mitochondrial RNA in mouse cells (hence the name), but subsequent research has revealed that RNase MRP is not associated with mitochondria and is now widely known as a nuclease for 5.8S rRNA processing. Notably, in humans, RNase P and RNase MRP share at least seven protein components (POP1, POP5, RPP20, RPP25, RPP30, RPP38, and RPP40) and have similar secondary and tertiary structures. Other than several protein components, RNase P and RNase MRP are distinguished by their unique ncRNA components: RPPH1 and RMRP RNA, respectively. Targets of RNase P/M