Molecular Mechanisms Driving mRNA Degradation by m6A Modification

Trends in Genetics, Journal Year: 2020, Volume and Issue: 36(3), P. 177 - 188

Published: Jan. 18, 2020

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

Language: Английский

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Modifications in an Emergency: The Role of N1-Methylpseudouridine in COVID-19 Vaccines

ACS Central Science, Journal Year: 2021, Volume and Issue: 7(5), P. 748 - 756

Published: April 6, 2021

The novel coronavirus SARS-CoV-2, the cause of COVID-19 pandemic, has inspired one most efficient vaccine development campaigns in human history. A key aspect mRNA vaccines is use modified nucleobase N1-methylpseudouridine (m1Ψ) to increase their effectiveness. In this Outlook, we summarize and function m1Ψ synthetic mRNAs. By demystifying how a element within these medicines works, aim foster understanding highlight future opportunities for chemical innovation.

Language: Английский

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m6A demethylase ALKBH5 inhibits tumor growth and metastasis by reducing YTHDFs-mediated YAP expression and inhibiting miR-107/LATS2–mediated YAP activity in NSCLC

Molecular Cancer, Journal Year: 2020, Volume and Issue: 19(1)

Published: Feb. 27, 2020

The importance of mRNA methylation erased by ALKBH5 in biogenesis, decay, and translation control is an emerging research focus. Ectopically activated YAP associated with the development many human cancers. However, mechanism whereby regulates expression activity to inhibit NSCLC tumor growth metastasis not clear.Protein transcript interactions were analyzed normal lung cell cells. Gene was evaluated qPCR reporter assays. Protein levels determined immunochemical approaches. Nucleic acid status immunoprecipitation. Cell behavior standard biochemical tests. m6A modification MeRIP.Our results show that negatively correlated plays opposite role regulation cellular proliferation, invasion, migration, EMT reduced YAP. YTHDF3 combined pre-mRNA depending on modification. YTHDF1 YTHDF2 competitively interacted m6A-independent manner regulate expression. facilitated decay via AGO2 system, whereas promoted interacting eIF3a; both these activities are regulated Furthermore, decreased regulating miR-107/LATS2 axis HuR-dependent manner. Further, inhibited vivo reducing YAP.The presented findings suggest demethylase inhibits YTHDFs-mediated inhibiting miR-107/LATS2-mediated NSCLC. Moreover, effective inhibition might constitute a potential treatment strategy for cancer.

Language: Английский

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METTL3 regulates heterochromatin in mouse embryonic stem cells

Nature, Journal Year: 2021, Volume and Issue: 591(7849), P. 317 - 321

Published: Jan. 27, 2021

Language: Английский

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The m6A epitranscriptome: transcriptome plasticity in brain development and function

Nature reviews. Neuroscience, Journal Year: 2019, Volume and Issue: 21(1), P. 36 - 51

Published: Dec. 5, 2019

Language: Английский

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METTL3-mediated m ⁶ A modification of ATG7 regulates autophagy-GATA4 axis to promote cellular senescence and osteoarthritis progression

Annals of the Rheumatic Diseases, Journal Year: 2021, Volume and Issue: 81(1), P. 85 - 97

Published: Oct. 27, 2021

Objective The aim of the study was to investigate role and regulatory mechanisms fibroblast-like synoviocytes (FLSs) their senescence in progression osteoarthritis (OA). Methods Synovial tissues from normal patients with OA were collected. Synovium FLS analysed by immunofluorescence western blotting. methyltransferase-like 3 (METTL3) autophagy regulation explored using N6-methyladenosine (m 6 A)-methylated RNA immunoprecipitation assays. Mice subjected destabilisation medial meniscus (DMM) surgery intra-articularly injected or without pAAV9 loaded small interfering (siRNA) targeting METTL3. Histological analysis performed determine cartilage damage. Results Senescent FLSs markedly increased mouse models. We determined that impaired occurred OA-FLS, resulting upregulation senescence-associated secretory phenotype (SASP). Re-establishment reversed senescent suppressing GATA4. Further, we observed for first time excessive m A modification negatively regulated OA-FLS. Mechanistically, METTL3-mediated decreased expression autophagy-related 7, an E-1 enzyme crucial formation autophagosomes, attenuating its stability. Silencing METTL3 enhanced autophagic flux inhibited SASP Intra-articular injection synovium-targeted siRNA suppressed cellular propagation joints ameliorated DMM-induced destruction. Conclusions Our revealed important progression. Targeted inhibition could alleviate limit development experimental animal models, providing a potential strategy therapy.

Language: Английский

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Programmable m6A modification of cellular RNAs with a Cas13-directed methyltransferase

Nature Biotechnology, Journal Year: 2020, Volume and Issue: 38(12), P. 1431 - 1440

Published: June 29, 2020

Language: Английский

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Landscape and Regulation of m6A and m6Am Methylome across Human and Mouse Tissues

Molecular Cell, Journal Year: 2019, Volume and Issue: 77(2), P. 426 - 440.e6

Published: Oct. 30, 2019

Language: Английский

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m6A RNA methylation regulates the fate of endogenous retroviruses

Nature, Journal Year: 2021, Volume and Issue: 591(7849), P. 312 - 316

Published: Jan. 13, 2021

Language: Английский

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Biological roles of adenine methylation in RNA

Nature Reviews Genetics, Journal Year: 2022, Volume and Issue: 24(3), P. 143 - 160

Published: Oct. 19, 2022

Language: Английский

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