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Membrane linked RNA glycosylation as new trend to envision epi-transcriptome epoch

  • 1.

    Murn J, Shi Y. The winding path of protein methylation research: milestones and new frontiers. Nat Rev Mol Cell Biol. 2017;18:517–27.

    CAS 
    PubMed 

    Google Scholar 

  • 2.

    Narita T, Weinert BT, Choudhary C. Author Correction: Functions and mechanisms of non-histone protein acetylation. Nat Rev Mol Cell Biol. 2019;20:508.

    CAS 
    PubMed 

    Google Scholar 

  • 3.

    Cohen P. The origins of protein phosphorylation. Nat Cell Biol. 2002;4:E127–30.

    CAS 
    PubMed 

    Google Scholar 

  • 4.

    Swatek KN, Komander D. Ubiquitin modifications. Cell Res. 2016;26:399–422.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 5.

    Spicer CD, Davis BG. Selective chemical protein modification. Nat Commun. 2014;5:4740.

    CAS 
    PubMed 

    Google Scholar 

  • 6.

    Schubeler D. Function and information content of DNA methylation. Nature. 2015;517:321–6.

    CAS 
    PubMed 

    Google Scholar 

  • 7.

    Wyatt GR. Occurrence of 5-methylcytosine in nucleic acids. Nature. 1950;166:237–8.

    CAS 
    PubMed 

    Google Scholar 

  • 8.

    Adams JM, Cory S. Modified nucleosides and bizarre 5’-termini in mouse myeloma mRNA. Nature. 1975;255:28–33.

    CAS 
    PubMed 

    Google Scholar 

  • 9.

    Perry RP, Kelley DE, Friderici K, Rottman F. The methylated constituents of L cell messenger RNA: evidence for an unusual cluster at the 5’ terminus. Cell. 1975;4:387–94.

    CAS 
    PubMed 

    Google Scholar 

  • 10.

    Roundtree IA, Evans ME, Pan T, He C. Dynamic RNA modifications in gene expression regulation. Cell. 2017;169:1187–1200.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 11.

    Norbury CJ. Cytoplasmic RNA: a case of the tail wagging the dog. Nat Rev Mol Cell Biol. 2013;14:643–53.

    CAS 
    PubMed 

    Google Scholar 

  • 12.

    Chang H, Lim J, Ha M, Kim VN. TAIL-seq: genome-wide determination of poly(A) tail length and 3’ end modifications. Mol Cell. 2014;53:1044–52.

    CAS 
    PubMed 

    Google Scholar 

  • 13.

    Sierant M, Leszczynska G, Sadowska K, Komar P, Radzikowska-Cieciura E, Sochacka E, et al. Escherichia coli tRNA 2-selenouridine synthase (SelU) converts S2U-RNA to Se2U-RNA via S-geranylated-intermediate. FEBS Lett. 2018;592:2248–58.

    CAS 
    PubMed 

    Google Scholar 

  • 14.

    Kasai H, Nakanishi K, Macfarlane RD, Torgerson DF, Ohashi Z, McCloskey JA, et al. Letter: The structure of Q* nucleoside isolated from rabbit liver transfer ribonucleic acid. J Am Chem Soc. 1976;98:5044–6.

    CAS 
    PubMed 

    Google Scholar 

  • 15.

    Sinha KM, Gu J, Chen Y, Reddy R. Adenylation of small RNAs in human cells. Development of a cell-free system for accurate adenylation on the 3’-end of human signal recognition particle RNA. J Biol Chem. 1998;273:6853–9.

    CAS 
    PubMed 

    Google Scholar 

  • 16.

    Mullen TE, Marzluff WF. Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5’ to 3’ and 3’ to 5’. Genes Dev. 2008;22:50–65.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 17.

    Rissland OS, Norbury CJ. Decapping is preceded by 3’ uridylation in a novel pathway of bulk mRNA turnover. Nat Struct Mol Biol. 2009;16:616–23.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 18.

    Yoluc Y, Ammann G, Barraud P, Jora M, Limbach PA, Motorin Y, et al. Instrumental analysis of RNA modifications. Crit Rev Biochem Mol Biol. 2021;56:178–204.

    CAS 
    PubMed 

    Google Scholar 

  • 19.

    Luo X, Li H, Liang J, Zhao Q, Xie Y, Ren J, et al. RMVar: an updated database of functional variants involved in RNA modifications. Nucleic Acids Res. 2021;49:D1405–D1412.

    CAS 
    PubMed 

    Google Scholar 

  • 20.

    Boccaletto P, Machnicka MA, Purta E, Piatkowski P, Baginski B, Wirecki TK, et al. MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Res. 2018;46:D303–D307.

    CAS 
    PubMed 

    Google Scholar 

  • 21.

    Rottman F, Shatkin AJ, Perry RP. Sequences containing methylated nucleotides at the 5’ termini of messenger RNAs: possible implications for processing. Cell. 1974;3:197–9.

    CAS 
    PubMed 

    Google Scholar 

  • 22.

    Liu N, Dai Q, Zheng G, He C, Parisien M, Pan T. N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature. 2015;518:560–4.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 23.

    Alarcon CR, Goodarzi H, Lee H, Liu X, Tavazoie S, Tavazoie SF. HNRNPA2B1 is a mediator of m(6)A-dependent nuclear RNA processing events. Cell. 2015;162:1299–308.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 24.

    Kawai G, Yamamoto Y, Kamimura T, Masegi T, Sekine M, Hata T, et al. Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2’-hydroxyl group. Biochemistry. 1992;31:1040–6.

    CAS 
    PubMed 

    Google Scholar 

  • 25.

    Sheng J, Zhang W, Hassan AE, Gan J, Soares AS, Geng S, et al. Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone. Nucleic Acids Res. 2012;40:8111–8.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 26.

    Taoka M, Nobe Y, Yamaki Y, Sato K, Ishikawa H, Izumikawa K, et al. Landscape of the complete RNA chemical modifications in the human 80S ribosome. Nucleic Acids Res. 2018;46:9289–98.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 27.

    Kim YK, Heo I, Kim VN. Modifications of small RNAs and their associated proteins. Cell. 2010;143:703–9.

    CAS 
    PubMed 

    Google Scholar 

  • 28.

    Karijolich J, Yu YT. Spliceosomal snRNA modifications and their function. RNA Biol. 2010;7:192–204.

    CAS 
    PubMed 

    Google Scholar 

  • 29.

    Trixl L, Lusser A. The dynamic RNA modification 5-methylcytosine and its emerging role as an epitranscriptomic mark. Wiley Interdiscip Rev RNA. 2019;10:e1510.

    PubMed 

    Google Scholar 

  • 30.

    Keffer-Wilkes LC, Soon EF, Kothe U. The methyltransferase TrmA facilitates tRNA folding through interaction with its RNA-binding domain. Nucleic Acids Res. 2020;48:7981–90.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 31.

    Di Timoteo G, Dattilo D, Centron-Broco A, Colantoni A, Guarnacci M, Rossi F, et al. Modulation of circRNA Metabolism by m(6)A Modification. Cell Rep. 2020;31:107641.

    PubMed 

    Google Scholar 

  • 32.

    Yang Y, Fan X, Mao M, Song X, Wu P, Zhang Y, et al. Extensive translation of circular RNAs driven by N(6)-methyladenosine. Cell Res. 2017;27:626–41.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 33.

    Chen YG, Chen R, Ahmad S, Verma R, Kasturi SP, Amaya L, et al. N6-methyladenosine modification controls circular RNA immunity. Mol Cell. 2019;76:96–109 e9.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 34.

    Okada N, Nishimura S. Enzymatic synthesis of Q nucleoside containing mannose in the anticodon of tRNA: isolation of a novel mannosyltransferase from a cell-free extract of rat liver. Nucleic Acids Res. 1977;4:2931–8.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 35.

    Flynn RA, Pedram K, Malaker SA, Batista PJ, Smith BAH, Johnson AG, et al. Small RNAs are modified with N-glycans and displayed on the surface of living cells. Cell. 2021;184:3109–24 e22.

    CAS 
    PubMed 

    Google Scholar 

  • 36.

    Tarentino AL, Plummer TH Jr. Enzymatic deglycosylation of asparagine-linked glycans: purification, properties, and specificity of oligosaccharide-cleaving enzymes from Flavobacterium meningosepticum. Methods Enzymol. 1994;230:44–57.

    CAS 
    PubMed 

    Google Scholar 

  • 37.

    Duan S, Paulson JC. Siglecs as immune cell checkpoints in disease. Annu Rev Immunol. 2020;38:365–95.

    CAS 
    PubMed 

    Google Scholar 

  • 38.

    Macauley MS, Crocker PR, Paulson JC. Siglec-mediated regulation of immune cell function in disease. Nat Rev Immunol. 2014;14:653–66.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 39.

    Chang YC, Nizet V. Siglecs at the host-pathogen interface. Adv Exp Med Biol. 2020;1204:197–214.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 40.

    Fraschilla I, Pillai S. Viewing Siglecs through the lens of tumor immunology. Immunol Rev. 2017;276:178–91.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 41.

    Stanczak MA, Siddiqui SS, Trefny MP, Thommen DS, Boligan KF, von Gunten S, et al. Self-associated molecular patterns mediate cancer immune evasion by engaging Siglecs on T cells. J Clin Investig. 2018;128:4912–23.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 42.

    Flores R, Zhang P, Wu W, Wang X, Ye P, Zheng P, et al. Siglec genes confer resistance to systemic lupus erythematosus in humans and mice. Cell Mol Immunol. 2019;16:154–64.

    CAS 
    PubMed 

    Google Scholar 

  • 43.

    Angata T. Associations of genetic polymorphisms of Siglecs with human diseases. Glycobiology. 2014;24:785–93.

    CAS 
    PubMed 

    Google Scholar 

  • 44.

    Wang Y, Neumann H. Alleviation of neurotoxicity by microglial human Siglec-11. J Neurosci. 2010;30:3482–8.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 45.

    Tsai CM, Riestra AM, Ali SR, Fong JJ, Liu JZ, Hughes G, et al. Siglec-14 enhances NLRP3-inflammasome activation in macrophages. J innate Immun. 2020;12:333–43.

    CAS 
    PubMed 

    Google Scholar 

  • 46.

    Liu YC, Yu MM, Chai YF, Shou ST. Sialic acids in the immune response during sepsis. Front Immunol. 2017;8:1601.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 47.

    Huang N, Fan X, Zaleta-Rivera K, Nguyen TC, Zhou J, Luo Y, et al. Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction. Genome Biol. 2020;21:225.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 48.

    Janas T, Yarus M. Visualization of membrane RNAs. RNA. 2003;9:1353–61.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 49.

    Morozkin ES, Laktionov PP, Rykova EY, Vlassov VV. Extracellular nucleic acids in cultures of long-term cultivated eukaryotic cells. Ann N. Y Acad Sci. 2004;1022:244–9.

    CAS 
    PubMed 

    Google Scholar 

  • 50.

    Block KF, Puerta-Fernandez E, Wallace JG, Breaker RR. Association of OLE RNA with bacterial membranes via an RNA-protein interaction. Mol Microbiol. 2011;79:21–34.

    CAS 
    PubMed 

    Google Scholar 

  • 51.

    Janas T, Janas T, Yarus M. Human tRNA(Sec) associates with HeLa membranes, cell lipid liposomes, and synthetic lipid bilayers. RNA. 2012;18:2260–8.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 52.

    Lin A, Hu Q, Li C, Xing Z, Ma G, Wang C, et al. The LINK-A lncRNA interacts with PtdIns(3,4,5)P3 to hyperactivate AKT and confer resistance to AKT inhibitors. Nat Cell Biol. 2017;19:238–51.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 53.

    Hirschberg CB, Snider MD. Topography of glycosylation in the rough endoplasmic reticulum and Golgi apparatus. Annu Rev Biochem. 1987;56:63–87.

    CAS 
    PubMed 

    Google Scholar 

  • 54.

    Aebi M. N-linked protein glycosylation in the ER. Bioch et Biophys Acta. 2013;1833:2430–7.

    CAS 

    Google Scholar 

  • 55.

    Hirschberg CB, Robbins PW, Abeijon C. Transporters of nucleotide sugars, ATP, and nucleotide sulfate in the endoplasmic reticulum and Golgi apparatus. Annu Rev Biochem. 1998;67:49–69.

    CAS 
    PubMed 

    Google Scholar 

  • 56.

    Gandini R, Reichenbach T, Tan TC, Divne C. Structural basis for dolichylphosphate mannose biosynthesis. Nat Commun. 2017;8:120.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 57.

    Moremen KW, Tiemeyer M, Nairn AV. Vertebrate protein glycosylation: diversity, synthesis and function. Nat Rev Mol Cell Biol. 2012;13:448–62.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 58.

    Helm M. Post-transcriptional nucleotide modification and alternative folding of RNA. Nucleic Acids Res. 2006;34:721–33.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 59.

    Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell. 1982;31:147–57.

    CAS 
    PubMed 

    Google Scholar 

  • 60.

    Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell. 1983;35:849–57.

    CAS 
    PubMed 

    Google Scholar 

  • 61.

    Chan CT, Pang YL, Deng W, Babu IR, Dyavaiah M, Begley TJ, et al. Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. Nat Commun. 2012;3:937.

    PubMed 

    Google Scholar 

  • 62.

    Begley U, Dyavaiah M, Patil A, Rooney JP, DiRenzo D, Young CM, et al. Trm9-catalyzed tRNA modifications link translation to the DNA damage response. Mol Cell. 2007;28:860–70.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 63.

    Endres L, Dedon PC, Begley TJ. Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses. RNA Biol. 2015;12:603–14.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 64.

    Nachtergaele S, Krishnan Y. New Vistas for Cell-Surface GlycoRNAs. N. Engl J Med. 2021;385:658–60.

    PubMed 

    Google Scholar 

  • 65.

    Silsirivanit A. Glycosylation markers in cancer. Adv Clin Chem. 2019;89:189–213.

    CAS 
    PubMed 

    Google Scholar 

  • 66.

    Narayanan S. Sialic acid as a tumor marker. Ann Clin Lab Sci. 1994;24:376–84.

    CAS 
    PubMed 

    Google Scholar 

  • 67.

    Boligan KF, Mesa C, Fernandez LE, von Gunten S. Cancer intelligence acquired (CIA): tumor glycosylation and sialylation codes dismantling antitumor defense. Cell Mol Life Sci. 2015;72:1231–48.

    CAS 
    PubMed 

    Google Scholar 

  • 68.

    Pinho SS, Reis CA. Glycosylation in cancer: mechanisms and clinical implications. Nat Rev Cancer. 2015;15:540–55.

    CAS 
    PubMed 

    Google Scholar 

  • 69.

    Tkach M, Thery C. Communication by extracellular vesicles: where we are and where we need to go. Cell. 2016;164:1226–32.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 70.

    Robertson JD. Membrane structure. J Cell Biol. 1981;91:189s–204s.

    CAS 
    PubMed 

    Google Scholar 

  • 71.

    Singer SJ, Nicolson GL. The fluid mosaic model of the structure of cell membranes. Science. 1972;175:720–31.

    CAS 
    PubMed 

    Google Scholar 

  • 72.

    Lombard J. Once upon a time the cell membranes: 175 years of cell boundary research. Biol Direct. 2014;9:32.

    PubMed 
    PubMed Central 

    Google Scholar 

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