The Importance of Being RNA-est: considering RNA-mediated ribosome plasticity

References

• Melnikov S, Ben-Shem A, de LN, et al. One core, two shells: bacterial and eukaryotic ribosomes. Nat Struct Mol Biol. 2012;19(6):560–567.
   PubMed Web of Science ®Google Scholar
• Borovinskaya MA, Pai RD, Zhang W, et al. Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Nat Struct Mol Biol. 2007;14:727–732.
   PubMed Web of Science ®Google Scholar
• Ben-Shem A, de LN, Melnikov S, et al. The structure of the eukaryotic ribosome at 3.0 Å resolution. Science. 2011;334:1524–1529.
   PubMed Web of Science ®Google Scholar
• Khatter H, Myasnikov AG, Natchiar SK, et al. Structure of the human 80S ribosome. Nature. 2015;520:640–645.
   PubMed Web of Science ®Google Scholar
• Bowman JC, Petrov AS, Frenkel-Pinter M, et al. Root of the tree: the significance, evolution, and origins of the ribosome. Chem Rev. 2020;120(11):4848–4878.
   PubMed Web of Science ®Google Scholar
• Melnikov S, Manakongtreecheep K, Söll D. Revising the structural diversity of ribosomal proteins across the three domains of life. Mol Biol Evol. 2018;35(7):1588–1598.
   PubMed Web of Science ®Google Scholar
• Londei P, Ferreira-Cerca S. Ribosome biogenesis in Archaea. Front Microbiol. 2021;12:686977.
   PubMed Web of Science ®Google Scholar
• Ban N, Beckmann R, Cate JH, et al. A new system for naming ribosomal proteins. Curr Opin Struc Biol. 2014;24:165–169.
   PubMed Web of Science ®Google Scholar
• Gay DM, Lund AH, Jansson MD. Translational control through ribosome heterogeneity and functional specialization. Trends Biochem Sci. 2022;47(1):66–81.
   PubMed Web of Science ®Google Scholar
• Xue S, Barna M. Specialized ribosomes: a new frontier in gene regulation and organismal biology. Nat Rev Mol Cell Bio. 2012;13(6):355–369.
   PubMed Web of Science ®Google Scholar
• Kellis M, Birren BW, Lander ES. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 2004;428:617–624.
   PubMed Web of Science ®Google Scholar
• Bauer JW, Brandl C, Haubenreisser O, et al. Specialized yeast ribosomes: a customized tool for selective mRNA translation. PLoS ONE. 2013;8:e67609.
   PubMed Web of Science ®Google Scholar
• Ghulam MM, Catala M, Elela SA. Differential expression of duplicated ribosomal protein genes modifies ribosome composition in response to stress. Nucleic Acids Res. 2020;48(4):1954–1968.
   PubMed Web of Science ®Google Scholar
• Genuth NR, Barna M. The discovery of ribosome heterogeneity and its implications for gene regulation and organismal life. Mol Cell. 2018;71(3):364–374.
   PubMed Web of Science ®Google Scholar
• Gerst JE. Pimp my ribosome: ribosomal protein paralogs specify translational control. Trends Genet. 2018;34(11):832–845.
   PubMed Web of Science ®Google Scholar
• Petrov AS, Bernier CR, Hsiao C, et al. Evolution of the ribosome at atomic resolution. Proc Natl Acad Sci. 2014;111(28):10251–10256. DOI:10.1073/pnas.1407205111
   PubMed Web of Science ®Google Scholar
• Petrov AS, Gulen B, Norris AM, et al. History of the ribosome and the origin of translation. Proc Natl Acad Sci. 2015;112(50):15396–15401. DOI:10.1073/pnas.1509761112
   PubMed Web of Science ®Google Scholar
• Hariharan N, Ghosh S, Palakodeti D. The story of rRNA expansion segments: finding functionality amidst diversity. Wiley Interdiscip Rev RNA. 2023;14(1):e1732.
   PubMed Web of Science ®Google Scholar
• Norris K, Hopes T, Aspden JL. Ribosome heterogeneity and specialization in development. Wiley Interdiscip Rev RNA. 2021;12(4):e1644.
   PubMed Web of Science ®Google Scholar
• Li D, Wang J. Ribosome heterogeneity in stem cells and development. J Cell Bio. 2020;219(6):e202001108.
   PubMed Web of Science ®Google Scholar
• Simsek D, Tiu GC, Flynn RA, et al. The mammalian ribo-interactome reveals ribosome functional diversity and heterogeneity. Cell. 2017;169(6):1051–1065.e18.
   PubMed Web of Science ®Google Scholar
• Warner JR. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci. 1999;24(11):437–440.
   PubMed Web of Science ®Google Scholar
• Henras AK, Plisson‐chastang C, O’Donohue M, et al. An overview of pre‐ribosomal RNA processing in eukaryotes. Wiley Interdiscip Rev RNA. 2015;6(2):225–242.
   PubMed Web of Science ®Google Scholar
• Parks MM, Kurylo CM, Dass RA, et al. Variant ribosomal RNA alleles are conserved and exhibit tissue-specific expression. Sci Adv. 2018;4(2):eaao0665.
   PubMed Web of Science ®Google Scholar
• Parks MM, Kurylo CM, Batchelder JE, et al. Implications of sequence variation on the evolution of rRNA. Chromosome Res. 2019;27(1–2):89–93.
   PubMed Web of Science ®Google Scholar
• Leffers H, Andersen AH. The sequence of 28S ribosomal RNA varies within and between human cell lines. Nucleic Acids Res. 1993;21(6):1449–1455.
   PubMed Web of Science ®Google Scholar
• Gonzalez IL, Sylvester JE, Schmickel RD. Human 28S ribosomal RNA sequence heterogeneity. Nucleic Acids Res. 1988;16(21):10213–10224.
   PubMed Web of Science ®Google Scholar
• Babaian A. Intra- and Inter-individual genetic variation in human ribosomal RNAs. bioRxiv. 2017;118760. DOI:10.1101/118760
   Google Scholar
• Symonová R. Integrative rDnaomics—importance of the oldest repetitive fraction of the eukaryote genome. Genes-Basel. 2019;10:345.
   PubMed Web of Science ®Google Scholar
• Torres‐machorro AL, Hernández R, Cevallos AM, et al. Ribosomal RNA genes in eukaryotic microorganisms: witnesses of phylogeny? FEMS Microbiol Rev. 2010;34(1):59–86.
   PubMed Web of Science ®Google Scholar
• Eickbush TH, Eickbush DG. Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics. 2007;175:477–485.
   PubMed Web of Science ®Google Scholar
• Jüttner M, Ferreira-Cerca S, Battistuzzi FU. Looking through the lens of the ribosome biogenesis evolutionary history: possible implications for archaeal phylogeny and eukaryogenesis. Mol Biol Evol. 2022;39(4):msac054.
   PubMed Web of Science ®Google Scholar
• Wormington WM, Brown DD. Onset of 5 S RNA gene regulation during Xenopus embryogenesis. Dev Biol. 1983;99(1):248–257.
   PubMed Web of Science ®Google Scholar
• Brown DD. A tribute to the xenopus laevis oocyte and egg. J Biol Chem. 2004;279(44):45291–45299.
   PubMed Web of Science ®Google Scholar
• Locati MD, Pagano JFB, Girard G, et al. Expression of distinct maternal and somatic 5.8S, 18S, and 28S rRNA types during zebrafish development. RNA. 2017;23(8):1188–1199. DOI:10.1261/rna.061515.117
   PubMed Web of Science ®Google Scholar
• Locati MD, Pagano JFB, Ensink WA, et al. Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons. RNA. 2017;23(4):446–456. DOI:10.1261/rna.059642.116
   PubMed Web of Science ®Google Scholar
• Rogers MJ, Gutell RR, Damberger SH, et al. Structural features of the large subunit rRNA expressed in Plasmodium falciparum sporozoites that distinguish it from the asexually expressed subunit rRNA. Rna New York N Y. 1996;2(2):134–145.
   PubMed Web of Science ®Google Scholar
• Vembar SS, Droll D, Scherf A. Translational regulation in blood stages of the malaria parasite Plasmodium spp.: systems-wide studies pave the way. Wiley Interdiscip Rev RNA. 2016;7(6):772–792.
   PubMed Web of Science ®Google Scholar
• Biesiada M, Hu MY, Williams LD, et al. rRNA expansion segment 7 in eukaryotes: from signature fold to tentacles. Nucleic Acids Res. 2022;50(18):10717–10732.
   PubMed Web of Science ®Google Scholar
• Penev PI, Fakhretaha-Aval S, Patel VJ, et al. Supersized ribosomal RNA expansion segments in asgard archaea. Genome Biol Evol. 2020;12(10):1694–1710.
   PubMed Web of Science ®Google Scholar
• Fujii K, Susanto TT, Saurabh S, et al. Decoding the function of expansion segments in ribosomes. Mol Cell. 2018;72(6):1013–1020.e6.
   PubMed Web of Science ®Google Scholar
• Armache J-P, Jarasch A, Anger AM, et al. Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-Å resolution. Proc Natl Acad Sci. 2010;107(46):19748–19753. DOI:10.1073/pnas.1009999107
   PubMed Web of Science ®Google Scholar
• Ramos LMG, Smeekens JM, Kovacs NA, et al. Yeast rRNA expansion segments: folding and function. J Mol Biol. 2016;428(20):4048–4059.
   PubMed Web of Science ®Google Scholar
• Knorr AG, Schmidt C, Tesina P, et al. Ribosome–nata architecture reveals that rRNA expansion segments coordinate N-terminal acetylation. Nat Struct Mol Biol. 2019;26(1):35–39.
   PubMed Web of Science ®Google Scholar
• Jeeninga RE, Delft YV, de GVM, et al. Variable regions V13 and V3 of Saccharomyces cerevisiae contain structural features essential for normal biogenesis and stability of 5.8S and 25S rRNA. Rna New York N Y. 1997;3(5):476–488.
   PubMed Web of Science ®Google Scholar
• Ramesh M, Woolford JL. Eukaryote-specific rRNA expansion segments function in ribosome biogenesis. RNA. 2016;22:1153–1162.
   PubMed Web of Science ®Google Scholar
• Shedlovskiy D, Zinskie JA, Gardner E, et al. Endonucleolytic cleavage in the expansion segment 7 of 25S rRNA is an early marker of low-level oxidative stress in yeast. J Biol Chem. 2017;292(45):18469–18485.
   PubMed Web of Science ®Google Scholar
• Parker MS, Sallee FR, Park EA, et al. Homoiterons and expansion in ribosomal RNAs. FEBS Open Bio. 2015;5:864–876.
   PubMed Web of Science ®Google Scholar
• Pfeffer S, Brandt F, Hrabe T, et al. Structure and 3D arrangement of endoplasmic reticulum membrane-associated ribosomes. Structure. 2012;20:1508–1518.
   PubMed Web of Science ®Google Scholar
• Halic M, Becker T, Pool MR, et al. Structure of the signal recognition particle interacting with the elongation-arrested ribosome. Nature. 2004;427(6977):808–814.
   PubMed Web of Science ®Google Scholar
• Wild K, Aleksić M, Lapouge K, et al. MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments. Nat Commun. 2020;11(1):776.
   PubMed Web of Science ®Google Scholar
• Kraushar ML, Krupp F, Harnett D, et al. Protein Synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit. Mol Cell. 2021;81(2):304–322.e16. DOI:10.1016/j.molcel.2020.11.037
   PubMed Web of Science ®Google Scholar
• Pánek J, Kolář M, Vohradský J, et al. An evolutionary conserved pattern of 18S rRNA sequence complementarity to mRNA 5′ UTRs and its implications for eukaryotic gene translation regulation. Nucleic Acids Res. 2013;41(16):7625–7634.
   PubMed Web of Science ®Google Scholar
• Parker MS, Balasubramaniam A, Sallee FR, et al. The expansion segments of 28S ribosomal RNA extensively match human messenger RNAs. Frontiers Genetics. 2018;9:66.
   PubMed Web of Science ®Google Scholar
• Leppek K, Fujii K, Quade N, et al. Gene- and species-specific hox mRNA translation by ribosome expansion segments. Mol Cell. 2020;80(6):980–995.e13.
   PubMed Web of Science ®Google Scholar
• Leppek K, Byeon GW, Fujii K, et al. VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide. Cell Rep. 2021;34:108629.
   PubMed Web of Science ®Google Scholar
• Mallo M, Alonso CR. The regulation of Hox gene expression during animal development. Development. 2013;140:3951–3963.
   PubMed Web of Science ®Google Scholar
• Teixeira FK, Lehmann R. Translational control during developmental transitions. Csh Perspect Biol. 2019;11(6):a032987.
   PubMed Web of Science ®Google Scholar
• Taoka M, Nobe Y, Yamaki Y, et al. Landscape of the complete RNA chemical modifications in the human 80S ribosome. Nucleic Acids Res. 2018;46(18):gky811. DOI:10.1093/nar/gky811
   Web of Science ®Google Scholar
• Yip WSV, Vincent NG, Baserga SJ. Ribonucleoproteins in archaeal pre-Rrna processing and modification. Archaea. 2013;2013:614735.
   PubMed Web of Science ®Google Scholar
• Czekay DP, Kothe U. H/ACA small ribonucleoproteins: structural and functional comparison between archaea and eukaryotes. Front Microbiol. 2021;12:654370.
   PubMed Web of Science ®Google Scholar
• Breuer R, Gomes-Filho J-V, Randau L. Conservation of archaeal C/D box srna-guided RNA modifications. Front Microbiol. 2021;12:654029.
   PubMed Web of Science ®Google Scholar
• Polikanov YS, Melnikov SV, Söll D, et al. Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly. Nat Struct Mol Biol. 2015;22(4):342–344.
   PubMed Web of Science ®Google Scholar
• Lareau LF, Hite DH, Hogan GJ, et al. Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments. Elife. 2014;3:e01257.
   PubMed Web of Science ®Google Scholar
• Sas-Chen A, Thomas JM, Matzov D, et al. Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping. Nature. 2020;583(7817):638–643. DOI:10.1038/s41586-020-2418-2
   PubMed Web of Science ®Google Scholar
• Marchand V, Pichot F, Neybecker P, et al. HydraPsiSeq: a method for systematic and quantitative mapping of pseudouridines in RNA. Nucleic Acids Res. 2020;48(19):e110.
   PubMed Web of Science ®Google Scholar
• Marchand V, Ayadi L, Bourguignon-Igel V, et al. RNA modifications, methods and protocols. Methods Mol Biology Clifton N J. 2021;2298:77–95.
   PubMedGoogle Scholar
• Taoka M, Nobe Y, Hori M, et al. A mass spectrometry-based method for comprehensive quantitative determination of post-transcriptional RNA modifications: the complete chemical structure of Schizosaccharomyces pombe ribosomal RNAs. Nucleic Acids Res. 2015;43(18):e115.
   PubMed Web of Science ®Google Scholar
• Baudin-Baillieu A, Namy O. Saccharomyces cerevisiae, a powerful model for studying rRNA modifications and their effects on translation fidelity. Int J Mol Sci. 2021;22(14):7419.
   PubMed Web of Science ®Google Scholar
• Sloan KE, Warda AS, Sharma S, et al. Tuning the ribosome: the influence of rRNA modification on eukaryotic ribosome biogenesis and function. RNA Biol. 2016;14(9):1138–1152.
   PubMed Web of Science ®Google Scholar
• Taoka M, Nobe Y, Yamaki Y, et al. The complete chemical structure of Saccharomyces cerevisiae rRNA: partial pseudouridylation of U2345 in 25S rRNA by snoRNA snR9. Nucleic Acids Res. 2016;44(18):8951–8961.
   PubMed Web of Science ®Google Scholar
• Motorin Y, Quinternet M, Rhalloussi W, et al. Constitutive and variable 2’-O-methylation (Nm) in human ribosomal RNA. RNA Biol. 2021;18(sup1):88–97.
   PubMedGoogle Scholar
• Demirci H, Murphy F, Belardinelli R, et al. Modification of 16S ribosomal RNA by the KsgA methyltransferase restructures the 30S subunit to optimize ribosome function. RNA. 2010;16:2319–2324.
   PubMed Web of Science ®Google Scholar
• Desaulniers J-P, Chang Y-C, Aduri R, et al. Pseudouridines in rRNA helix 69 play a role in loop stacking interactions. Org Biomol Chem. 2008;6(21):3892–3895.
   PubMed Web of Science ®Google Scholar
• Sumita M, Jiang J, SantaLucia J, et al. Comparison of solution conformations and stabilities of modified helix 69 rRNA analogs from bacteria and human. Biopolymers. 2012;97:94–106.
   PubMed Web of Science ®Google Scholar
• King TH, Liu B, McCully RR, et al. Ribosome structure and activity are altered in cells lacking snoRnps that form pseudouridines in the peptidyl transferase center. Mol Cell. 2003;11(2):425–435.
   PubMed Web of Science ®Google Scholar
• Baxter-Roshek JL, Petrov AN, Dinman JD. Optimization of ribosome structure and function by rRNA base modification. PLoS ONE. 2007;2(1):e174.
   PubMed Web of Science ®Google Scholar
• Hirabayashi N, Sato NS, Suzuki T. Conserved loop sequence of helix 69 in Escherichia coli 23 S rRNA is involved in A-site tRNA binding and translational fidelity*. J Biol Chem. 2006;281(25):17203–17211.
   PubMed Web of Science ®Google Scholar
• Liang X, Liu Q, Fournier MJ. rRNA modifications in an intersubunit bridge of the ribosome strongly affect both ribosome biogenesis and activity. Mol Cell. 2007;28(6):965–977.
   PubMed Web of Science ®Google Scholar
• Baudin-Baillieu A, Fabret C, Liang X, et al. Nucleotide modifications in three functionally important regions of the Saccharomyces cerevisiae ribosome affect translation accuracy. Nucleic Acids Res. 2009;37(22):7665–7677.
   PubMed Web of Science ®Google Scholar
• Esguerra J, Warringer J, Blomberg A. Functional importance of individual rRNA 2′-O-ribose methylations revealed by high-resolution phenotyping. RNA. 2008;14:649–656.
   PubMed Web of Science ®Google Scholar
• Jansson M, Hafner S, Altinel K, et al. Ribosomal RNA methylation induced by MYC regulates translation. Nat Struct Mol Biol. 2021 Nov;28(11): 889–899. DOI:10.1038/s41594-021-00669- . Epub 2021 Nov 10. PMID: 34759377.
   PubMed Web of Science ®Google Scholar
• Piekna-Przybylska D, Przybylski P, Baudin-Baillieu A, et al. Ribosome performance is enhanced by a rich cluster of pseudouridines in the A-site finger region of the large subunit*. J Biol Chem. 2008;283(38):26026–26036.
   PubMed Web of Science ®Google Scholar
• Koh CM, Gurel B, Sutcliffe S, et al. Alterations in nucleolar structure and gene expression programs in prostatic neoplasia are driven by the MYC oncogene. Am J Pathol. 2011;178(4):1824–1834. DOI:10.1016/j.ajpath.2010.12.040
   PubMed Web of Science ®Google Scholar
• Marcel V, Ghayad SE, Belin S, et al. P53 acts as a safeguard of translational control by regulating fibrillarin and rRNA methylation in cancer. Cancer Cell. 2013;24(3):318–330. DOI:10.1016/j.ccr.2013.08.013
   PubMed Web of Science ®Google Scholar
• Su H, Xu T, Ganapathy S, et al. Elevated snoRNA biogenesis is essential in breast cancer. Oncogene. 2014;33:1348–1358.
   PubMed Web of Science ®Google Scholar
• Belin S, Beghin A, Solano-Gonzàlez E, et al. Dysregulation of ribosome biogenesis and translational capacity is associated with tumor progression of human breast cancer cells. PLoS ONE. 2009;4(9):e7147.
   PubMed Web of Science ®Google Scholar
• Janin M, Coll-SanMartin L, Esteller M. Disruption of the RNA modifications that target the ribosome translation machinery in human cancer. Mol Cancer. 2020;19(1):70.
   PubMed Web of Science ®Google Scholar
• Sharma S, Marchand V, Motorin Y, et al. Identification of sites of 2′-O-methylation vulnerability in human ribosomal RNAs by systematic mapping. Sci Rep-UK. 2017;7(1):11490.
   PubMedGoogle Scholar
• Garus A, Autexier AC. Dyskerin: an essential pseudouridine synthase with multifaceted roles in ribosome biogenesis, splicing, and telomere maintenance. RNA. 2021;27(12):rna.078953.121.
   PubMedGoogle Scholar
• Penzo M, Rocchi L, Brugiere S, et al. Human ribosomes from cells with reduced dyskerin levels are intrinsically altered in translation. Faseb J. 2015;29(8):3472–3482.
   PubMed Web of Science ®Google Scholar
• Babaian A, Rothe K, Girodat D, et al. Loss of m1acp3Ψ ribosomal RNA modification is a major feature of cancer. Cell Rep. 2020;31:107611.
   PubMed Web of Science ®Google Scholar
• Schosserer M, Minois N, Angerer TB, et al. Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan. Nat Commun. 2015;6(1):6158. DOI:10.1038/ncomms7158
   PubMedGoogle Scholar
• Heissenberger C, Liendl L, Nagelreiter F, et al. Loss of the ribosomal RNA methyltransferase NSUN5 impairs global protein synthesis and normal growth. Nucleic Acids Res. 2019;47(22):11807–11825. DOI:10.1093/nar/gkz1043
   PubMed Web of Science ®Google Scholar
• Janin M, Ortiz-Barahona V, de MM, et al. Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program. Acta Neuropathol. 2019;138(6):1053–1074. DOI:10.1007/s00401-019-02062-4
   PubMed Web of Science ®Google Scholar
• Liberman N, O’Brown ZK, Earl AS, et al. N6-adenosine methylation of ribosomal RNA affects lipid oxidation and stress resistance. Sci Adv. 2020;6(17):eaaz4370. DOI:10.1126/sciadv.aaz4370
   PubMed Web of Science ®Google Scholar
• Liu K, Santos DA, Hussmann JA, et al. Regulation of translation by methylation multiplicity of 18S rRNA. Cell Rep. 2021;34:108825.
   PubMed Web of Science ®Google Scholar
• Chen H, Liu Q, Yu D, et al. METTL5, an 18S rRNA-specific m6A methyltransferase, modulates expression of stress response genes. bioRxiv. 2020;1–44. DOI:10.1101/2020.04.27.064162
   Google Scholar
• Lafontaine D, Delcour J, Glasser AL, et al. The DIM1 gene responsible for the conserved m62Am62A dimethylation in the 3′-terminal loop of 18 S rRNA is essential in yeast. J Mol Biol. 1994;241(3):492–497.
   PubMed Web of Science ®Google Scholar
• Ramachandran S, Krogh N, Jørgensen TE, et al. The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2′-O-Me sites. RNA. 2020;26:1919–1934.
   PubMed Web of Science ®Google Scholar
• Hebras J, Krogh N, Marty V, et al. Developmental changes of rRNA ribose methylations in the mouse. RNA Biol. 2020;17(1):150–164.
   PubMed Web of Science ®Google Scholar
• Higa-Nakamine S, Suzuki T, Uechi T, et al. Loss of ribosomal RNA modification causes developmental defects in zebrafish. Nucleic Acids Res. 2012;40(1):391–398.
   PubMed Web of Science ®Google Scholar
• Jacq B. Sequence homologies between eukaryotic 5.8S rRNA and the 5′ end of prokaryotic 23S rRNA: evidences for a common evolutionary origin. Nucleic Acids Res. 1981;9(12):2913–2932.
   PubMed Web of Science ®Google Scholar
• Consortium TR, Sweeney BA, Petrov AI, et al. Rnacentral: a hub of information for non-coding RNA sequences. Nucleic Acids Res. 2018;47:gky1206.
   Web of Science ®Google Scholar
• Wang M, Parshin AV, Shcherbik N, et al. Reduced expression of the mouse ribosomal protein Rpl17 alters the diversity of mature ribosomes by enhancing production of shortened 5.8S rRNA. RNA. 2015;21:1240–1248.
   PubMed Web of Science ®Google Scholar
• Rubin GM. Three forms of the 5.8‐S ribosomal RNA species in Saccharomyces cerevisiae. Eur J Biochem. 1974;41(1):197–202.
   PubMedGoogle Scholar
• Henry Y, Wood H, Morrissey JP, et al. The 5′ end of yeast 5.8S rRNA is generated by exonucleases from an upstream cleavage site. Embo J. 1994;13(10):2452–2463.
   PubMed Web of Science ®Google Scholar
• Venturi G, Zacchini F, Vaccari CL, et al. Primer extension coupled with fragment analysis for rapid and quantitative evaluation of 5.8S rRNA isoforms. PLoS ONE. 2021;16:e0261476.
   PubMed Web of Science ®Google Scholar
• Oeffinger M, Zenklusen D, Ferguson A, et al. Rrp17p is a eukaryotic exonuclease required for 5′ end processing of pre-60S ribosomal RNA. Mol Cell. 2009;36(5):768–781.
   PubMed Web of Science ®Google Scholar
• Faber AW, Vos HR, Vos JC, et al. 5′-end formation of yeast 5.8SL rRNA is an endonucleolytic event. Biochem Biophys Res Commun. 2006;345(2):796–802.
   PubMed Web of Science ®Google Scholar
• Allmang C, Henry Y, Morrissey JP, et al. Processing of the yeast pre-Rrna at sites A(2) and A(3) is linked. Rna New York N Y. 1996;2(1):63–73.
   PubMed Web of Science ®Google Scholar
• Schmitt ME, Clayton DA. Nuclear RNase MRP is required for correct processing of pre-5.8S rRNA in Saccharomyces cerevisiae. Mol Cell Biol. 1993;13(12):7935–7941.
   PubMed Web of Science ®Google Scholar
• Chu S, Archer RH, Zengel JM, et al. The RNA of RNase MRP is required for normal processing of ribosomal RNA. Proc Natl Acad Sci. 1994;91(2):659–663.
   PubMed Web of Science ®Google Scholar
• Wang M, Pestov DG. 5′-end surveillance by Xrn2 acts as a shared mechanism for mammalian pre-Rrna maturation and decay. Nucleic Acids Res. 2011;39(5):1811–1822.
   PubMed Web of Science ®Google Scholar
• Sloan KE, Mattijssen S, Lebaron S, et al. Both endonucleolytic and exonucleolytic cleavage mediate ITS1 removal during human ribosomal RNA processing. J Cell Biol. 2013;200(5):577–588.
   PubMed Web of Science ®Google Scholar
• Li X, Zengel JM, Lindahl L. A novel model for the RNase MRP-Induced switch between the formation of different forms of 5.8S rRNA. Int J Mol Sci. 2021;22(13):6690.
   PubMed Web of Science ®Google Scholar
• Eppens NA, Faber AW, Rondaij M, et al. Deletions in the S1 domain of Rrp5p cause processing at a novel site in ITS1 of yeast pre‐rRNA that depends on Rex4p. Nucleic Acids Res. 2002;30:4222–4231.
   PubMed Web of Science ®Google Scholar
• Aubert M, O’Donohue M-F, Lebaron S, et al. Pre-ribosomal RNA processing in human cells: from mechanisms to congenital diseases. Biomol. 2018;8:123.
   Google Scholar
• Decatur WA, Schnare MN. Different mechanisms for pseudouridine formation in yeast 5S and 5.8S rRnas. Mol Cell Biol. 2008;28:3089–3100.
   PubMed Web of Science ®Google Scholar
• Mauro VP, Edelman GM. The ribosome filter hypothesis. Proc Natl Acad Sci. 2002;99:12031–12036.
   PubMed Web of Science ®Google Scholar
• Mauro VP, Edelman GM. The ribosome filter redux. Cell Cycle Georget Tex. 2007;6:2246–2251.
   PubMed Web of Science ®Google Scholar
• Ferretti MB, Karbstein K. Does functional specialization of ribosomes really exist? Rna New York N Y. 2019;25:521–538.
   PubMed Web of Science ®Google Scholar
• Shigeoka T, Koppers M, Wong H-W, et al. On-site ribosome remodeling by locally synthesized ribosomal proteins in axons. Cell Rep. 2019;29:3605–3619.e10.
   PubMed Web of Science ®Google Scholar