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An Examination of Mechanisms by which Synonymous Mutations may Alter Protein Levels, Structure and Functions

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Single Nucleotide Polymorphisms

Abstract

In this chapter, we review mechanisms by which synonymous codon variations influence gene expression at the mRNA or protein levels. These changes may alter the structure and function of the encoded proteins, leading to diseases, altered disease phenotype, or interfering with protein-drug interactions. In order to appreciate the significance of synonymous mutations, we first look at the concept of codon redundancy and the steps of protein biogenesis which can be influenced by synonymous codon variations.

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References

  • Adzhubei AA, Adzhubei IA, Krasheninnikov IA, Neidle S (1996) Non-random usage of ‘degenerate’ codons is related to protein three-dimensional structure. FEBS Lett 399:78–82

    CAS  Google Scholar 

  • Ahner A, Gong X, Frizzell RA (2013) Cystic fibrosis transmembrane conductance regulator degradation: cross-talk between the ubiquitylation and SUMOylation pathways. FEBS J 280:4430–4438

    CAS  Google Scholar 

  • Antunes D, Jorge NAN, Caffarena ER, Passetti F (2017) Using RNA sequence and structure for the prediction of riboswitch aptamer: a comprehensive review of available software and tools. Front Genet 8:231

    Google Scholar 

  • Austin F, Oyarbide U, Massey G, Grimes M, Corey SJ (2017) Synonymous mutation in TP53 results in a cryptic splice site affecting its DNA-binding site in an adolescent with two primary sarcomas. Pediatr Blood Cancer 64

    Google Scholar 

  • Bali V, Lazrak A, Guroji P, Fu L, Matalon S, Bebok Z (2016a) A synonymous codon change alters the drug sensitivity of DeltaF508 cystic fibrosis transmembrane conductance regulator. FASEB J 30:201–213

    CAS  Google Scholar 

  • Bali V, Lazrak A, Guroji P, Matalon S, Bebok Z (2016b) Mechanistic approaches to improve correction of the most common disease-causing mutation in cystic fibrosis. PLoS One 11:e0155882

    Google Scholar 

  • Bampi GB, Ramalho AS, Santos LA, Wagner J, Dupont L, Cuppens H, De Boeck K, Ignatova Z (2020) The effect of synonymous single-nucleotide polymorphisms on an atypical cystic fibrosis clinical presentation. Life (Basel) 11

    Google Scholar 

  • Barrett LW, Fletcher S, Wilton SD (2012) Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements. Cell Mol Life Sci 69:3613–3634

    CAS  Google Scholar 

  • Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215–233

    CAS  Google Scholar 

  • Bartel DP (2018) Metazoan microRNAs. Cell 173:20–51

    CAS  Google Scholar 

  • Bartoszewski RA, Jablonsky M, Bartoszewska S, Stevenson L, Dai Q, Kappes J, Collawn JF, Bebok Z (2010) A synonymous single nucleotide polymorphism in DeltaF508 CFTR alters the secondary structure of the mRNA and the expression of the mutant protein. J Biol Chem 285:28741–28748

    CAS  Google Scholar 

  • Bartoszewski R, Kroliczewski J, Piotrowski A, Jasiecka AJ, Bartoszewska S, Vecchio-Pagan B, Fu L, Sobolewska A, Matalon S, Cutting GR, Rowe SM, Collawn JF (2016) Codon bias and the folding dynamics of the cystic fibrosis transmembrane conductance regulator. Cell Mol Biol Lett 21:23

    Google Scholar 

  • Bebok Z, Lianwu F (2018) Stressors and Stress responses in Cystic Fibrosis. Cell Pathology 5:11–29. https://doi.org/10.1515/ersc-2018-0002

    Article  Google Scholar 

  • Bebok Z, Tousson A, Schwiebert LM, Venglarik CJ (2001) Improved oxygenation promotes CFTR maturation and trafficking in MDCK monolayers. Am J Physiol Cell Physiol 280:C135–C145

    CAS  Google Scholar 

  • Bebok Z, Varga K, Hicks JK, Venglarik CJ, Kovacs T, Chen L, Hardiman KM, Collawn JF, Sorscher EJ, Matalon S (2002) Reactive oxygen nitrogen species decrease cystic fibrosis transmembrane conductance regulator expression and cAMP-mediated Cl- secretion in airway epithelia. J Biol Chem 277:43041–43049

    CAS  Google Scholar 

  • Berg OG, Kurland CG (1997) Growth rate-optimised tRNA abundance and codon usage. J Mol Biol 270:544–550

    CAS  Google Scholar 

  • Berg MD, Giguere DJ, Dron JS, Lant JT, Genereaux J, Liao C, Wang J, Robinson JF, Gloor GB, Hegele RA, O’Donoghue P, Brandl CJ (2019) Targeted sequencing reveals expanded genetic diversity of human transfer RNAs. RNA Biol 16:1574–1585

    Google Scholar 

  • Blount A, Zhang S, Chestnut M, Hixon B, Skinner D, Sorscher EJ, Woodworth BA (2011) Transepithelial ion transport is suppressed in hypoxic sinonasal epithelium. Laryngoscope 121:1929–1934

    CAS  Google Scholar 

  • Brest P, Lapaquette P, Souidi M, Lebrigand K, Cesaro A, Vouret-Craviari V, Mari B, Barbry P, Mosnier JF, Hebuterne X, Harel-Bellan A, Mograbi B, Darfeuille-Michaud A, Hofman P (2011) A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn’s disease. Nat Genet 43:242–245

    CAS  Google Scholar 

  • Brini E, Simmerling C, Dill K (2020) Protein storytelling through physics. Science 370

    Google Scholar 

  • Bruijn LI, Becher MW, Lee MK, Anderson KL, Jenkins NA, Copeland NG, Sisodia SS, Rothstein JD, Borchelt DR, Price DL, Cleveland DW (1997) ALS-linked SOD1 mutant G85R mediates damage to astrocytes and promotes rapidly progressive disease with SOD1-containing inclusions. Neuron 18:327–338

    CAS  Google Scholar 

  • Buhr F, Jha S, Thommen M, Mittelstaet J, Kutz F, Schwalbe H, Rodnina MV, Komar AA (2016) Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations. Mol Cell 61:341–351

    CAS  Google Scholar 

  • Canson D, Glubb D, Spurdle AB (2020) Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: strategies to enhance bioinformatic prediction using hereditary cancer genes as exemplars. Hum Mutat 41

    Google Scholar 

  • Cardozo AK, De Meirleir L, Liebaers I, Lissens W (2000) Analysis of exonic mutations leading to exon skipping in patients with pyruvate dehydrogenase E1 alpha deficiency. Pediatr Res 48:748–753

    CAS  Google Scholar 

  • Carrocci TJ, Neugebauer KM (2019) Pre-mRNA Splicing in the Nuclear Landscape. Cold Spring Harb Symp Quant Biol 84:11–20

    Google Scholar 

  • Cassaignau AME, Cabrita LD, Christodoulou J (2020) How does the ribosome fold the proteome? Annu Rev Biochem 89:389–415

    CAS  Google Scholar 

  • Chao HK, Hsiao KJ, Su TS (2001) A silent mutation induces exon skipping in the phenylalanine hydroxylase gene in phenylketonuria. Hum Genet 108:14–19

    CAS  Google Scholar 

  • Cheng SH, Gregory RJ, Marshall J, Paul S, Souza DW, White GA, O’Riordan CR, Smith AE (1990) Defective intracellular transport and processing of CFTR is the molecular basis of most cystic fibrosis. Cell 63:827–834

    CAS  Google Scholar 

  • Claverie-Martin F, Gonzalez-Paredes FJ, Ramos-Trujillo E (2015) Splicing defects caused by exonic mutations in PKD1 as a new mechanism of pathogenesis in autosomal dominant polycystic kidney disease. RNA Biol 12:369–374

    Google Scholar 

  • Cleveland DW, Rothstein JD (2001) From Charcot to Lou Gehrig: deciphering selective motor neuron death in ALS. Nat Rev Neurosci 2:806–819

    CAS  Google Scholar 

  • Collart MA, Weiss B (2020) Ribosome pausing, a dangerous necessity for co-translational events. Nucleic Acids Res 48:1043–1055

    CAS  Google Scholar 

  • Cutting GR (2015) Cystic fibrosis genetics: from molecular understanding to clinical application. Nat Rev Genet 16:45–56

    CAS  Google Scholar 

  • Czech A, Fedyunin I, Zhang G, Ignatova Z (2010) Silent mutations in sight: co-variations in tRNA abundance as a key to unravel consequences of silent mutations. Mol Biosyst 6:1767–1772

    CAS  Google Scholar 

  • De Meirleir L, Lissens W, Benelli C, Ponsot G, Desguerre I, Marsac C, Rodriguez D, Saudubray JM, Poggi F, Liebaers I (1994) Aberrant splicing of exon 6 in the pyruvate dehydrogenase-E1 alpha mRNA linked to a silent mutation in a large family with Leigh’s encephalomyelopathy. Pediatr Res 36:707–712

    CAS  Google Scholar 

  • Dhindsa RS, Copeland BR, Mustoe AM, Goldstein DB (2020) Natural selection shapes codon usage in the human genome. Am J Hum Genet 107:83–95

    CAS  Google Scholar 

  • Diatchenko L, Slade GD, Nackley AG, Bhalang K, Sigurdsson A, Belfer I, Goldman D, Xu K, Shabalina SA, Shagin D, Max MB, Makarov SS, Maixner W (2005) Genetic basis for individual variations in pain perception and the development of a chronic pain condition. Hum Mol Genet 14:135–143

    CAS  Google Scholar 

  • Dickinson KM, Collaco JM (2021) Cystic fibrosis. Pediatr Rev 42:55–67

    Google Scholar 

  • Dittmar KA, Goodenbour JM, Pan T (2006) Tissue-specific differences in human transfer RNA expression. PLoS Genet 2:e221

    Google Scholar 

  • Domingo J, Baeza-Centurion P, Lehner B (2019) The Causes and Consequences of Genetic Interactions (Epistasis). Annu Rev Genomics Hum Genet 20:433–460

    CAS  Google Scholar 

  • Dork T, Dworniczak B, Aulehla-Scholz C, Wieczorek D, Bohm I, Mayerova A, Seydewitz HH, Nieschlag E, Meschede D, Horst J, Pander HJ, Sperling H, Ratjen F, Passarge E, Schmidtke J, Stuhrmann M (1997) Distinct spectrum of CFTR gene mutations in congenital absence of vas deferens. Hum Genet 100:365–377

    CAS  Google Scholar 

  • Du K, Lukacs GL (2009) Cooperative assembly and misfolding of CFTR domains in vivo. Mol Biol Cell 20:1903–1915

    CAS  Google Scholar 

  • Duan J, Wainwright MS, Comeron JM, Saitou N, Sanders AR, Gelernter J, Gejman PV (2003) Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor. Hum Mol Genet 12:205–216

    CAS  Google Scholar 

  • Dufton MJ (1983) The significance of redundancy in the genetic code. J Theor Biol 102:521–526

    CAS  Google Scholar 

  • Edwards NC, Hing ZA, Perry A, Blaisdell A, Kopelman DB, Fathke R, Plum W, Newell J, Allen CESG, Shapiro A, Okunji C, Kosti I, Shomron N, Grigoryan V, Przytycka TM, Sauna ZE, Salari R, Mandel-Gutfreund Y, Komar AA, Kimchi-Sarfaty C (2012) Characterization of coding synonymous and non-synonymous variants in ADAMTS13 using ex vivo and in silico approaches. PLoS One 7:e38864

    CAS  Google Scholar 

  • Eny KM, Corey PN, El-Sohemy A (2009) Dopamine D2 receptor genotype (C957T) and habitual consumption of sugars in a free-living population of men and women. J Nutrigenet Nutrigenomics 2:235–242

    CAS  Google Scholar 

  • Faa V, Coiana A, Incani F, Costantino L, Cao A, Rosatelli MC (2010) A synonymous mutation in the CFTR gene causes aberrant splicing in an italian patient affected by a mild form of cystic fibrosis. J Mol Diagn 12:380–383

    CAS  Google Scholar 

  • Forman JJ, Coller HA (2010) The code within the code: microRNAs target coding regions. Cell Cycle 9:1533–1541

    CAS  Google Scholar 

  • Forman JJ, Legesse-Miller A, Coller HA (2008) A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc Natl Acad Sci U S A 105:14879–14884

    CAS  Google Scholar 

  • Fredrick K, Ibba M (2010) How the sequence of a gene can tune its translation. Cell 141:227–229

    CAS  Google Scholar 

  • Fujishima K, Kanai A (2014) tRNA gene diversity in the three domains of life. Front Genet 5:142

    Google Scholar 

  • Fung KL, Pan J, Ohnuma S, Lund PE, Pixley JN, Kimchi-Sarfaty C, Ambudkar SV, Gottesman MM (2014) MDR1 synonymous polymorphisms alter transporter specificity and protein stability in a stable epithelial monolayer. Cancer Res 74:598–608

    CAS  Google Scholar 

  • Gartner JJ, Parker SC, Prickett TD, Dutton-Regester K, Stitzel ML, Lin JC, Davis S, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Morken MA, Bhanot UK, Program NCS, Chen G, Elnitski LL, Davies MA, Gershenwald JE, Carter H, Karchin R, Robinson W, Robinson S, Rosenberg SA, Collins FS, Parmigiani G, Komar AA, Kimchi-Sarfaty C, Hayward NK, Margulies EH, Samuels Y (2013) Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc Natl Acad Sci U S A 110:13481–13486

    CAS  Google Scholar 

  • Gingold H, Tehler D, Christoffersen NR, Nielsen MM, Asmar F, Kooistra SM, Christophersen NS, Christensen LL, Borre M, Sorensen KD, Andersen LD, Andersen CL, Hulleman E, Wurdinger T, Ralfkiaer E, Helin K, Gronbaek K, Orntoft T, Waszak SM, Dahan O, Pedersen JS, Lund AH, Pilpel Y (2014) A dual program for translation regulation in cellular proliferation and differentiation. Cell 158:1281–1292

    CAS  Google Scholar 

  • Golimbet VE, Garakh ZV, Zaytseva Y, Alfimova MV, Lezheiko TV, Kondratiev NV, Shmukler AB, Gurovich IY, Strelets VB (2017) The dopamine receptor D2 C957T polymorphism modulates early components of event-related potentials in visual word recognition task. Neuropsychobiology 76:143–150

    CAS  Google Scholar 

  • Gonzalez-Paredes FJ, Ramos-Trujillo E, Claverie-Martin F (2014) Defective pre-mRNA splicing in PKD1 due to presumed missense and synonymous mutations causing autosomal dominant polycystic disease. Gene 546:243–249

    CAS  Google Scholar 

  • Gorochowski TE, Ignatova Z, Bovenberg RA, Roubos JA (2015) Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate. Nucleic Acids Res 43:3022–3032

    CAS  Google Scholar 

  • Gottesman MM, Fojo T, Bates SE (2002) Multidrug resistance in cancer: role of ATP-dependent transporters. Nat Rev Cancer 2:48–58

    CAS  Google Scholar 

  • Grzanka M, Piekielko-Witkowska A (2021) The role of TCOF1 gene in health and disease: beyond treacher collins syndrome. Int J Mol Sci 22

    Google Scholar 

  • Guimaraes JC, Mittal N, Gnann A, Jedlinski D, Riba A, Buczak K, Schmidt A, Zavolan M (2020) A rare codon-based translational program of cell proliferation. Genome Biol 21:44

    CAS  Google Scholar 

  • Guimbellot JS, Fortenberry JA, Siegal GP, Moore B, Wen H, Venglarik C, Chen YF, Oparil S, Sorscher EJ, Hong JS (2008) Role of oxygen availability in CFTR expression and function. Am J Respir Cell Mol Biol 39:514–521

    CAS  Google Scholar 

  • Guo H, Ingolia NT, Weissman JS, Bartel DP (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466:835–840

    CAS  Google Scholar 

  • Hamasaki-Katagiri N, Lin BC, Simon J, Hunt RC, Schiller T, Russek-Cohen E, Komar AA, Bar H, Kimchi-Sarfaty C (2017) The importance of mRNA structure in determining the pathogenicity of synonymous and non-synonymous mutations in haemophilia. Haemophilia 23:e8–e17

    CAS  Google Scholar 

  • Hansen TV, Steffensen AY, Jonson L, Andersen MK, Ejlertsen B, Nielsen FC (2010) The silent mutation nucleotide 744 G → A, Lys172Lys, in exon 6 of BRCA2 results in exon skipping. Breast Cancer Res Treat 119:547–550

    CAS  Google Scholar 

  • Hanson G, Coller J (2018) Codon optimality, bias and usage in translation and mRNA decay. Nat Rev Mol Cell Biol 19:20–30

    CAS  Google Scholar 

  • Hauber DJ, Grogan DW, DeBry RW (2016) Mutations to less-preferred synonymous codons in a highly expressed gene of escherichia coli: fitness and epistatic interactions. PLoS One 11:e0146375

    Google Scholar 

  • He L, Aleksandrov AA, An J, Cui L, Yang Z, Brouillette CG, Riordan JR (2015) Restoration of NBD1 thermal stability is necessary and sufficient to correct F508 CFTR folding and assembly. J Mol Biol 427:106–120

    CAS  Google Scholar 

  • Hill AE, Plyler ZE, Tiwari H, Patki A, Tully JP, McAtee CW, Moseley LA, Sorscher EJ (2014) Longevity and plasticity of CFTR provide an argument for noncanonical SNP organization in hominid DNA. PLoS One 9:e109186

    Google Scholar 

  • Hing ZA, Schiller T, Wu A, Hamasaki-Katagiri N, Struble EB, Russek-Cohen E, Kimchi-Sarfaty C (2013) Multiple in silico tools predict phenotypic manifestations in congenital thrombotic thrombocytopenic purpura. Br J Haematol 160:825–837

    CAS  Google Scholar 

  • Hirvonen M, Laakso A, Nagren K, Rinne JO, Pohjalainen T, Hietala J (2004) C957T polymorphism of the dopamine D2 receptor (DRD2) gene affects striatal DRD2 availability in vivo. Mol Psychiatry 9:1060–1061

    CAS  Google Scholar 

  • Hirvonen MM, Laakso A, Nagren K, Rinne JO, Pohjalainen T, Hietala J (2009) C957T polymorphism of dopamine D2 receptor gene affects striatal DRD2 in vivo availability by changing the receptor affinity. Synapse 63:907–912

    CAS  Google Scholar 

  • Hoagland MB, Stephenson ML, Scott JF, Hecht LI, Zamecnik PC (1958) A soluble ribonucleic acid intermediate in protein synthesis. J Biol Chem 231:241–257

    CAS  Google Scholar 

  • Hoelen H, Kleizen B, Schmidt A, Richardson J, Charitou P, Thomas PJ, Braakman I (2010) The primary folding defect and rescue of DeltaF508 CFTR emerge during translation of the mutant domain. PLoS One 5:e15458

    CAS  Google Scholar 

  • Hoenicka J, Aragues M, Rodriguez-Jimenez R, Ponce G, Martinez I, Rubio G, Jimenez-Arriero MA, Palomo T, Psychosis, and Addictions Research, G. (2006) C957T DRD2 polymorphism is associated with schizophrenia in Spanish patients. Acta Psychiatr Scand 114:435–438

    CAS  Google Scholar 

  • Hunt R, Hettiarachchi G, Katneni U, Hernandez N, Holcomb D, Kames J, Alnifaidy R, Lin B, Hamasaki-Katagiri N, Wesley A, Kafri T, Morris C, Bouche L, Panico M, Schiller T, Ibla J, Bar H, Ismail A, Morris H, Komar A, Kimchi-Sarfaty C (2019) A single synonymous variant (c.354G>A [p.P118P]) in ADAMTS13 confers enhanced specific activity. Int J Mol Sci 20

    Google Scholar 

  • Ikemura T (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol 151:389–409

    CAS  Google Scholar 

  • Jacobsen LK, Pugh KR, Mencl WE, Gelernter J (2006) C957T polymorphism of the dopamine D2 receptor gene modulates the effect of nicotine on working memory performance and cortical processing efficiency. Psychopharmacology (Berl) 188:530–540

    CAS  Google Scholar 

  • Joly BS, Coppo P, Veyradier A (2019) An update on pathogenesis and diagnosis of thrombotic thrombocytopenic purpura. Expert Rev Hematol 12:383–395

    CAS  Google Scholar 

  • Joruiz SM, Bourdon JC (2016) p53 Isoforms: key regulators of the cell fate decision. Cold Spring Harb Perspect Med 6

    Google Scholar 

  • Karalija N, Papenberg G, Wahlin A, Johansson J, Andersson M, Axelsson J, Riklund K, Lovden M, Lindenberger U, Backman L, Nyberg L (2019) C957T-mediated Variation in Ligand Affinity Affects the Association between (11)C-raclopride Binding Potential and Cognition. J Cogn Neurosci 31:314–325

    Google Scholar 

  • Kerem B, Rommens JM, Buchanan JA, Markiewicz D, Cox TK, Chakravarti A, Buchwald M, Tsui LC (1989) Identification of the cystic fibrosis gene: genetic analysis. Science 245:1073–1080

    CAS  Google Scholar 

  • Kim SJ, Skach WR (2012) Mechanisms of CFTR folding at the endoplasmic reticulum. Front Pharmacol 3:201

    CAS  Google Scholar 

  • Kim B, Hing ZA, Wu A, Schiller T, Struble EB, Liuwantara D, Kempert PH, Broxham EJ, Edwards NC, Marder VJ, Simhadri VL, Sauna ZE, Howard TE, Kimchi-Sarfaty C (2014) Single-nucleotide variations defining previously unreported ADAMTS13 haplotypes are associated with differential expression and activity of the VWF-cleaving protease in a Salvadoran congenital thrombotic thrombocytopenic purpura family. Br J Haematol 165:154–158

    CAS  Google Scholar 

  • Kim SJ, Yoon JS, Shishido H, Yang Z, Rooney LA, Barral JM, Skach WR (2015) Protein folding. Translational tuning optimizes nascent protein folding in cells. Science 348:444–448

    CAS  Google Scholar 

  • Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM (2007) A “silent” polymorphism in the MDR1 gene changes substrate specificity. Science 315:525–528

    CAS  Google Scholar 

  • Kircher M, Witten DM, Jain P, O’Roak BJ, Cooper GM, Shendure J (2014) A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46:310–315

    CAS  Google Scholar 

  • Kirchner S, Ignatova Z (2015) Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. Nat Rev Genet 16:98–112

    CAS  Google Scholar 

  • Kirchner S, Cai Z, Rauscher R, Kastelic N, Anding M, Czech A, Kleizen B, Ostedgaard LS, Braakman I, Sheppard DN, Ignatova Z (2017) Alteration of protein function by a silent polymorphism linked to tRNA abundance. PLoS Biol 15:e2000779

    Google Scholar 

  • Kleizen B, Braakman I, de Jonge HR (2000) Regulated trafficking of the CFTR chloride channel. Eur J Cell Biol 79:544–556

    CAS  Google Scholar 

  • Kleizen B, van Vlijmen T, de Jonge HR, Braakman I (2005) Folding of CFTR is predominantly cotranslational. Mol Cell 20:277–287

    CAS  Google Scholar 

  • Komar AA, Jaenicke R (1995) Kinetics of translation of gamma B crystallin and its circularly permutated variant in an in vitro cell-free system: possible relations to codon distribution and protein folding. FEBS Lett 376:195–198

    CAS  Google Scholar 

  • Kramer G, Shiber A, Bukau B (2019) Mechanisms of cotranslational maturation of newly synthesized proteins. Annu Rev Biochem 88:337–364

    CAS  Google Scholar 

  • Lazrak A, Fu L, Bali V, Bartoszewski R, Rab A, Havasi V, Keiles S, Kappes J, Kumar R, Lefkowitz E, Sorscher EJ, Matalon S, Collawn JF, Bebok Z (2013) The silent codon change I507-ATC->ATT contributes to the severity of the DeltaF508 CFTR channel dysfunction. FASEB J 27:4630–4645

    CAS  Google Scholar 

  • Li H, Sheppard DN, Hug MJ (2004) Transepithelial electrical measurements with the Ussing chamber. J Cyst Fibros 3(Suppl 2):123–126

    CAS  Google Scholar 

  • Li X, Qiu S, Shi J, Wang S, Wang M, Xu Y, Nie Z, Liu C, Liu C (2019) A new function of copper zinc superoxide dismutase: as a regulatory DNA-binding protein in gene expression in response to intracellular hydrogen peroxide. Nucleic Acids Res 47:5074–5085

    CAS  Google Scholar 

  • Liu HX, Zhang M, Krainer AR (1998) Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes Dev 12:1998–2012

    CAS  Google Scholar 

  • Liu Y, Yang Q, Zhao F (2021) Synonymous but not silent: the codon usage code for gene expression and protein folding. Annu Rev Biochem 90:375

    CAS  Google Scholar 

  • Lukacs GL, Mohamed A, Kartner N, Chang XB, Riordan JR, Grinstein S (1994) Conformational maturation of CFTR but not its mutant counterpart (delta F508) occurs in the endoplasmic reticulum and requires ATP. EMBO J 13:6076–6086

    CAS  Google Scholar 

  • Macaya D, Katsanis SH, Hefferon TW, Audlin S, Mendelsohn NJ, Roggenbuck J, Cutting GR (2009) A synonymous mutation in TCOF1 causes Treacher Collins syndrome due to mis-splicing of a constitutive exon. Am J Med Genet A 149A:1624–1627

    CAS  Google Scholar 

  • Mannisto PT, Kaakkola S (1999) Catechol-O-methyltransferase (COMT): biochemistry, molecular biology, pharmacology, and clinical efficacy of the new selective COMT inhibitors. Pharmacol Rev 51:593–628

    CAS  Google Scholar 

  • Marin M (2008) Folding at the rhythm of the rare codon beat. Biotechnol J 3:1047–1057

    CAS  Google Scholar 

  • Marinko JT, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR (2019) Folding and misfolding of human membrane proteins in health and disease: from single molecules to cellular proteostasis. Chem Rev 119:5537–5606

    CAS  Google Scholar 

  • Martel JC, Gatti McArthur S (2020) Dopamine receptor subtypes, physiology and pharmacology: new ligands and concepts in schizophrenia. Front Pharmacol 11:1003

    CAS  Google Scholar 

  • Mauger DM, Cabral BJ, Presnyak V, Su SV, Reid DW, Goodman B, Link K, Khatwani N, Reynders J, Moore MJ, McFadyen IJ (2019) mRNA structure regulates protein expression through changes in functional half-life. Proc Natl Acad Sci U S A 116:24075–24083

    CAS  Google Scholar 

  • McCarthy C, Carrea A, Diambra L (2017) Bicodon bias can determine the role of synonymous SNPs in human diseases. BMC Genomics 18:227

    Google Scholar 

  • McClure ML, Wen H, Fortenberry J, Hong JS, Sorscher EJ (2014) S-palmitoylation regulates biogenesis of core glycosylated wild-type and F508del CFTR in a post-ER compartment. Biochem J 459:417–425

    CAS  Google Scholar 

  • Meyer IM, Miklos I (2005) Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs. Nucleic Acids Res 33:6338–6348

    CAS  Google Scholar 

  • Mijnders M, Kleizen B, Braakman I (2017) Correcting CFTR folding defects by small-molecule correctors to cure cystic fibrosis. Curr Opin Pharmacol 34:83–90

    CAS  Google Scholar 

  • Minucci A, Concolino P, De Bonis M, Costella A, Paris I, Scambia G, Capoluongo E (2018) Preliminary molecular evidence associating a novel BRCA1 synonymous variant with hereditary ovarian cancer syndrome. Hum Genome Var 5:2

    Google Scholar 

  • Miranda GG, Rodrigue KM, Kennedy KM (2021) Cortical thickness mediates the relationship between DRD2 C957T polymorphism and executive function across the adult lifespan. Brain Struct Funct 226:121–136

    CAS  Google Scholar 

  • Monani UR, Lorson CL, Parsons DW, Prior TW, Androphy EJ, Burghes AH, McPherson JD (1999) A single nucleotide difference that alters splicing patterns distinguishes the SMA gene SMN1 from the copy gene SMN2. Hum Mol Genet 8:1177–1183

    CAS  Google Scholar 

  • Nackley AG, Shabalina SA, Tchivileva IE, Satterfield K, Korchynskyi O, Makarov SS, Maixner W, Diatchenko L (2006) Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science 314:1930–1933

    CAS  Google Scholar 

  • Nielsen KB, Sorensen S, Cartegni L, Corydon TJ, Doktor TK, Schroeder LD, Reinert LS, Elpeleg O, Krainer AR, Gregersen N, Kjems J, Andresen BS (2007) Seemingly neutral polymorphic variants may confer immunity to splicing-inactivating mutations: a synonymous SNP in exon 5 of MCAD protects from deleterious mutations in a flanking exonic splicing enhancer. Am J Hum Genet 80:416–432

    CAS  Google Scholar 

  • O’Brien EP, Ciryam P, Vendruscolo M, Dobson CM (2014) Understanding the influence of codon translation rates on cotranslational protein folding. Acc Chem Res 47:1536–1544

    Google Scholar 

  • Okiyoneda T, Veit G, Sakai R, Aki M, Fujihara T, Higashi M, Susuki-Miyata S, Miyata M, Fukuda N, Yoshida A, Xu H, Apaja PM, Lukacs GL (2018) Chaperone-independent peripheral quality control of CFTR by RFFL E3 ligase. Dev Cell 44(694-708):e697

    Google Scholar 

  • Pagani F, Stuani C, Tzetis M, Kanavakis E, Efthymiadou A, Doudounakis S, Casals T, Baralle FE (2003) New type of disease causing mutations: the example of the composite exonic regulatory elements of splicing in CFTR exon 12. Hum Mol Genet 12:1111–1120

    CAS  Google Scholar 

  • Pagani F, Raponi M, Baralle FE (2005) Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution. Proc Natl Acad Sci U S A 102:6368–6372

    CAS  Google Scholar 

  • Pal S, Tiwari A, Sharma K, Sharma SK (2020) Does conserved domain SOD1 mutation has any role in ALS severity and therapeutic outcome? BMC Neurosci 21:42

    CAS  Google Scholar 

  • Pankow S, Bamberger C, Yates JR 3rd. (2019) A posttranslational modification code for CFTR maturation is altered in cystic fibrosis. Sci Signal 12

    Google Scholar 

  • Parkes M, Barrett JC, Prescott NJ, Tremelling M, Anderson CA, Fisher SA, Roberts RG, Nimmo ER, Cummings FR, Soars D, Drummond H, Lees CW, Khawaja SA, Bagnall R, Burke DA, Todhunter CE, Ahmad T, Onnie CM, McArdle W, Strachan D, Bethel G, Bryan C, Lewis CM, Deloukas P, Forbes A, Sanderson J, Jewell DP, Satsangi J, Mansfield JC, Wellcome Trust Case Control C, Cardon L, Mathew CG (2007) Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat Genet 39:830–832

    CAS  Google Scholar 

  • Pechmann S (2018) Coping with stress by regulating tRNAs. Sci Signal 11

    Google Scholar 

  • Pechmann S, Frydman J (2013) Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding. Nat Struct Mol Biol 20:237–243

    CAS  Google Scholar 

  • Pechmann S, Chartron JW, Frydman J (2014) Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo. Nat Struct Mol Biol 21:1100–1105

    CAS  Google Scholar 

  • Polte C, Wedemeyer D, Oliver KE, Wagner J, Bijvelds MJC, Mahoney J, de Jonge HR, Sorscher EJ, Ignatova Z (2019) Assessing cell-specific effects of genetic variations using tRNA microarrays. BMC Genomics 20:549

    Google Scholar 

  • Presnyak V, Alhusaini N, Chen YH, Martin S, Morris N, Kline N, Olson S, Weinberg D, Baker KE, Graveley BR, Coller J (2015) Codon optimality is a major determinant of mRNA stability. Cell 160:1111–1124

    CAS  Google Scholar 

  • Rab A, Bartoszewski R, Jurkuvenaite A, Wakefield J, Collawn JF, Bebok Z (2007) Endoplasmic reticulum stress and the unfolded protein response regulate genomic cystic fibrosis transmembrane conductance regulator expression. Am J Physiol Cell Physiol 292:C756–C766

    CAS  Google Scholar 

  • Rak R, Dahan O, Pilpel Y (2018) Repertoires of tRNAs: the couplers of genomics and proteomics. Annu Rev Cell Dev Biol 34:239–264

    CAS  Google Scholar 

  • Raponi M, Baralle FE, Pagani F (2007) Reduced splicing efficiency induced by synonymous substitutions may generate a substrate for natural selection of new splicing isoforms: the case of CFTR exon 12. Nucleic Acids Res 35:606–613

    CAS  Google Scholar 

  • Rauscher R, Ignatova Z (2018) Timing during translation matters: synonymous mutations in human pathologies influence protein folding and function. Biochem Soc Trans 46:937–944

    CAS  Google Scholar 

  • Rauscher R, Bampi GB, Guevara-Ferrer M, Santos LA, Joshi D, Mark D, Strug LJ, Rommens JM, Ballmann M, Sorscher EJ, Oliver KE, Ignatova Z (2021) Positive epistasis between disease-causing missense mutations and silent polymorphism with effect on mRNA translation velocity. Proc Natl Acad Sci U S A 118

    Google Scholar 

  • Reczko M, Maragkakis M, Alexiou P, Grosse I, Hatzigeorgiou AG (2012) Functional microRNA targets in protein coding sequences. Bioinformatics 28:771–776

    CAS  Google Scholar 

  • Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M (2019) CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res 47:D886–D894

    CAS  Google Scholar 

  • Rentzsch P, Schubach M, Shendure J, Kircher M (2021) CADD-Splice-improving genome-wide variant effect prediction using deep learning-derived splice scores. Genome Med 13:31

    CAS  Google Scholar 

  • Riordan JR, Rommens JM, Kerem B, Alon N, Rozmahel R, Grzelczak Z, Zielenski J, Lok S, Plavsic N, Chou JL et al (1989) Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA. Science 245:1066–1073

    CAS  Google Scholar 

  • Rodnina MV, Wintermeyer W (2016) Protein elongation, co-translational folding and targeting. J Mol Biol 428:2165–2185

    CAS  Google Scholar 

  • Rommens JM, Iannuzzi MC, Kerem B, Drumm ML, Melmer G, Dean M, Rozmahel R, Cole JL, Kennedy D, Hidaka N et al (1989) Identification of the cystic fibrosis gene: chromosome walking and jumping. Science 245:1059–1065

    CAS  Google Scholar 

  • Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J (2013) The RNAsnp web server: predicting SNP effects on local RNA secondary structure. Nucleic Acids Res 41:W475–W479

    Google Scholar 

  • Santos M, Fidalgo A, Varanda AS, Oliveira C, Santos MAS (2019) tRNA deregulation and its consequences in cancer. Trends Mol Med 25:853–865

    CAS  Google Scholar 

  • Sato S, Ward CL, Kopito RR (1998) Cotranslational ubiquitination of cystic fibrosis transmembrane conductance regulator in vitro. J Biol Chem 273:7189–7192

    CAS  Google Scholar 

  • Saunders R, Deane CM (2010) Synonymous codon usage influences the local protein structure observed. Nucleic Acids Res 38:6719–6728

    CAS  Google Scholar 

  • Saunders R, Mann M, Deane CM (2011) Signatures of co-translational folding. Biotechnol J 6:742–751

    CAS  Google Scholar 

  • Scherrer K (2018) Primary transcripts: from the discovery of RNA processing to current concepts of gene expression – review. Exp Cell Res 373:1–33

    CAS  Google Scholar 

  • Schimmel P (2018) The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis. Nat Rev Mol Cell Biol 19:45–58

    CAS  Google Scholar 

  • Schroeder SJ (2018) Challenges and approaches to predicting RNA with multiple functional structures. RNA 24:1615–1624

    CAS  Google Scholar 

  • Schwarz A, Beck M (2019) The benefits of cotranslational assembly: a structural perspective. Trends Cell Biol 29:791–803

    CAS  Google Scholar 

  • Shah K, Cheng Y, Hahn B, Bridges R, Bradbury NA, Mueller DM (2015) Synonymous codon usage affects the expression of wild type and F508del CFTR. J Mol Biol 427:1464–1479

    CAS  Google Scholar 

  • Sharma M, Benharouga M, Hu W, Lukacs GL (2001) Conformational and temperature-sensitive stability defects of the delta F508 cystic fibrosis transmembrane conductance regulator in post-endoplasmic reticulum compartments. J Biol Chem 276:8942–8950

    CAS  Google Scholar 

  • Sharma Y, Miladi M, Dukare S, Boulay K, Caudron-Herger M, Gross M, Backofen R, Diederichs S (2019) A pan-cancer analysis of synonymous mutations. Nat Commun 10:2569

    Google Scholar 

  • Sharp PM, Li WH (1986) An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol 24:28–38

    CAS  Google Scholar 

  • Sharp PM, Li WH (1987) The codon Adaptation Index – a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281–1295

    CAS  Google Scholar 

  • Sheppard DN (2004) CFTR channel pharmacology: novel pore blockers identified by high-throughput screening. J Gen Physiol 124:109–113

    CAS  Google Scholar 

  • Sheppard DN (2011) Cystic fibrosis: CFTR correctors to the rescue. Chem Biol 18:145–147

    CAS  Google Scholar 

  • Sheppard DN, Ostedgaard LS, Winter MC, Welsh MJ (1995) Mechanism of dysfunction of two nucleotide binding domain mutations in cystic fibrosis transmembrane conductance regulator that are associated with pancreatic sufficiency. EMBO J 14:876–883

    CAS  Google Scholar 

  • Shishido H, Yoon JS, Yang Z, Skach WR (2020) CFTR trafficking mutations disrupt cotranslational protein folding by targeting biosynthetic intermediates. Nat Commun 11:4258

    CAS  Google Scholar 

  • Simhadri VL, Hamasaki-Katagiri N, Lin BC, Hunt R, Jha S, Tseng SC, Wu A, Bentley AA, Zichel R, Lu Q, Zhu L, Freedberg DI, Monroe DM, Sauna ZE, Peters R, Komar AA, Kimchi-Sarfaty C (2017) Single synonymous mutation in factor IX alters protein properties and underlies haemophilia B. J Med Genet 54:338–345

    CAS  Google Scholar 

  • Stegh AH, Kim H, Bachoo RM, Forloney KL, Zhang J, Schulze H, Park K, Hannon GJ, Yuan J, Louis DN, DePinho RA, Chin L (2007) Bcl2L12 inhibits post-mitochondrial apoptosis signaling in glioblastoma. Genes Dev 21:98–111

    CAS  Google Scholar 

  • Steingrimsdottir H, Rowley G, Dorado G, Cole J, Lehmann AR (1992) Mutations which alter splicing in the human hypoxanthine-guanine phosphoribosyltransferase gene. Nucleic Acids Res 20:1201–1208

    CAS  Google Scholar 

  • Tay Y, Zhang J, Thomson AM, Lim B, Rigoutsos I (2008a) MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 455:1124–1128

    CAS  Google Scholar 

  • Tay YM, Tam WL, Ang YS, Gaughwin PM, Yang H, Wang W, Liu R, George J, Ng HH, Perera RJ, Lufkin T, Rigoutsos I, Thomson AM, Lim B (2008b) MicroRNA-134 modulates the differentiation of mouse embryonic stem cells, where it causes post-transcriptional attenuation of Nanog and LRH1. Stem Cells 26:17–29

    CAS  Google Scholar 

  • Tellier M, Maudlin I, Murphy S (2020) Transcription and splicing: a two-way street. Wiley Interdiscip Rev RNA 11:e1593

    CAS  Google Scholar 

  • Torrent M, Chalancon G, de Groot NS, Wuster A, Madan Babu M (2018) Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions. Sci Signal 11

    Google Scholar 

  • Torres AG, Reina O, Stephan-Otto Attolini C, Ribas de Pouplana L (2019) Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments. Proc Natl Acad Sci U S A 116:8451–8456

    CAS  Google Scholar 

  • Tsai CJ, Sauna ZE, Kimchi-Sarfaty C, Ambudkar SV, Gottesman MM, Nussinov R (2008) Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. J Mol Biol 383:281–291

    CAS  Google Scholar 

  • Tsao D, Shabalina SA, Gauthier J, Dokholyan NV, Diatchenko L (2011) Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant. Nucleic Acids Res 39:6201–6212

    CAS  Google Scholar 

  • Tseng SC, Kimchi-Sarfaty C (2011) SNPs in ADAMTS13. Pharmacogenomics 12:1147–1160

    CAS  Google Scholar 

  • Tsui LC, Dorfman R (2013) The cystic fibrosis gene: a molecular genetic perspective. Cold Spring Harb Perspect Med 3:a009472

    Google Scholar 

  • Tuller T (2014) Challenges and obstacles related to solving the codon bias riddles. Biochem Soc Trans 42:155–159

    CAS  Google Scholar 

  • Tuller T, Waldman YY, Kupiec M, Ruppin E (2010a) Translation efficiency is determined by both codon bias and folding energy. Proc Natl Acad Sci U S A 107:3645–3650

    CAS  Google Scholar 

  • Tuller T, Carmi A, Vestsigian K, Navon S, Dorfan Y, Zaborske J, Pan T, Dahan O, Furman I, Pilpel Y (2010b) An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell 141:344–354

    CAS  Google Scholar 

  • Varga K, Jurkuvenaite A, Wakefield J, Hong JS, Guimbellot JS, Venglarik CJ, Niraj A, Mazur M, Sorscher EJ, Collawn JF, Bebok Z (2004) Efficient intracellular processing of the endogenous cystic fibrosis transmembrane conductance regulator in epithelial cell lines. J Biol Chem 279:22578–22584

    CAS  Google Scholar 

  • Veit G, Avramescu RG, Perdomo D, Phuan PW, Bagdany M, Apaja PM, Borot F, Szollosi D, Wu YS, Finkbeiner WE, Hegedus T, Verkman AS, Lukacs GL (2014) Some gating potentiators, including VX-770, diminish DeltaF508-CFTR functional expression. Sci Transl Med 6:246ra297

    Google Scholar 

  • Veit G, Avramescu RG, Chiang AN, Houck SA, Cai Z, Peters KW, Hong JS, Pollard HB, Guggino WB, Balch WE, Skach WR, Cutting GR, Frizzell RA, Sheppard DN, Cyr DM, Sorscher EJ, Brodsky JL, Lukacs GL (2016) From CFTR biology toward combinatorial pharmacotherapy: expanded classification of cystic fibrosis mutations. Mol Biol Cell 27:424–433

    CAS  Google Scholar 

  • Walsh IM, Bowman MA, Soto Santarriaga IF, Rodriguez A, Clark PL (2020) Synonymous codon substitutions perturb cotranslational protein folding in vivo and impair cell fitness. Proc Natl Acad Sci U S A 117:3528–3534

    CAS  Google Scholar 

  • Wang X, He Y, Jiang Y, Feng X, Zhang G, Xia Z, Zhou Y (2019) Screening and mutation analysis of hyperphenylalaninemia in newborns from Xiamen, China. Clin Chim Acta 498:161–166

    CAS  Google Scholar 

  • Ward CL, Kopito RR (1994) Intracellular turnover of cystic fibrosis transmembrane conductance regulator. Inefficient processing and rapid degradation of wild-type and mutant proteins. J Biol Chem 269:25710–25718

    CAS  Google Scholar 

  • Ward CL, Omura S, Kopito RR (1995) Degradation of CFTR by the ubiquitin-proteasome pathway. Cell 83:121–127

    CAS  Google Scholar 

  • Wen JD, Lancaster L, Hodges C, Zeri AC, Yoshimura SH, Noller HF, Bustamante C, Tinoco I (2008) Following translation by single ribosomes one codon at a time. Nature 452:598–603

    CAS  Google Scholar 

  • Whitesides GM, Grzybowski B (2002) Self-assembly at all scales. Science 295:2418–2421

    CAS  Google Scholar 

  • Wu X, Jornvall H, Berndt KD, Oppermann U (2004) Codon optimization reveals critical factors for high level expression of two rare codon genes in Escherichia coli: RNA stability and secondary structure but not tRNA abundance. Biochem Biophys Res Commun 313:89–96

    CAS  Google Scholar 

  • Xu B, Meng Y, Jin Y (2021) RNA structures in alternative splicing and back-splicing. Wiley Interdiscip Rev RNA 12:e1626

    CAS  Google Scholar 

  • Yu CH, Dang Y, Zhou Z, Wu C, Zhao F, Sachs MS, Liu Y (2015) Codon usage influences the local rate of translation elongation to regulate co-translational protein folding. Mol Cell 59:744–754

    CAS  Google Scholar 

  • Yue JK, Winkler EA, Rick JW, Burke JF, McAllister TW, Oh SS, Burchard EG, Hu D, Rosand J, Temkin NR, Korley FK, Sorani MD, Ferguson AR, Lingsma HF, Sharma S, Robinson CK, Yuh EL, Tarapore PE, Wang KK, Puccio AM, Mukherjee P, Diaz-Arrastia R, Gordon WA, Valadka AB, Okonkwo DO, Manley GT, Investigators T-T (2017) DRD2 C957T polymorphism is associated with improved 6-month verbal learning following traumatic brain injury. Neurogenetics 18:29–38

    CAS  Google Scholar 

  • Zeitlin PL (2006) Is it go or NO go for S-nitrosylation modification-based therapies of cystic fibrosis transmembrane regulator trafficking? Mol Pharmacol 70:1155–1158

    CAS  Google Scholar 

  • Zhang G, Ignatova Z (2009) Generic algorithm to predict the speed of translational elongation: implications for protein biogenesis. PLoS One 4:e5036

    Google Scholar 

  • Zhang F, Kartner N, Lukacs GL (1998) Limited proteolysis as a probe for arrested conformational maturation of delta F508 CFTR. Nat Struct Biol 5:180–183

    CAS  Google Scholar 

  • Zhang J, Long M, Li L (2005) Translational effects of differential codon usage among intragenic domains of new genes in Drosophila. Biochim Biophys Acta 1728:135–142

    CAS  Google Scholar 

  • Zhang G, Hubalewska M, Ignatova Z (2009) Transient ribosomal attenuation coordinates protein synthesis and co-translational folding. Nat Struct Mol Biol 16:274–280

    CAS  Google Scholar 

  • Zhang G, Fedyunin I, Miekley O, Valleriani A, Moura A, Ignatova Z (2010) Global and local depletion of ternary complex limits translational elongation. Nucleic Acids Res 38:4778–4787

    CAS  Google Scholar 

  • Zhang K, Zhang X, Cai Z, Zhou J, Cao R, Zhao Y, Chen Z, Wang D, Ruan W, Zhao Q, Liu G, Xue Y, Qin Y, Zhou B, Wu L, Nilsen T, Zhou Y, Fu XD (2018) A novel class of microRNA-recognition elements that function only within open reading frames. Nat Struct Mol Biol 25:1019–1027

    CAS  Google Scholar 

  • Zhou H, Rigoutsos I (2014) MiR-103a-3p targets the 5’ UTR of GPRC5A in pancreatic cells. RNA 20:1431–1439

    Google Scholar 

  • Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415

    CAS  Google Scholar 

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Zhang, Y., Bebok, Z. (2022). An Examination of Mechanisms by which Synonymous Mutations may Alter Protein Levels, Structure and Functions . In: Sauna, Z.E., Kimchi-Sarfaty, C. (eds) Single Nucleotide Polymorphisms. Springer, Cham. https://doi.org/10.1007/978-3-031-05616-1_6

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