Studies on nonsense mediated decay reveal novel therapeutic options for genetic diseases

Recent Patents on DNA and Gene Sequences

Volumn 3, Issue 1, 2009, Pages 7-15

  Bashyam, Murali D ^a  

^a CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS   (India)

Author keywords

Alternative splicing; Cystic fibrosis; Duchenne muscular distrophy; Exon; Genetic disorders; Gentamicin; Intron; mRNA; Nonsense mediated decay; PABPC1; Premature stop codon; Thalassemia; Therapy; Transcription; Translation; Upf1

Indexed keywords

AMINOGLYCOSIDE DERIVATIVE; CAFFEINE; DYSTROPHIN; PROTEIN P53; RNA POLYMERASE; T LYMPHOCYTE RECEPTOR; TRANSMEMBRANE CONDUCTANCE REGULATOR; WORTMANNIN; RNA;

3' UNTRANSLATED REGION; ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; BECKER MUSCULAR DYSTROPHY; CELL FUNCTION; CHOLESTEROL SYNTHESIS; CYSTIC FIBROSIS; DOWN REGULATION; DUCHENNE MUSCULAR DYSTROPHY; EUKARYOTE; FRAMESHIFT MUTATION; GENE DELETION; GENE MUTATION; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC DISORDER; GENETIC REGULATION; GENETIC VARIABILITY; HETEROZYGOSITY; HUMAN; INTRON; MUSCLE STRENGTH; NONSENSE MEDIATED DECAY; NONSENSE MUTATION; OPEN READING FRAME; PATENT; POLYADENYLATION; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN INTERACTION; PROTEIN PHOSPHORYLATION; PROTEIN SYNTHESIS; REVIEW; RNA SYNTHESIS; RNA TRANSLATION; STOP CODON; THALASSEMIA; TRANSLATION INITIATION; TUMOR SUPPRESSOR GENE; ANIMAL; BIOLOGICAL MODEL; BIOSYNTHESIS; GENE TARGETING; GENE THERAPY; GENETICS; LEGAL ASPECT; METHODOLOGY; PHYSIOLOGY; RNA STABILITY;

ANIMALS; CODON, NONSENSE; GENE TARGETING; GENE THERAPY; GENETIC DISEASES, INBORN; HUMANS; MODELS, BIOLOGICAL; PATENTS AS TOPIC; PROTEIN BIOSYNTHESIS; RNA; RNA STABILITY;

EID: 60549102070     PISSN: 18722156     EISSN: None     Source Type: Journal    
DOI: 10.2174/187221509787236219     Document Type: Review

References (66)

1. Lewis BP, Green RE, Brenner SE. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci USA 2003; 100: 189-192.
2. Lejeune F, Maquat LE. Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. Curr Opin Cell Biol 2005; 17: 9-15.
3. Mendell JT, Sharifi NA, Meyers JL, Martinez-Murillo F, Dietz HC. Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat Genet 2004; 36: 1073-1078.
4. Wittmann J, Hol EM, Jäck HM. hUPF2 silencing identifies physiologic substrates of mammalian nonsense-mediated mRNA decay. Mol Cell Biol 2006; 26: 1272-1287.
5. Tycowski KT, Shu M-D, Steitz JA. A mammalian gene with introns instead of exons generating stable RNA products. Nature 1996; 379: 464-466.
6. Oliveira CC, McCarthy JE. The relationship between eukaryotic translation and mRNA stability. A short upstream open reading frame strongly inhibits translational initiation and greatly accelerates mRNA degradation in the yeast Saccharomyces cerevisiae. J Biol Chem 1995; 270: 8936-8943.
7. Weischenfeldt J, Damgaard I, Bryder D, et al. NMD is essential for hematopoietic stem and progenitor cells and for eliminating byproducts of programmed DNA rearrangements. Genes Dev 2008; 22: 1381-1396.
8. Hir HL, Izaurralde E, Maquat LE, Moore MJ. The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J 2000; 19: 6860-6869.
9. Nagy E, Maquat LE. A rule for termination-codon position within intron-containing genes: When nonsense affects RNA abundance. Trends Biochem Sci 1998; 23: 198-199.
10. Longman D, Plasterk RH, Johnstone IL, Caceres JF. Mechanistic insights and identification of two novel factors in the C. elegans NMD pathway. Genes Dev 2007; 21: 1075-1085.
11. Gatfield D, Unterholzner L, Ciccarelli FD, Bork P, Izaurralde E. Nonsense-mediated mRNA decay in Drosophila: At the intersection of the yeast and mammalian pathways. EMBO J 2003; 22: 3960-3970.
12. Behm-Ansmant I, Gatfield D, Rehwinkel J, Hilgers V, Izaurralde E. A conserved role for cytoplasmic poly(A)-binding protein 1 (PABPC1) in nonsense-mediated mRNA decay. EMBO J 2007; 26: 1591-1601.
13. Singh G, Rebbapragada I, Lykke-Andersen J. A Competition between stimulators and antagonists of UPF complex recruitment governs human nonsense-mediated mRNA decay. PLoS Biol 2008; 6: 860-871.
14. Eberle AB, Stalder L, Mathys H, Orozco RZ, Mühlemann O. Posttranscriptional gene regulation by spatial rearrangement of the 3′ untranslated region. PLoS Biol 2008; 6: 849-859.
15. Farh KK, Grimson A, Jan C, et al. The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science 2005; 310: 1817-1821.
16. Eisenberg E, Levanon EY. Human housekeeping genes are compact. Trends Genet 2003; 19: 362-365.
17. Liu S, Zhang C, Zhou Y. Uneven size distribution of mammalian genes in the number of tissues expressed and in the number of coexpressed genes. Hum Mol Genet 2006; 15: 1313-1318.
18. Sironi M, Menozzi G, Comi GP, Cagliani R, Bresolin N, Pozzoli U. Analysis of intronic conserved elements indicates that functional complexity might represent a major source of negative selection on non-coding sequences. Hum Mol Genet 2005; 14: 2533-2546.
19. Isken O, Kim YK, Hosoda N, Mayeur GL, Hershey JWB, Maquat LE. UPF1 phosphorylation triggers translational repression during nonsense-mediated mRNA decay. Cell 2008; 133: 314-327.
20. Holbrook JA, Neu-Yilik G, Hentze MW, Kulozik AE. Nonsense-mediated decay approaches the clinic. Nat Genet 2004; 36: 801-808.
21. Lewis BP, Green RE, Brenner SE. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci USA 2003; 100: 189-192.
22. Medghalchi SM, Frischmeyer PA, Mendell JT, et al. Rent1, a transeffector of nonsense-mediated mRNA decay, is essential for mammalian embryonic viability. Hum Mol Genet 2001; 10: 99-105.
23. Culbertson MR. RNA surveillance: Unforeseen consequences for gene expression, inherited genetic disorders and cancer. Trends Genet 1999; 15: 74-80.
24. Jäck HM, Berg J, Wabl M. Translation affects immunoglobulin mRNA stability. Eur J Immunol 1989; 19: 843-847.
25. Carter MS, Doskow J, Morris P, et al. A regulatory mechanism that detects premature nonsense codons in T-cell receptor transcripts in vivo is reversed by protein synthesis inhibitors in vitro. J Biol Chem 1995; 270: 28995-29003.
26. Morrison M, Harris KS, Roth MB. SMG mutants affect the expression of alternatively spliced SR protein mRNAs in Caenorhabditis elegans. Proc Natl Acad Sci USA 1997; 94: 9782-9785.
27. Xing Y, Lee CJ. Negative selection pressure against premature protein truncation is reduced by alternative splicing and diploidy. Trends Genet 2004; 20: 472-475.
28. Lew JE, Enomoto S, Berman J. Telomere length regulation and telomeric chromatin require the nonsense-mediated mRNA decay pathway. Mol Cell Biol 1998; 18: 6121-6130.
29. Hall GW, Thein S. Nonsense codon mutations in the terminal exon of the beta-globin gene are not associated with a reduction in beta-mRNA accumulation: A mechanism for the phenotype of dominant beta-thalassemia. Blood 1994; 83: 2031-2037.
30. Fan S, Yuan R, Ma YX, Meng Q, Goldberg ID, Rosen EM. Mutant BRCA1 genes antagonize phenotype of wild-type BRCA1. Oncogene 2001; 20: 8215-8235.
31. Dietz HC, McIntosh I, Sakai LY, et al. Four novel FBN1 mutations: Significance for mutant transcript level and EGF-like domain calcium binding in the pathogenesis of Marfan syndrome. Genomics 1993; 17: 468-475.
32. Keeling KM, Du M, Bedwell D. Therapies of nonsense-associated diseases. Nonsense-mediated mRNA decay. In: Maquat LE, Ed. Landes Bioscience 2006; Vol. 84: pp. 121-136.
33. Deutekom JC. Functional analysis of 114 exon-internal AONs for targeted DMD exon skipping: Indication for steric hindrance of SR protein binding sites. Oligonucleotides 2005; 15: 284-297.
34. Aartsma-Rus A, De Winter CL, Janson AA, et al. Functional analysis of 114 exon-internal AONs for targeted DMD exon skipping: Indication for steric hindrance of SR protein binding sites. Oligonucleotides 2005; 15: 284-297.
35. Alter J, Lou F, Rabinowitz A, et al. Systemic delivery of morpholino oligonucleotide restores dystrophin expression bodywide and improves dystrophic pathology. Nat Med 2006; 12: 175-177.
36. Lu QL, Rabinowitz A, Chen YC, et al. Systemic delivery of antisense oligoribonucleotide restores dystrophin expression in body-wide skeletal muscles. Proc Natl Acad Sci USA 2005; 102: 198-203.
37. Sheppard DN, Ostedgaard LS, Rich DP, Welsh MJ. The amino-terminal portion of CFTR forms a regulated Cl- channel. Cell 1994; 76: 1091-1098.
38. Chu CS, Trapnell BC, Curristin SM, Cutting GR, Crystal RG. Extensive posttranscriptional deletion of the coding sequences for part of nucleotide-binding fold 1 in respiratory epithelial mRNA transcripts of the cystic fibrosis transmembrane conductance regulator gene is not associated with the clinical manifestations of cystic fibrosis. J Clin Invest 1992; 90: 785-790.
39. Abeliovich D, Lavon IP, Lerer I, et al. Screening for five mutations detects 97% of cystic fibrosis (CF) chromosomes and predicts a carrier frequency of 1:29 in the Jewish Ashkenazi population. Am J Hum Genet 1992; 51: 951-956.
40. Wilschanski M, Yahav Y, Yaacov Y, et al. Gentamycin-induced correction of CFTR function in patients with cystic fibrosis and CFTR stop mutations. N Engl J Med 2003; 349: 1433-1441.
41. Kerem E. Pharmacologic therapy for stop mutations: How much CFTR activity is enough? A Opin Pulm Med 2004; 10: 547-552.
42. Linde L, Boelz S, Nissim-Rafinia M, et al. Nonsense-mediated mRNA decay affects nonsense transcript levels and governs response of cystic fibrosis patients to gentamicin. J Clin Invest 2007; 117: 683-692.
43. Ainsworth C. Nonsense mutations: Running the red light. Nature 2005; 438: 726-728.
44. Du M, Liu X, Welch EM, Hirawat S, Peltz SW, Bedwell DM. PTC124 is an orally bioavailable compound that promotes suppression of the human CFTR-G542X nonsense allele in a CF mouse model. Proc Natl Acad Sci USA 2008; 105: 2064-2069.
45. Kerem E, Hirawat S, Armoni S, et al. Effectiveness of PTC124 treatment of cystic fibrosis caused by nonsense mutations: A prospective phase II trial. Lancet 2008; 372: 719-727.
46. Correa-Cerro LS, Wassif CA, Waye JS, et al. DHCR7 nonsense mutations and characterisation of mRNA nonsense mediated decay in Smith-Lemli-Opitz syndrome. J Med Genet 2005; 42: 350-357.
47. Barton-Davis ER, Cordier L, Shoturma DI, Leland SE, Sweeney HL. Aminoglycoside antibiotics restore dystrophin function to skeletal muscles of MDX mice. J Clin Invest 1999; 104: 375-381.
48. Yang C, Feng J, Song W, et al. A mouse model for nonsense mutation bypass therapy shows a dramatic multiday response to geneticin. Proc Natl Acad Sci USA 2007; 104: 15394-15399.
49. Usuki F, Yamashita A, Hiquchi, et al. Inhibition of nonsense-mediated mRNA decay rescues the phenotype in Ullrich's disease. Ann Neurol 2004; 55: 740-744.
50. Ohnishi T, Yamashita A, Kashima I, et al. Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7. Mol Cell 2003; 12: 1187-1200.
51. Durand S, Cougot N, Mahuteau-Betzer F, et al. Inhibition of nonsense-mediated mRNA decay (NMD) by a new chemical molecule reveals the dynamic of NMD factors in P-bodies. J Cell Biol 2007; 178: 1145-1160.
52. Li S, Leonard D, Wilkinson MF. T cell receptor (TCR) mini-gene mRNA expression regulated by nonsense codons: A nuclear-associated translation-like mechanism. J Exp Med 1997; 185: 985-992.
53. Temple GF, Dozy AM, Roy KL, Kan YW. Construction of a functional human suppressor tRNA gene: An approach to gene therapy for beta-thalassaemia. Nature 1982; 296: 537-540.
54. Kiselev AV, Ostapenko OV, Rogozhkina EV, et al. Suppression of nonsense mutations in the Dystrophin gene by a suppressor tRNA gene. Mol Biol (Mosk) 2002; 36: 43-47.
55. Reed R, Hurt E. A conserved mRNA export machinery coupled to pre-mRNA splicing. Cell 2002; 108: 523-531.
56. Deol JR, Danialou G, Larochelle N, et al. Successful compensation for dystrophin deficiency by a helper-dependent adenovirus expressing full-length utrophin. Mol Ther 2007; 15: 1767-1774.
57. Moll J, Barzaghi P, Lin S, et al. An agrin minigene rescues dystrophic symptoms in a mouse model for congenital muscular dystrophy. Nature 2001; 413: 302-307.
58. Maquat, L.: US20060154883 (2006).
59. Cao D, Parker R. Computational modeling and experimental analysis of nonsense-mediated decay in yeast. Cell 2003; 113: 533-545.
60. Brenner, S.E., Green, R.E., Lewis, B.P.: US20067149631 (2006).
61. Maquat, L.E., Kim, Y.K.: WO2006039399 (2006).
62. Arakawa, M., Matsuda, R.: CA2449950 (2002).
63. Wilde, R.G., Welch, E.M, Takasugi, J.J., Almstead, N.G., Rubenstein, S.M., Beckmann, H.: EP1525185 (2005).
64. Wilde, R.G., Kennedy, P.D., Almstead, N.G., Welch, E.M., Takasugi, J.J., Friesen, W.J.: EP1534726 (2005).
65. Matsuda, R., Shiozuka, M., Mackerell, J.A.: WO2008004610 (2008).
66. Almstead, N., Chen, G., Karp, G.M., Welch, E., Wilde, R., Campbell, J.A.: EP1815206 (2007).