БИОХИМИЯ, 2022, том 87, вып. 4, с. 508–522

УДК 575.2

Нонсенс-мутации у эукариот

Обзор

© 2022 Н.А. Потаповаnadezhdalpotapova@gmail.com

Федеральное государственное бюджетное учреждение науки Институт проблем передачи информации имени А.А. Харкевича Российской академии наук (ИППИ РАН), 127051 Москва, Россия

Поступила в редакцию 12.01.2022
После доработки 14.02.2022
Принята к публикации 22.03.2022

DOI: 10.31857/S0320972522040042

КЛЮЧЕВЫЕ СЛОВА: нонсенс-мутация, стоп-кодон, эукариоты, отрицательный отбор, положительный отбор.

Аннотация

Нонсенс-мутации представляют собой мутации, в результате которых появляется стоп-кодон. В то время как продолжает оставаться общепринятым рассмотрение этих мутаций как одних из самых вредных, приводящих к преждевременной терминации синтеза белка на рибосоме и, как следствие, к возникновению дефектного полипептида, накапливаются данные, согласно которым не все нонсенс-мутации вредны. Также существуют молекулярные механизмы, которые позволяют нивелировать потенциальное неблагоприятное воздействие данных мутаций. В представленном обзоре рассмотрены актуальные сведения о нонсенс-мутациях в геномах эукариот, характеристиках таковых мутаций и молекулярных механизмах предотвращения или смягчения их неблагоприятных эффектов.

Благодарности

Автор выражает благодарность Игорю Игоревичу Адамейко, Ольге Владимировне Черченко, Екатерине Юрьевне Царёвой, Эвелине Ильиничне Никельшпарг, Ивану Владимировичу Кулаковскому, а также Борису Романовичу Петрову за ценные комментарии.

Конфликт интересов

Автор заявляет об отсутствии конфликта интересов.

Соблюдение этических норм

Настоящая статья не содержит описания выполненных автором исследований с участием людей или использованием животных в качестве объектов.

Список литературы

1. Osawa, S., and Jukes, T.H. (1989) Codon reassignment (codon capture) in evolution, J. Mol. Evol., 28, 271-8, doi: 10.1007/BF02103422.

2. Campbell, J. H., O’Donoghue, P., Campbell, A. G., Schwientek, P., Sczyrba, A., et al. (2013) UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota, Proc. Natl. Acad. Sci. USA, 110, 5540-5, doi: 10.1073/pnas.1303090110.

3. Sánchez-Silva, R., Villalobo, E., Morin, L., and Torres, A. (2003) A new noncanonical nuclear genetic code: Translation of UAA into glutamate, Curr. Biol., 13, 442-447, doi: 10.1016/S0960-9822(03)00126-X.

4. Ring, K. L., and Cavalcanti, A. R. (2007) Consequences of stop codon reassignment on protein evolution in ciliates with alternative genetic codes, Mol. Biol. Evol., 25, 179-86, doi: 10.1093/molbev/msm237.

5. Keeling, P. J., and Doolittle, W. F. (1996) A non-canonical genetic code in an early diverging eukaryotic lineage, EMBO J., 15, 2285-90, doi: 10.1002/j.1460-2075.1996.tb00581.x.

6. Keeling, P. J., and Leander, B. S. (2003) Characterisation of a non-canonical genetic code in the oxymonad Streblomastix strix, J. Mol. Biol., 326, 1337-49, doi: 10.1016/s0022-2836(03)00057-3.

7. Záhonová, K., Kostygov, A., Ševčíková, T., Yurchenko, V., and Eliáš, M. (2016) An unprecedented non-canonical nuclear genetic code with all three termination codons reassigned as sense codons, Curr. Biol., 26, 2364-2369, doi: 10.1016/j.cub.2016.06.064.

8. Ohama, T., Inagaki, Y., Bessho, Y., and Osawa, S. (2008) Evolving genetic code, Proc. Jpn. Acad. Ser. B Phys. Biol. Sci., 84, 58-74, doi: 10.2183/pjab.84.58.

9. Cocquyt, E., Gile, G. H., Leliaert, F., Verbruggen, H., Keeling, P. J., et al. (2010) Complex phylogenetic distribution of a non-canonical genetic code in green algae, BMC Evol. Biol., 10, 327, doi: 10.1186/1471-2148-10-327.

10. Swart, E. C., Serra, V., Petroni, G., and Nowacki, M. (2016) Genetic codes with no dedicated stop codon: Context-dependent translation termination, Cell, 166, 3, 691-702, doi: 10.1016/j.cell.2016.06.020.

11. Pánek, T., Žihala, D., Sokol, M., Derelle, R., Klimeš, V., et al. (2017) Nuclear genetic codes with a different meaning of the UAG and the UAA codon, BMC Biol., 15, 8, doi: 10.1186/s12915-017-0353-y.

12. Mukai, T., Lajoie, M.J., Englert, M., and Söll, D. (20170 Rewriting the genetic code, Annu. Rev. Microbiol., 71, 557-577, doi: 10.1146/annurev-micro-090816-093247.

13. Ling, J., O’Donoghue, P., and Söll, D. (2015) Genetic code flexibility in microorganisms: Novel mechanisms and impact on physiology, Nat. Rev. Microbiol., 13, 707-721, doi: 10.1038/nrmicro3568.

14. Bezerra, A., Guimarães, A., and Santos, M. (2015) Non-standard genetic codes define new concepts for protein engineering, Life, 5, 1610-1628, doi: 10.3390/life5041610.

15. De Valles-Ibáñez, G., Hernandez-Rodriguez, J., Prado-Martinez, J., Luisi, P., Marquès-Bonet, T., et al. (2016) Genetic load of loss-of-function polymorphic variants in great apes, Genome Biol. Evol., 8, 871-877, doi: 10.1093/gbe/evw040.

16. Flowers, J. M., Hazzouri, K. M., Pham, G. M., Rosas, U., Bahmani, T., et al. (2015) Whole-genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii, Plant Cell, 27, 2353-2369, doi: 10.1105/tpc.15.00492.

17. MacArthur, D. G., Balasubramanian, S., Frankish, A., Huang, N., Morris, J., et al. (2012) A systematic survey of loss-of-function variants in human protein-coding genes, Science, 335, 823-828, doi: 10.1126/science.1215040.

18. Li, A. H., Morrison, A. C., Kovar, C., Cupples, L. A., Brody, J. A., et al. (2015) Analysis of loss-of-function variants and 20 risk factor phenotypes in 8,554 individuals identifies loci influencing chronic disease, Nat. Genet., 47, 640-642, doi: 10.1038/ng.3270.

19. Groenen, M. A., Archibald, A. L., Uenishi, H., Tuggle, C. K., Takeuchi, Y., et al. (2012) Analyses of pig genomes provide insight into porcine demography and evolution, Nature, 491, 393-398, doi: 10.1038/nature11622.

20. Lack, J. B., Cardeno, C. M., Crepeau, M. W., Taylor, W., Corbett-Detig, R. B., et al. (2015) The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population, Genetics, 199, 4, 1229-1241, doi: 10.1534/genetics.115.174664.

21. Yang, H., He, B. Z., Ma, H., Tsaur, S. C., Ma, C., et al. (2015) Expression profile and gene age jointly shaped the genome-wide distribution of premature termination codons in a Drosophila melanogaster population, Mol. Biol. Evol., 32, 216-228, doi: 10.1093/molbev/msu299.

22. Xu, Y. C., Niu, X. M., Li, X. X., He, W., Chen, J. F., et al. (2019) Adaptation and phenotypic diversification in arabidopsis through loss-of-function mutations in protein-coding genes, Plant Cell, 31, 5, 1012-1025, doi: 10.1105/tpc.18.00791.

23. Monroe, J. G., McKay, J. K., Weigel, D., and Flood, P. J. (2021) The population genomics of adaptive loss of function, Heredity, 126, 383-395, doi: 10.1038/s41437-021-00403-2.

24. MacArthur, D. G., and Tyler-Smith, C. (2010) Loss-of-function variants in the genomes of healthy humans, Hum. Mol. Genet., 19, R125-R130, doi: 10.1093/hmg/ddq365.

25. Mort, M., Ivanov, D., Cooper, D. N., and Chuzhanova, N. A. (2008) A meta-analysis of nonsense mutations causing human genetic disease, Hum. Mutat., 29, 8, 1037-1047, doi: 10.1002/humu.20763.

26. Gorlov, I. P., Kimmel, M., and Amos, C. I. (2006) Strength of the purifying selection against different categories of the point mutations in the coding regions of the human genome, Hum. Mol. Genet., 15, 7, 1143-1150, doi: 10.1093/hmg/ddl029.

27. Marth, G. T., Yu, F., Indap, A. R., Garimella, K., Gravel, S., et al. (2011) The functional spectrum of low-frequency coding variation, Genome Biol., 12, R84, doi: 10.1186/gb-2011-12-9-r84.

28. Lee, Y. C., and Reinhardt, J. A. (2012) Widespread polymorphism in the positions of stop codons in Drosophila melanogaster, Genome Biol. Evol., 4, 533-549, doi: 10.1093/gbe/evr113.

29. Hernandez-Gonzalez, I., Tenorio-Castano, J., Ochoa-Parra, N., Gallego, N., Pérez-Olivares, C., et al. (2021) Novel genetic and molecular pathways in pulmonary arterial hypertension associated with connective tissue disease, Cells, 10, 1488, doi: 10.3390/cells10061488.

30. Guerreiro, R., Brás, J., Wojtas, A., Rademakers, R., Hardy, J., et al. (2014) Nonsense mutation in PRNP associated with clinical Alzheimer’s disease, Neurobiol. Aging, 35, 2656.e13-2656.e16, doi: 10.1016/j.neurobiolaging.2014.05.013.

31. Nakamura, K., Sekijima, Y., Nagamatsu, K., Yoshida, K., and Ikeda, S. (2012) A novel nonsense mutation in the TITF-1 gene in a Japanese family with benign hereditary chorea, J. Neurol. Sci., 313, 189-192, doi: 10.1016/j.jns.2011.09.013.

32. Nieminen, P., Arte, S., Tanner, D., Paulin, L., Alaluusua, S., et al. (2001) Identification of a nonsense mutation in the PAX9 gene in molar oligodontia, Eur. J. Human Genet., 9, 743-746, doi: 10.1038/sj.ejhg.5200715.

33. Ruwald, M. H., Xu Parks, X., Moss, A. J., Zareba, W., Baman, J., et al. (2016), Stop-codon and C-terminal nonsense mutations are associated with a lower risk of cardiac events in patients with long QT syndrome type 1, Heart Rhythm, 13, 122-131, doi: 10.1016/j.hrthm.2015.08.033.

34. Yamaguchi-Kabata, Y., Shimada, M. K., Hayakawa, Y., Minoshima, S., et al. (2008), Distribution and effects of nonsense polymorphisms in human genes, PLoS One, 3, 10, e3393, doi: 10.1371/journal.pone.0003393.

35. DeBoever, C., Tanigawa, Y., Lindholm, M. E., McInnes, G., Lavertu, A., et al. (2018) Medical relevance of protein-truncating variants across 337,205 individuals in the UK Biobank study, Nat. Commun., 9, 1612, doi: 10.1038/s41467-018-03910-9.

36. Xu, H., Zhen, Q., Bai, M., Fang, L., Zhang, Y., et al. (2021) Deep sequencing of 1320 genes reveals the landscape of protein-truncating variants and their contribution to psoriasis in 19,973 Chinese individuals, Genome Res., 31, 1150-1158, doi: 10.1101/gr.267963.120.

37. Xu, Y. C., and Guo, Y. L. (2020) Less is more, natural loss-of-function mutation is a strategy for adaptation, Plant Commun., 1, 100103, doi: 10.1016/j.xplc.2020.100103.

38. Kaler, S. G., Tang, J., Donsante, A., and Kaneski, C. R. (2009) Translational read-through of a nonsense mutation in ATP7A impacts treatment outcome in Menkes disease, Ann. Neurol., 65, 108-113, doi: 10.1002/ana.21576.

39. Roosing, S., Rosti, R. O., Rosti, B., de Vrieze, E., Silhavy, J. L., et al. (2016) Identification of a homozygous nonsense mutation in KIAA0556 in a consanguineous family displaying Joubert syndrome, Hum. Genet., 135, 919-921, doi: 10.1007/s00439-016-1689-z.

40. Perez, H., Abdallah, M. F., Chavira, J. I., Norris, A. S., Egeland, M. T., et al. (2021) A novel, ataxic mouse model of ataxia telangiectasia caused by a clinically relevant nonsense mutation, eLife, 10, e64695, doi: 10.7554/eLife.64695.

41. Yang, C., Feng, J., Song, W., Wang, J., Tsai, B., et al. (2007) A mouse model for nonsense mutation bypass therapy shows a dramatic multiday response to geneticin, Proc. Natl. Acad. Sci. USA, 104, 15394-15399, doi: 10.1073/pnas.0610878104.

42. McHugh, D. R., Steele, M. S., Valerio, D. M., Miron, A., Mann, R. J., et al. (2018) A G542X cystic fibrosis mouse model for examining nonsense mutation directed therapies, PLoS One, 13, e0199573, doi: 10.1371/journal.pone.0199573.

43. Flossmann, G., Wurmser, C., Pausch, H., Tenghe, A., Doddenhoff, J., et al. (2021) A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs, BMC Genomics, 22, 38, doi: 10.1186/s12864-020-07343-x.

44. Derks, M., Gjuvsland, A. B., Bosse, M., Lopes, M. S., van Son, M., et al. (2019) Loss of function mutations in essential genes cause embryonic lethality in pigs, PLoS Genet., 15, e1008055, doi: 10.1371/journal.pgen.1008055.

45. Sonstegard, T. S., Cole, J. B., VanRaden, P. M., Van Tassell, C. P., Null, D. J., et al. (2013) Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle, PLoS One, 8, e54872, doi: 10.1371/journal.pone.0054872.

46. Ricketts, M. H., Simons, M. J., Parma, J., Mercken, L., Dong, Q., et al. (1987) A nonsense mutation causes hereditary goitre in the Afrikander cattle and unmasks alternative splicing of thyroglobulin transcripts, Proc. Natl. Acad. Sci. USA, 84, 3181-3184, doi: 10.1073/pnas.84.10.3181.

47. Wells, K. L., Hadad, Y., Ben-Avraham, D., Hillel, J., Cahaner, A., et al. (2012) Genome-wide SNP scan of pooled DNA reveals nonsense mutation in FGF20 in the scaleless line of featherless chickens, BMC Genomics, 13, 257, doi: 10.1186/1471-2164-13-257.

48. Damé, M. C., Xavier, G. M., Oliveira-Filho, J. P., Borges, A. S., Oliveira, H. N., et al. (2012) A nonsense mutation in the tyrosinase gene causes albinism in water buffalo, BMC Genetics, 13, 62, doi: 10.1186/1471-2156-13-62.

49. Chintamaneni, C. D., Halaban, R., Kobayashi, Y., Witkop, C. J., Jr, and Kwon, B. S. (1991) A single base insertion in the putative transmembrane domain of the tyrosinase gene as a cause for tyrosinase-negative oculocutaneous albinism. Proc. Natl. Acad. Sci. USA, 88, 5272-5276, doi: 10.1073/pnas.88.12.5272.

50. Rafique, M. Z., Carvalho, E., Stracke, R., Palmieri, L., Herrera, L., et al. (2016) Nonsense mutation inside anthocyanidin synthase gene controls pigmentation in yellow raspberry (Rubus idaeus L.), Front. Plant Sci., 7, 1892, doi: 10.3389/fpls.2016.01892.

51. Ishishita, S., Takahashi, M., Yamaguchi, K., Kinoshita, K., Nakano, M., et al. (2018) Nonsense mutation in PMEL is associated with yellowish plumage colour phenotype in Japanese quail, Sci. Rep., 8, 1, 16732, doi: 10.1038/s41598-018-34827-4.

52. Wu, W., Liu, X., Wang, M., Meyer, R. S., Luo, X., et al. (2017) A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication, Nat. Plants, 3, 17064, doi: 10.1038/nplants.2017.64.

53. Amrad, A., Moser, M., Mandel, T., de Vries, M., Schuurink, R. C., et al. (2016) Gain and loss of floral scent production through changes in structural genes during pollinator-mediated speciation, Curr. Biol., 26, 3303-3312, doi: 10.1016/j.cub.2016.10.023.

54. Zhao, Y., Wang, H., Poole, R. J., and Gems, D. (2019) A fln-2 mutation affects lethal pathology and lifespan in C. elegans, Nat. Commun., 10, 5087, doi: 10.1038/s41467-019-13062-z.

55. Hoehn, K. B., McGaugh, S. E., and Noor, M. A. (2012) Effects of premature termination codon polymorphisms in the Drosophila pseudoobscura subclade, J. Mol. Evol., 75, 141-150, doi: 10.1007/s00239-012-9528-x.

56. MacArthur, D. G., Seto, J. T., Raftery, J. M., Quinlan, K. G., Huttley, G. A., et al. (2007) Loss of ACTN3 gene function alters mouse muscle metabolism and shows evidence of positive selection in humans, Nat. Genet., 39, 1261-1265, doi: 10.1038/ng2122.

57. North, K. N., Yang, N., Wattanasirichaigoon, D., Mills, M., Easteal, S., et al. (1999) A common nonsense mutation results in alpha-actinin-3 deficiency in the general population, Nat. Genetics, 21, 353-354, doi: 10.1038/7675.

58. Xue, Y., Daly, A., Yngvadottir, B., Liu, M., Coop, G., et al. (2006) Spread of an inactive form of caspase-12 in humans is due to recent positive selection, Am. J. Hum. Genet., 78, 659-670, doi: 10.1086/503116.

59. Fry, A. E., Ghansa, A., Small, K. S., Palma, A., Auburn, S., et al. (2009) Positive selection of a CD36 nonsense variant in sub-Saharan Africa, but no association with severe malaria phenotypes, Hum. Mol. Genet., 18, 2683-2692, doi: 10.1093/hmg/ddp192.

60. Flannick, J., Thorleifsson, G., Beer, N. L., Jacobs, S. B., Grarup, N., et al. (2014) Loss-of-function mutations in SLC30A8 protect against type 2 diabetes, Nat. Genet., 46, 357-363, doi: 10.1038/ng.2915.

61. Dwivedi, O. P., Lehtovirta, M., Hastoy, B., Chandra, V., Krentz, N., et al. (2019) Loss of ZnT8 function protects against diabetes by enhanced insulin secretion, Nat. Genet., 51, 1596-1606, doi: 10.1038/s41588-019-0513-9.

62. Olson M. V. (1999) When less is more: Gene loss as an engine of evolutionary change, Am. J. Hum. Genet, 64, 18-23, doi: 10.1086/302219.

63. Mills, M., Yang, N., Weinberger, R., Vander Woude, D. L., Beggs, A. H., et al. (2001) Differential expression of the actin-binding proteins, alpha-actinin-2 and -3, in different species: implications for the evolution of functional redundancy, Hum. Mol. Genet., 10, 1335-1346, doi: 10.1093/hmg/10.13.1335.

64. Niemi, A. K., and Majamaa, K. (2005) Mitochondrial DNA and ACTN3 genotypes in Finnish elite endurance and sprint athletes, Eur. J. Hum. Genet., 13, 965-969, doi: 10.1038/sj.ejhg.5201438.

65. Wang, X., Grus, W. E., and Zhang, J. (2006) Gene losses during human origins, PLoS Biol., 4, e52, doi: 10.1371/journal.pbio.0040052.

66. Xiang, Y., Song, B., Née, G., Kramer, K., Finkemeier, I., et al. (2016) Sequence Polymorphisms at the reduced DORMANCY5 pseudophosphatase underlie natural variation in Arabidopsis dormancy, Plant Physiol., 171, 2659-2670, doi: 10.1104/pp.16.00525.

67. Matika, O., Robledo, D., Pong-Wong, R., Bishop, S. C., Riggio, V., et al. (2019) Balancing selection at a premature stop mutation in the myostatin gene underlies a recessive leg weakness syndrome in pigs, PLoS Genet., 15, e1007759, doi: 10.1371/journal.pgen.1007759.

68. Landrum, M. J., Lee, J. M., Benson, M., Brown, G. R., Chao, C., et al. (2018) ClinVar: improving access to variant interpretations and supporting evidence, Nucleic Acids Res., 46, D1062-D1067, doi: 10.1093/nar/gkx1153.

69. Karczewski, K. J., Francioli, L. C., Tiao, G., Cummings, B. B., Alföldi, J., et al. (2020) The mutational constraint spectrum quantified from variation in 141,456 humans, Nature, 581, 434-443, doi: 10.1038/s41586-020-2308-7.

70. Stenson, P. D., Mort, M., Ball, E. V., Chapman, M., Evans, K., et al. (2020) The human gene mutation database (HGMD®): Optimizing its use in a clinical diagnostic or research setting, Hum. Genet., 139, 1197-1207, doi: 10.1007/s00439-020-02199-3.

71. Tate, J. G., Bamford, S., Jubb, H. C., Sondka, Z., Beare, D. M., et al. (2019) COSMIC: The catalogue of somatic mutations in cancer, Nucleic Acids Res., 47, D941-D947, doi: 10.1093/nar/gky1015.

72. McKusick, V. A. (1998) Mendelian Inheritance in Man. A Catalog of Human Genes and Genetic Disorders (12th edition) Baltimore: Johns Hopkins University Press.

73. Fokkema, I. F., Taschner, P. E., Schaafsma, G. C., Celli, J., Laros, J. F., et al. (2011) LOVD v.2.0: The next generation in gene variant databases, Hum. Mutat., 32, 557-563, doi: 10.1002/humu.21438.

74. Blake, J. A., Baldarelli, R., Kadin, J. A., Richardson, J. E., Smith, C. L., et al. (2021) Mouse Genome Database (MGD): Knowledgebase for mouse-human comparative biology, Nucleic Acids Res., 49, D981-D987, doi: 10.1093/nar/gkaa1083.

75. Chen, N., Fu, W., Zhao, J., Shen, J., Chen, Q., et al. (2020) BGVD: An integrated database for bovine sequencing variations and selective signatures, Genom. Proteom. Bioinform., 18, 186-193, doi: 10.1016/j.gpb.2019.03.007.

76. Rhee, S. Y., Beavis, W., Berardini, T. Z., Chen, G., Dixon, D., et al. (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community, Nucleic Acids Res., 31, 1, 224-228, doi: 10.1093/nar/gkg076.

77. Li, W. H., Gojobori, T., and Nei, M. (1981) Pseudogenes as a paradigm of neutral evolution, Nature, 292, 237-239, doi: 10.1038/292237a0.

78. Li, W. H., Gojobori, T., and Nei, M. (1981) Evolution of pseudogenes and its relevance to the neutrality vs selection controversy, Genetics, 97, 1.

79. Singleton, B. K., Green, C. A., Avent, N. D., Martin, P. G., Smart, E., et al. (2000) The presence of an RHD pseudogene containing a 37 base pair duplication and a nonsense mutation in africans with the Rh D-negative blood group phenotype, Blood, 95, 12-18.

80. Harrison, P. M., Milburn, D., Zhang, Z., Bertone, P., and Gerstein, M. (2003) Identification of pseudogenes in the Drosophila melanogaster genome, Nucleic Acids Res., 31, 1033-1037, doi: 10.1093/nar/gkg169.

81. Potapova, N. A., Andrianova, M. A., Bazykin, G. A., and Kondrashov, A. S. (2018) Are nonsense alleles of Drosophila melanogaster genes under any selection? Gen. Biol. Evol., 10, 1012-1018, doi: 10.1093/gbe/evy032.

82. Prieto-Godino, L. L., Rytz, R., Bargeton, B., Abuin, L., Arguello, J. R., et al. (2016) Olfactory receptor pseudo-pseudogenes, Nature, 539, 93-97, doi: 10.1038/nature19824.

83. Dos Santos, G., Schroeder, A. J., Goodman, J. L., Strelets, V. B., Crosby, M. A., et al. (2015) FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations, Nucleic Acids Res., 43, D690-D697, doi: 10.1093/nar/gku1099.

84. Wetterbom, A., Gyllensten, U., Cavelier, L., and Bergström, T. F. (2009) Genome-wide analysis of chimpanzee genes with premature termination codons, BMC Genom., 10, 56, doi: 10.1186/1471-2164-10-56.

85. Xu, J., and Zhang, J. (2016). Are human translated pseudogenes functional? Mol. Biol. Evol., 33, 755-760, doi: 10.1093/molbev/msv268.

86. Torella, A., Zanobio, M., Zeuli, R., Del Vecchio Blanco, F., Savarese, M., et al. (2020) The position of nonsense mutations can predict the phenotype severity: A survey on the DMD gene, PLoS One, 15, 8, e0237803, doi: 10.1371/journal.pone.0237803.

87. Valentine, C. R. (1998) The association of nonsense codons with exon skipping, Mutat. Res., 411, 87-117, doi: 10.1016/s1383-5742(98)00010-6.

88. Thein, S. L. (2004) Genetic insights into the clinical diversity of beta thalassaemia, Br. J. Haematol., 124, 264-274, doi: 10.1046/j.1365-2141.2003.04769.x.

89. Skraban, C. M., Wells, C. F., Markose, P., Cho, M. T., Nesbitt, A. I., et al. (2017) WDR26 haploinsufficiency causes a recognizable syndrome of intellectual disability, seizures, abnormal gait, and distinctive facial features, Am. J. Hum. Genet., 101, 139-148, doi: 10.1016/j.ajhg.2017.06.002.

90. Kuehn, H. S., Bernasconi, A., Niemela, J. E., Almejun, M. B., Gallego, W., et al. (2020) A nonsense N-terminus NFKB2 mutation leading to haploinsufficiency in a patient with a predominantly antibody deficiency, J. Clin. Immunol., 40, 1093-1101, doi: 10.1007/s10875-020-00842-2.

91. Zhang, X., Chai, J., Azhar, G., Sheridan, P., Borras, A. M., et al. (2001) Early postnatal cardiac changes and premature death in transgenic mice overexpressing a mutant form of serum response factor, J. Biol. Chem., 276, 40033-40040, doi: 10.1074/jbc.M104934200.

92. Yngvadottir, B., Xue, Y., Searle, S., Hunt, S., Delgado, M., et al. (2009) A genome-wide survey of the prevalence and evolutionary forces acting on human nonsense SNPs, Am. J. Hum. Genet., 84, 224-234, doi: 10.1016/j.ajhg.2009.01.008.

93. Casci, T. (2011) Molecular evolution: Dealing with nonsense, Nat. Rev. Genet., 12, 805, doi: 10.1038/nrg3109.

94. Cusack, B. P., Arndt, P. F., Duret, L., and Roest Crollius, H. (2011) Preventing dangerous nonsense: Selection for robustness to transcriptional error in human genes, PLoS Genet., 7, e1002276, doi: 10.1371/journal.pgen.1002276.

95. Ma, Z., and Chen, J. (2020) Premature termination codon-bearing mRNA mediates genetic compensation response, Zebrafish, doi: 10.1089/zeb.2019.1824.

96. Ma, Z., Zhu, P., Shi, H., Guo, L., Zhang, Q., et al. (2019) PTC-bearing mRNA elicits a genetic compensation response via Upf3a and COMPASS components, Nature, 568, 259-263, doi: 10.1038/s41586-019-1057-y.

97. Ma, Z. P., and Chen, J. (2019) Hereditas, 41, 359-364, doi: 10.16288/j.yczz.19-101.

98. El-Brolosy, M. A., and Stainier, D. (2017) Genetic compensation: A phenomenon in search of mechanisms, PLoS Genet., 13, e1006780, doi: 10.1371/journal.pgen.1006780.

99. Chang, Y. F., Imam, J. S., and Wilkinson, M. F. (2007) The nonsense-mediated decay RNA surveillance pathway, Annu. Rev. Biochem., 76, 51-74, doi: 10.1146/annurev.biochem.76.050106.093909.

100. Riehs-Kearnan, N., Gloggnitzer, J., Dekrout, B., Jonak, C., and Riha, K. (2012) Aberrant growth and lethality of Arabidopsis deficient in nonsense-mediated RNA decay factors is caused by autoimmune-like response, Nucleic Acids Res., 40, 5615-5624, doi: 10.1093/nar/gks195.

101. Maquat, L. E. (2005) Nonsense-mediated mRNA decay in mammals, J. Cell Sci., 118, 1773-1776, doi: 10.1242/jcs.01701.

102. Kurosaki, T., Popp, M. W., and Maquat, L. E. (2019) Quality and quantity control of gene expression by nonsense-mediated mRNA decay, Nat. Rev. Mol. Cell Biol., 20, 406-420, doi: 10.1038/s41580-019-0126-2.

103. Stalder, L., and Mühlemann, O. (2008) The meaning of nonsense, Trends Cell Biol., 18, 315-321, doi: 10.1016/j.tcb.2008.04.005.

104. Khajavi, M., Inoue, K., and Lupski, J. R. (2006) Nonsense-mediated mRNA decay modulates clinical outcome of genetic disease, Eur. J. Hum. Genet., 14, 1074-1081, doi: 10.1038/sj.ejhg.5201649.

105. Holbrook, J. A., Neu-Yilik, G., Hentze, M. W., and Kulozik, A. E. (2004) Nonsense-mediated decay approaches the clinic, Nat. Genet., 36, 801-808, doi: 10.1038/ng1403.

106. Lindeboom, R. G., Supek, F., and Lehner, B. (2016) The rules and impact of nonsense-mediated mRNA decay in human cancers, Nat. Genet., 48, 1112-1118, doi: 10.1038/ng.3664.

107. Hwang, J., and Kim, Y. K. (2013) When a ribosome encounters a premature termination codon, BMB Rep., 46, 9-16, doi: 10.5483/bmbrep.2013.46.1.002.

108. Nickless, A., Bailis, J. M., and You, Z. (2017) Control of gene expression through the nonsense-mediated RNA decay pathway, Cell Biosci., 7, 26, doi: 10.1186/s13578-017-0153-7.

109. Kervestin, S., and Jacobson, A. (2012). NMD: A multifaceted response to premature translational termination, Nat. Rev. Mol. Cell Biol., 13, 700-712, doi: 10.1038/nrm3454.

110. Kalyna, M., Simpson, C. G., Syed, N. H., Lewandowska, D., Marquez, Y., et al. (2012) Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis, Nucleic Acids Res., 40, 2454-2469, doi: 10.1093/nar/gkr932.

111. Rayson, S., Arciga-Reyes, L., Wootton, L., De Torres Zabala, M., Truman, W., et al. (2012) A role for nonsense-mediated mRNA decay in plants: pathogen responses are induced in Arabidopsis thaliana NMD mutants, PLoS One, 7, e31917, doi: 10.1371/journal.pone.0031917.

112. Shi, C., Baldwin, I. T., and Wu, J. (2012) Arabidopsis plants having defects in nonsense-mediated mRNA decay factors UPF1, UPF2, and UPF3 show photoperiod-dependent phenotypes in development and stress responses, J. Integr. Plant Biol., 54, 99-114, doi: 10.1111/j.1744-7909.2012.01093.x.

113. Sato, H., and Singer, R. H. (2021) Cellular variability of nonsense-mediated mRNA decay, Nat. Commun., 12, 7203, doi: 10.1038/s41467-021-27423-0.

114. Zetoune, A. B., Fontanière, S., Magnin, D., Anczuków, O., Buisson, M., et al. (2008) Comparison of nonsense-mediated mRNA decay efficiency in various murine tissues, BMC Genet., 9, 83, doi: 10.1186/1471-2156-9-83.

115. Teran, N. A., Nachun, D. C., Eulalio, T., Ferraro, N. M., Smail, C., et al. (2021) Nonsense-mediated decay is highly stable across individuals and tissues, Am. J. Hum. Genet., 108, 1401-1408, doi: 10.1016/j.ajhg.2021.06.008.

116. Nagy, E., and Maquat, L. E. (1998) A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance, Trends Biochem. Sci., 23, 198-199, doi: 10.1016/s0968-0004(98)01208-0.

117. Neu-Yilik, G., Amthor, B., Gehring, N. H., Bahri, S., Paidassi, H., et al. (2011) Mechanism of escape from nonsense-mediated mRNA decay of human beta-globin transcripts with nonsense mutations in the first exon, RNA, 17, 843-854, doi: 10.1261/rna.2401811.

118. Inácio, A., Silva, A. L., Pinto, J., Ji, X., Morgado, A., et al. (2004) Nonsense mutations in close proximity to the initiation codon fail to trigger full nonsense-mediated mRNA decay, J. Biol. Chem., 279, 32170-32180, doi: 10.1074/jbc.M405024200.

119. Perrin-Vidoz, L., Sinilnikova, O. M., Stoppa-Lyonnet, D., Lenoir, G. M., and Mazoyer, S. (2002) The nonsense-mediated mRNA decay pathway triggers degradation of most BRCA1 mRNAs bearing premature termination codons, Hum. Mol. Genet., 11, 2805-2814, doi: 10.1093/hmg/11.23.2805.

120. Dyle, M. C., Kolakada, D., Cortazar, M. A., and Jagannathan, S. (2020) How to get away with nonsense: Mechanisms and consequences of escape from nonsense-mediated RNA decay, Wiley Interdiscip. Rev RNA, 11, e1560, doi: 10.1002/wrna.1560.

121. Jungreis, I., Lin, M. F., Spokony, R., Chan, C. S., Negre, N., et al. (2011) Evidence of abundant stop codon readthrough in Drosophila and other metazoa, Genome Res., 21, 2096-2113, doi: 10.1101/gr.119974.110.

122. Adachi, H., and Yu, Y. T. (2020) Pseudouridine-mediated stop codon readthrough in S. cerevisiae is sequence context-independent, RNA, 26, 1247-1256, doi: 10.1261/rna.076042.120.

123. McCaughan, K. K., Brown, C. M., Dalphin, M. E., Berry, M. J., and Tate, W. P. (1995) Translational termination efficiency in mammals is influenced by the base following the stop codon, Proc. Natl. Acad. Sci. USA, 92, 5431-5435, doi: 10.1073/pnas.92.12.5431.

124. Cassan, M., and Rousset, J. P. (2001) UAG readthrough in mammalian cells: Effect of upstream and downstream stop codon contexts reveal different signals, BMC Mol. Biol., 2, 3, doi: 10.1186/1471-2199-2-3.

125. Stiebler, A. C., Freitag, J., Schink, K. O., Stehlik, T., Tillmann, B. A., et al. (2014) Ribosomal readthrough at a short UGA stop codon context triggers dual localization of metabolic enzymes in Fungi and animals, PLoS Genet., 10, e1004685, doi: 10.1371/journal.pgen.1004685.

126. Chen, Y., Sun, T., Bi, Z., Ni, J. Q., Pastor-Pareja, J. C., et al. (2020) Premature termination codon readthrough in Drosophila varies in a developmental and tissue-specific manner, Sci. Rep., 10, 1, 8485, doi: 10.1038/s41598-020-65348-8.

127. Böck, A., Forchhammer, K., Heider, J., Leinfelder, W., Sawers, G., et al. (1991) Selenocysteine: The 21st amino acid, Mol. Microbiol., 5, 515-520, doi: 10.1111/j.1365-2958.1991.tb00722.x.

128. Keeling, K. M., Xue, X., Gunn, G., and Bedwell, D. M. (2014) Therapeutics based on stop codon readthrough, Annu. Rev. Genom. Hum. Genet., 15, 371-394, doi: 10.1146/annurev-genom-091212-153527.

129. Peltz, S. W., Morsy, M., Welch, E. M., and Jacobson, A. (2013) Ataluren as an agent for therapeutic nonsense suppression, Annu. Rev. Med., 64, 407-425, doi: 10.1146/annurev-med-120611-144851.

130. Roy, B., Friesen, W. J., Tomizawa, Y., Leszyk, J. D., Zhuo, J., et al. (2016) Ataluren stimulates ribosomal selection of near-cognate tRNAs to promote nonsense suppression, Proc. Natl. Acad. Sci. USA, 113, 12508-12513, doi: 10.1073/pnas.1605336113.

131. Peled, A., Samuelov, L., Sarig, O., Bochner, R., Malki, L., et al. (2020) Treatment of hereditary hypotrichosis simplex of the scalp with topical gentamicin, Br. J. Dermatol., 183, 114-120, doi: 10.1111/bjd.18718.

132. Leubitz, A., Vanhoutte, F., Hu, M. Y., Porter, K., Gordon, E., et al. (2021) A randomized, double-blind, placebo-controlled, multiple dose escalation study to evaluate the safety and pharmacokinetics of ELX-02 in healthy subjects, Clin. Pharmacol. Drug Dev., 10, 859-869, doi: 10.1002/cpdd.914.

133. Martins-Dias, P., and Romão, L. (2021) Nonsense suppression therapies in human genetic diseases, Cell. Mol. Life Sci., 78, 4677-4701, doi: 10.1007/s00018-021-03809-7.

134. Morais, P., Adachi, H., and Yu, Y. T. (2020) Suppression of nonsense mutations by new emerging technologies, Int. J. Mol. Sci., 21, 4394, doi: 10.3390/ijms21124394.

135. Melfi, R., Cancemi, P., Chiavetta, R., Barra, V., Lentini, L., et al. (2020) Investigating REPAIRv2 as a tool to edit CFTR mRNA with premature stop codons, Int. J. Mol. Sci., 21, 4781, doi: 10.3390/ijms21134781.