Uloga kodirajućih i nekodirajućih DNA regija u razvoju genetskih poremećaja
DOI:
https://doi.org/10.13112/pc.1047Ključne riječi:
GENETIČKE BOLESTI, UROĐENE, INTRONI, EGZONI, STRUKTURE KROMOSOMASažetak
Cilj: Ovaj pregledni članak analizira ulogu kodirajućih i nekodirajućih regija ljudskog genoma u razvoju genetskih poremećaja, s posebnim naglaskom na različite tipove genetskih varijanti i mehanizme njihovog djelovanja.
Metode: Provedena je detaljna analiza dostupne znanstvene literature koja se bavi utjecajem varijanti pojedinačnih nukleotida, insercija, delecija i varijanti broja kopija u kodirajućim i nekodirajućim regijama genoma. Posebna pažnja posvećena je mehanizmima poput promjena u strukturi i funkciji proteina, regulaciji ekspresije gena te utjecaju na stabilnost mRNA.
Rezultati: Kodirajuće varijante, uključujući sinonimne, besmislene i pogrešne varijante, mogu značajno utjecati na strukturu, funkciju i stabilnost proteina, što dovodi do različitih genetskih poremećaja. Nekodirajuće varijante, smještene u cis i trans regulatornim elementima, igraju ključnu ulogu u regulaciji ekspresije gena, organizaciji i stabilizaciji genoma. Varijante u nekodirajućim regijama mogu utjecati na prekrajanje gena, transkripciju, translaciju te stabilnost RNA, što također može rezultirati patološkim stanjima.
Zaključak: Razumijevanje utjecaja genetskih varijanti u kodirajućim i nekodirajućim regijama genoma ključno je za bolje razumijevanje mehanizama patogeneze i genetske osnove brojnih bolesti. Uključivanje nekodirajućih varijanti u istraživanja može doprinijeti poboljšanju dijagnostičkih i terapijskih pristupa u medicini.
Reference
1. Nurk S, Koren S, Rhie A, et al. The complete sequence of a human genome. Science. 2022;376(6588):44–53. doi:10.1126/science.abj6987
2. Maurano MT, Humbert R, Rynes E, et al. Systematic localization of common disease-associated variation in regulatory DNA. Science. 2012;337(6099):1190–5. doi:10.1126/science.1222794
3. Stenson PD, Ball EV, Mort M, et al. Human Gene Mutation Database (HGMD®): 2003 update. Hum Mutat. 2003;21(6):577–81. doi:10.1002/humu.10216
4. Antonarakis SE, Cooper DN. Human Gene Mutation in Inherited Disease. In: Emery and Rimoin’s Principles and Practice of Medical Genetics. 2013;1–48.
5. Dhindsa RS, Copeland BR, Mustoe AM, Goldstein DB. Natural selection shapes codon usage in the human genome. Am J Hum Genet. 2020;107(1):83–95. doi:10.1016/j.ajhg.2020.05.014
6. Rosen EM, Fan S, Pestell RG, Goldberg ID. BRCA1 gene in breast cancer. J Cell Physiol. 2003;196(1):19–41. doi:10.1002/jcp.10212
7. Montera M, Piaggio F, Marchese C, et al. A silent mutation in exon 14 of the APC gene is associated with exon skipping in a FAP family. J Med Genet. 2001;38(12):863–7. doi:10.1136/jmg.38.12.863
8. Temaj G, Telkoparan-Akillilar P, Nuhii N, Chichiarelli S, Saha S, Saso L. Recoding of Nonsense Mutation as a Pharmacological Strategy. Biomedicines. 2023;11(3):659. doi:10.3390/biomedicines11030659
9. Boyle MP, De Boeck K. A new era in the treatment of cystic fibrosis: correction of the underlying CFTR defect. Lancet Respir Med. 2013;1(2):158–63. doi:10.1016/S2213-2600(13)70010-8
10. Sharma J, Du M, Wong E, et al. A small molecule that induces translational readthrough of CFTR nonsense mutations by eRF1 depletion. Nat Commun. 2021;12(1):4358. doi:10.1038/s41467-021-24613-z
11. Petrosino M, Novak L, Pasquo A, et al. Analysis and interpretation of the impact of missense variants in cancer. Int J Mol Sci. 2021;22(11):5416. doi:10.3390/ijms22115416
12. Morais VA, Verstreken P, Roethig A, et al. Parkinson’s disease mutations in PINK1 result in decreased Complex I activity and deficient synaptic function. EMBO Mol Med. 2009;1(2):99–111. doi:10.1002/emmm.200900032
13. Webster MK, Donoghue DJ. Constitutive activation of fibroblast growth factor receptor 3 by the transmembrane domain point mutation found in achondroplasia. EMBO J. 1996;15(3):520–7. doi:10.1002/j.1460-2075.1996.tb00317.x
14. Bellus GA, Spector EB, Speiser PW, et al. Distinct missense mutations of the FGFR3 lys650 codon modulate receptor kinase activation and the severity of the skeletal dysplasia phenotype. Am J Hum Genet. 2000;67(6):1411-21. doi:10.1086/316876
15. Ball EV, Stenson PD, Abeysinghe SS, Krawczak M, Cooper DN, Chuzhanova NA. Microdeletions and microinsertions causing human genetic disease: common mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum Mutat. 2005;26:205-213. doi:10.1002/humu.20239
16. Walsh T, Mcclellan JM, Mccarthy SE, et al. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science. 2008;320:539–43. doi:10.1126/science.1155176
17. Yu CE, Dawson G, Munson J, et al. Presence of large deletions in kindreds with autism. Am J Hum Genet. 2002;71(1):100–15. doi:10.1086/341702
18. Mao G, Pan X, Bei B, et al. Identification and characterization of OGG1 mutations in patients with Alzheimer’s disease. Nucleic Acids Res. 2007;35(8):2759–66. doi:10.1093/nar/gkm182
19. Monaco AP, Bertelson CJ, Liechti-Gallati S, Moser H, Kunkel LM. An explanation for the phenotypic differences between patients bearing partial deletions of the DMD locus. Genomics. 1988;2(1):90–5. doi:10.1016/0888-7543(88)90126-2
20. Waldmüller S, Sakthivel S, Saadi AV, et al. Novel deletions in MYH7 and MYBPC3 identified in Indian families with familial hypertrophic cardiomyopathy. J Mol Cell Cardiol. 2003;35(6):623–36. doi:10.1016/S0022-2828(03)00079-2
21. Herman DS, Lam L, Taylor MRG, et al. Truncations of titin causing dilated cardiomyopathy. N Engl J Med. 2012;366(7):619–28. doi:10.1056/NEJMoa1110180
22. Keum JW, Shin A, Gillis T, et al. The HTT CAG-expansion mutation determines age at death but not disease duration in Huntington disease. Am J Hum Genet. 2016;98(2):287–98. doi:10.1016/j.ajhg.2015.12.010
23. Cremer M, Cremer T. Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences. Genes Chromosomes Cancer. 2019;58(7):427–36. doi:10.1002/gcc.22730
24. Ellingford JM, Ahn JW, Bagnall RD, et al. Recommendations for clinical interpretation of variants found in non-coding regions of the genome. Genome Med. 2022;14(1):73. doi:10.1186/s13073-022-01026-2
25. Peña-Martínez EG, Rodríguez-Martínez JA. Decoding non-coding variants: Recent approaches to studying their role in gene regulation and human diseases. Front Biosci (Schol Ed). 2024;16(1):4. doi:10.2741/S485
26. Lee JA, Madrid RE, Sperle K, et al. Spastic paraplegia type 2 associated with axonal neuropathy and apparent PLP1 position effect. Ann Neurol. 2006;59(2):398–403. doi:10.1002/ana.20861
27. Benito-Sanz S, Royo JL, Barroso E, et al. Identification of the first recurrent PAR1 deletion in Léri-Weill dyschondrosteosis and idiopathic short stature reveals the presence of a novel SHOX enhancer. J Med Genet. 2012;49(7):442–50. doi:10.1136/jmedgenet-2012-100832
28. Pop R, Conz C, Lindenberg KS, et al. Screening of the 1 Mb SOX9 5’ control region by array CGH identifies a large deletion in a case of campomelic dysplasia with XY sex reversal. J Med Genet. 2004;41(4):e47. doi:10.1136/jmg.2003.015229
29. Cox JJ, Willatt L, Homfray T, Woods CG. A SOX9 duplication and familial 46,XX developmental testicular disorder. N Engl J Med. 2011;364(1):91–3. doi:10.1056/NEJMc1012413
30. Benko S, Fantes JA, Amiel J, et al. Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence. Nat Genet. 2009;41(3):359–64. doi:10.1038/ng.333
31. Klopocki E, Schulze H, Strauss G, et al. Complex inheritance pattern resembling autosomal recessive inheritance involving a microdeletion in thrombocytopenia-absent radius syndrome. Am J Hum Genet. 2007;80(2):232–40. doi:10.1086/510690
32. Albers CA, Paul DS, Schulze H, et al. Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome. Nat Genet. 2012;44(4):435–9, S1-2. doi:10.1038/ng.2209
33. Wieczorek D, Newman WG, Wieland T, et al. Compound heterozygosity of low-frequency promoter deletions and rare loss-of-function mutations in TXNL4A causes Burn-McKeown syndrome. Am J Hum Genet. 2014;95(6):698–707. doi:10.1016/j.ajhg.2014.11.001
34. Dixon JR, Selvaraj S, Yue F, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485(7398):376–80. doi:10.1038/nature11082
35. Lupiáñez DG, Kraft K, Heinrich V, et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell. 2015;161(5):1012–25. doi:10.1016/j.cell.2015.04.004
36. Tena JJ, Santos-Pereira JM. Topologically associating domains and regulatory landscapes in development, evolution and disease. Front Cell Dev Biol. 2021;9:702787. doi:10.3389/fcell.2021.702787
37. Zhang P, Philippot Q, Ren W, et al. Genome-wide detection of human variants that disrupt intronic branchpoints. Proc Natl Acad Sci U S A. 2022;119(44):e2211194119. doi:10.1073/pnas.2211194119
38. King K, Flinter FA, Nihalani V, Green PM. Unusual deep intronic mutations in the COL4A5 gene cause X linked Alport syndrome. Hum Genet. 2002;111(6):548–54. doi:10.1007/s00439-002-0849-5
39. Richards AJ, McNinch A, Whittaker J, et al. Splicing analysis of unclassified variants in COL2A1 and COL11A1 identifies deep intronic pathogenic mutations. Eur J Hum Genet. 2012;20(5):552–8. doi:10.1038/ejhg.2011.211
40. Popp MW-L, Maquat LE. Organizing principles of mammalian nonsense-mediated mRNA decay. Annu Rev Genet. 2013;47(1):139–65. doi:10.1146/annurev-genet-111312-085539
41. Dobkin C, Pergolizzi RG, Bahre P, Bank A. Abnormal splice in a mutant human beta-globin gene not at the site of a mutation. Proc Natl Acad Sci U S A. 1983;80(5):1184–8. doi:10.1073/pnas.80.5.1184
42. Cunha K, Oliveira N, Fausto A, et al. Hybridization capture-based next-generation sequencing to evaluate coding sequence and deep intronic mutations in the NF1 gene. Genes (Basel). 2016;7(12):133. doi:10.3390/genes7120133
43. Gonorazky H, Liang M, Cummings B, et al. RNA seq analysis for the diagnosis of muscular dystrophy. Ann Clin Transl Neurol. 2016;3(1):55–60. doi:10.1002/acn3.255
44. Antonellis A, Dennis MY, Burzynski G, et al. A rare myelin protein zero (MPZ) variant alters enhancer activity in vitro and in vivo. PLoS One. 2010;5(12):e14346. doi:10.1371/journal.pone.0014346
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