Defective pre-mRNA splicing in PKD1 due to presumed missense and synonymous mutations causing autosomal dominant polycystic disease

Gene

Volumn 546, Issue 2, 2014, Pages 243-249

  Gonzalez Paredes, Francisco J ^a   Ramos Trujillo, Elena ^a   Claverie Martin, Felix ^a  

^a HOSPITAL UNIVERSITARIO NUESTRA SEÑORA DE CANDELARIA   (Spain)

Author keywords

ADPKD; Donor splice site; Exonic mutation; Genetic kidney disease; Minigene analysis

Indexed keywords

POLYCYSTIN 1; POLYCYSTIN 2; RNA;

ANIMAL CELL; ARTICLE; BIOINFORMATICS; CELL CULTURE; DNA SEQUENCE; EXON; GENE MUTATION; HUMAN; INTRON; KIDNEY POLYCYSTIC DISEASE; MAJOR CLINICAL STUDY; MISSENSE MUTATION; MOUSE; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SPLICING; CONTROLLED STUDY; SITE DIRECTED MUTAGENESIS; SPLICING DEFECT;

ADPKD; DONOR SPLICE SITE; EXONIC MUTATION; GENETIC KIDNEY DISEASE; MINIGENE ANALYSIS;

ANIMALS; CERCOPITHECUS AETHIOPS; COS CELLS; DATABASES, NUCLEIC ACID; EXONS; FEMALE; HUMANS; INTRONS; MALE; MUTATION, MISSENSE; POLYCYSTIC KIDNEY, AUTOSOMAL DOMINANT; RNA PRECURSORS; RNA SPLICE SITES; RNA SPLICING; TRPP CATION CHANNELS;

EID: 84903526606     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2014.06.004     Document Type: Article

References (42)

1. Aguiari G., Savelli S., Garbo M., Bozza A., Augello G., et al. Novel splicing and missense mutations in autosomal dominant polycystic kidney disease 1 (PKD1) gene: expression of mutated genes. Hum. Mutat. 2000, 16:444-445.
2. Bergmann C., von Bothmer J., Ortiz Brüchle N., Venghaus A., Frank V., et al. Mutations in multiple PKD genes may explain early and severe polycystic kidney disease. J. Am. Soc. Nephrol. 2011, 22:2047-2056.
3. Blanchette M., Chabot B. Modulation of exon skipping by high-affinity hnRNP A1-binding sites and by intron elements that repress splice site utilization. EMBO J. 1999, 18:1939-1952.
4. Bonnet C., Krieger S., Vezain M., Rousselin A., Tournier I., et al. Screening BRCA1 and BRCA2 unclassified variants for splicing mutations using reverse transcription PCR on patient RNA and an ex vivo assay based on a splicing reporter minigene. J. Med. Genet. 2008, 45:438-446.
5. Buratti E., Baralle M., Baralle F.E. Defective splicing, disease and therapy: searching for master checkpoints in exon definition. Nucleic Acids Res. 2006, 34:3494-3510.
6. Campos B., Díez O., Domènech M., Baena M., Balmaña J., et al. RNA analysis of eight BRCA1 and BRCA2 unclassified variants identified in breast/ovarian cancer families from Spain. Hum. Mutat. 2003, 22:337.
7. Cartegni L., Chew S.L., Krainer A.R. Listening to silence. Nat. Rev. Genet. 2002, 3:285-298.
8. Cartegni L., Wang J., Zhu Z., Zhang M.Q., Krainer A.R. ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Res. 2003, 31:3568-3571.
9. Cartegni L., Hastings M.L., Calarco J.A., de Stanchina E., Krainer A.R. Determinants of exon 7 splicing in the spinal muscular atrophy genes, SMN1 and SMN2. Am. J. Hum. Genet. 2006, 78:63-77.
10. Casuscelli J., Schmidt S., DeGray B., Petri E.T., Celić A., et al. Analysis of the cytoplasmic interaction between polycystin-1 and polycystin-2. Am. J. Physiol. Renal Physiol. 2009, 297:F1310-F1315.
11. Claverie-Martín F., Flores C., Antón-Gamero M., González-Acosta H., García-Nieto V. The Alu insertion in the CLCN5 gene of a patient with Dent's disease leads to exon 11 skipping. J. Hum. Genet. 2005, 50:370-374.
12. Del Gatto-Konczak F., Olive M., Gesnel M.C., Breathnach R. hnRNP A1 recruited to an exon in vivo can function as an exon splicing silencer. Mol. Cell. Biol. 1999, 19:251-260.
13. Desmet F.O., Hamroun D., Lalande M., Collod-Béroud G., Claustres M., et al. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res. 2009, 37:e67.
14. Drögemüller C., Reichart U., Seuberlich T., Oevermann A., Baumgartner M., et al. An unusual splice defect in the mitofusin 2 gene (MFN2) is associated with degenerative axonopathy in Tyrolean Grey cattle. PLoS One 2011, 6:e18931.
15. Gaildrat P., Krieger S., Théry J.C., et al. The BRCA1 c.5434C->G (p.Pro1812Ala) variant induces a deleterious exon 23 skipping by affecting exonic splicing regulatory elements. J. Med. Genet. 2010, 47:398-403.
16. Garcia-Gonzalez M.A., Jones J.G., Allen S.K., Palatucci C.M., Batish S.D., et al. Evaluating the clinical utility of a molecular genetic test for polycystic kidney disease. Mol. Genet. Metab. 2007, 92:160-167.
17. Gout A.M., Martin N.C., Brown A.F., Ravine D. PKDB: Polycystic Kidney Disease Mutation Database - a gene variant database for autosomal dominant polycystic kidney disease. Hum. Mutat. 2007, 28:654-659.
18. Harris P.C., Torres V.E. Polycystic kidney disease. Annu. Rev. Med. 2009, 60:321-337.
19. Hopp K., Ward C.J., Hommerding C.J., Nasr S.H., Tuan H.F., et al. Functional polycystin-1 dosage governs autosomal dominant polycystic kidney disease severity. J. Clin. Invest. 2012, 122:4257-4273.
20. Houdayer C., Dehainault C., Mattler C., Michaux D., Caux-Moncoutier V., et al. Evaluation of in silico splice tools for decision-making in molecular diagnosis. Hum. Mutat. 2008, 29:975-982.
21. International Polycystic Kidney Disease Consortium Polycystic kidney disease: the complete structure of the PKD1 gene and its protein. Cell 1995, 81:289-298.
22. Kim U.K., Jin D.K., Ahn C., Shin J.H., Lee K.B., et al. Novel mutations of the PKD1 gene in Korean patients with autosomal dominant polycystic kidney disease. Mutat. Res. 2000, 432:39-45.
23. Lantinga-van Leeuwen I.S., Dauwerse J.G., Baelde H.J., Leonhard W.N., van de Wal A., et al. Lowering of Pkd1 expression is sufficient to cause polycystic kidney disease. Hum. Mol. Genet. 2004, 13:3069-3077.
24. Lastella P., Surdo N.C., Resta N., Guanti G., Stella A. In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects. BMC Genomics 2006, 7:243.
25. Liu H.X., Cartegni L., Zhang M.Q., Krainer A.R. A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes. Nat. Genet. 2001, 27:55-58.
26. Mochizuki T., Wu G., Hayashi T., Xenophontos S.L., Veldhuisen B., et al. PKD2, a gene for polycystic kidney disease that encodes an integral membrane protein. Science 1996, 272:1339-1342.
27. Nauli S.M., Alenghat F.J., Luo Y., Williams E., Vassilev P., et al. Polycystins 1 and 2 mediate mechanosensation in the primary cilium of kidney cells. Nat. Genet. 2003, 33:129-137.
28. Nicholson P., Mühlemann O. Cutting the nonsense: the degradation of PTC-containing mRNAs. Biochem. Soc. Trans. 2010, 38:1615-1620.
29. Parsam V.L., Ali M.J., Honavar S.G., Vemuganti G.K., Kannabiran C. Splicing aberrations caused by constitutional RB1 gene mutations in retinoblastoma. J. Biosci. 2011, 36:281-287.
30. Raevaara T.E., Korhonen M.K., Lohi H., Hampel H., Lynch E., et al. Functional significance and clinical phenotype of nontruncating mismatch repair variants of MLH1. Gastroenterology 2005, 129:537-549.
31. Reese M.G., Eeckman F.H., Kulp D., Haussler D. Improved splice site detection in Genie. J. Comput. Biol. 1997, 4:311-323.
32. Rossetti S., Strmecki L., Gamble V., Burton S., Sneddon V., et al. Mutation analysis of the entire PKD1 gene: genetic and diagnostic implications. Am. J. Hum. Genet. 2001, 68:46-63.
33. Rossetti S., Consugar M.B., Chapman A.B., Torres V.E., Guay-Woodford L.M., et al. Comprehensive molecular diagnostics in autosomal dominant polycystic kidney disease. J. Am. Soc. Nephrol. 2007, 18:2143-2160.
34. Rossetti S., Kubly V.J., Consugar M.B., Hopp K., Roy S., et al. Incompletely penetrant PKD1 alleles suggest a role for gene dosage in cyst initiation in polycystic kidney disease. Kidney Int. 2009, 75:848-855.
35. Sharp A., Pichert G., Lucassen A., Eccles D. RNA analysis reveals splicing mutations and loss of expression defects in MLH1 and BRCA1. Hum. Mutat. 2004, 24:272.
36. Sironi M., Menozzi G., Riva L., Cagliani R., Comi G.P., et al. Silencer elements as possible inhibitors of pseudoexon splicing. Nucleic Acids Res. 2004, 32:1783-1791.
37. Thomas R., McConnell R., Whittacker J., Kirkpatrick P., Bradley J., et al. Identification of mutations in the repeated part of the autosomal dominant polycystic kidney disease type 1 gene, PKD1, by long-range PCR. Am. J. Hum. Genet. 1999, 65:39-49.
38. Tournier I., Vezain M., Martins A., Charbonnier F., Baert-Desurmont S., et al. A large fraction of unclassified variants of the mismatch repair genes MLH1 and MSH2 is associated with splicing defects. Hum. Mutat. 2008, 29:1412-1424.
39. Vujic M., Heyer C.M., Ars E., Hopp K., Markoff A., et al. Incompletely penetrant PKD1 alleles mimic the renal manifestations of ARPKD. J. Am. Soc. Nephrol. 2010, 21:1097-1102.
40. Wang R., Crystal R.G., Hackett N.R. Identification of an exonic splicing silencer in exon 6A of the human VEGF gene. BMC Mol. Biol. 2009, 10:103.
41. Watnick T.J., Piontek K.B., Cordal T.M., Weber H., Gandolph M.A., et al. An unusual pattern of mutation in the duplicated portion of PKD1 is revealed by use of a novel strategy for mutation detection. Hum. Mol. Genet. 1997, 6:1473-1478.
42. Yeo G.W., Van Nostrand E., Holste D., Poggio T., Burge C.B. Identification and analysis of alternative splicing events conserved in human and mouse. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:2850-2855.