A compensatory effect upon splicing results in normal function of the CYP2A6*14 allele

Pharmacogenetics and Genomics

Volumn 23, Issue 3, 2013, Pages 107-116

  Bloom, A Joseph ^a   Harari, Oscar ^a   Martinez, Maribel ^a   Zhang, Xiaochun ^a   McDonald, Sandra A ^a   Murphy, Sharon E ^b   Goate, Alison ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

CYP2A6; exonic splice enhancer; exonic splice suppressor; nicotine metabolism; splicing

Indexed keywords

COMPLEMENTARY DNA; CYTOCHROME P450 2A6; MESSENGER RNA; NICOTINE;

ALLELE; ARTICLE; EXON; GENE EXPRESSION; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HETEROZYGOTE; HOMOZYGOTE; HUMAN; IN VIVO STUDY; LIVER BIOPSY; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RNA SPLICING; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84873411419     PISSN: 17446872     EISSN: 17446880     Source Type: Journal    
DOI: 10.1097/FPC.0b013e32835caf7d     Document Type: Article

References (32)

1. Mwenifumbo JC, Tyndale RF. Molecular genetics of nicotine metabolism. Handb Exp Pharmacol 2009; 192:235-259.
2. Bloom J, Hinrichs AL, Wang JC, von Weymarn LB, Kharasch ED, Bierut LJ, et al. The contribution of common CYP2A6 alleles to variation in nicotine metabolism among European-Americans. Pharmacogenet Genomics 2011; 21:403-416.
3. Haberl M, Anwald B, Klein K, Weil R, Fuss C, Gepdiremen A, et al. Three haplotypes associated with CYP2A6 phenotypes in Caucasians. Pharmacogenet Genomics 2005; 15:609-624.
4. Pitarque M, von Richter O, Rodriguez-Antona C, Wang J, Oscarson M, Ingelman-Sundberg M. A nicotine C-oxidase gene (CYP2A6) polymorphism important for promoter activity. Hum Mutat 2004; 23:258-266.
5. Mwenifumbo JC, Al Koudsi N, Ho MK, Zhou Q, Hoffmann EB, Sellers EM, et al. Novel and established CYP2A6 alleles impair in vivo nicotine metabolism in a population of Black African descent. Hum Mutat 2008; 29:679-688.
6. Keren H, Lev-Maor G, Ast G. Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet 2010; 11: 345-355.
7. Mukherjee O, Wang J, Gitcho M, Chakraverty S, Taylor-Reinwald L, Shears S, et al. Molecular characterization of novel progranulin (GRN) mutations in frontotemporal dementia. Hum Mutat 2008; 29:512-521.
8. Wang GS, Cooper TA. Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet 2007; 8:749-761.
9. Cartegni L, Chew SL, Krainer AR. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 2002; 3:285-298.
10. McVety S, Li L, Gordon PH, Chong G, Foulkes WD. Disruption of an exon splicing enhancer in exon 3 of MLH1 is the cause of HNPCC in a Quebec family. J Med Genet 2006; 43:153-156.
11. Suphapeetiporn K, Kongkam P, Tantivatana J, Sinthuwiwat T, Tongkobpetch S, Shotelersuk V. PTEN c.511C > T nonsense mutation in a BRRS family disrupts a potential exonic splicing enhancer and causes exon skipping. Jpn J Clin Oncol 2006; 36:814-821.
12. Nielsen KB, Sorensen S, Cartegni L, Corydon TJ, Doktor TK, Schroeder LD, et al. 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 2007; 80:416-432.
13. Kashima T, Rao N, David CJ, Manley JL. hnRNP A1 functions with specificity in repression of SMN2 exon 7 splicing. Hum Mol Genet 2007; 16: 3149-3159.
14. Gaildrat P, Krieger S, Di Giacomo D, Abdat J, Revillion F, Caputo S, et al. Multiple sequence variants of BRCA2 exon 7 alter splicing regulation. J Med Genet 2012; 49:609-617.
15. Burgess R, MacLaren RE, Davidson AE, Urquhart JE, Holder GE, Robson AG, et al. ADVIRC is caused by distinct mutations in BEST1 that alter pre-mRNA splicing. J Med Genet 2009; 46:620-625.
16. Hofmann MH, Blievernicht JK, Klein K, Saussele T, Schaeffeler E, Schwab M, et al. Aberrant splicing caused by single nucleotide polymorphism c.516G > T [Q172H], a marker of CYP2B6&z.ast;6, is responsible for decreased expression and activity of CYP2B6 in liver. J Pharmacol Exp Ther 2008; 325:284-292.
17. Fairbrother WG, Holste D, Burge CB, Sharp PA. Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol 2004; 2:E268.
18. Carlini DB, Genut JE. Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers. J Mol Evol 2006; 62: 89-98.
19. Ke S, Zhang XH, Chasin LA. Positive selection acting on splicing motifs reflects compensatory evolution. Genome Res 2008; 18:533-543.
20. Bloom AJ, Harari O, Martinez M, Madden PA, Martin NG, Montgomery GW, et al. Use of a predictive model derived from in vivo endophenotype measurements to demonstrate associations with a complex locus, CYP2A6. Hum Mol Genet 2012; 21:3050-3062.
21. Yoshida R, Nakajima M, Nishimura K, Tokudome S, Kwon JT, Yokoi T. Effects of polymorphism in promoter region of human CYP2A6 gene (CYP2A6&z.ast;9) on expression level of messenger ribonucleic acid and enzymatic activity in vivo and in vitro. Clin Pharmacol Ther 2003; 74:69-76.
22. von Richter O, Pitarque M, Rodriguez-Antona C, Testa A, Mantovani R, Oscarson M, et al. Polymorphic NF-Y dependent regulation of human nicotine C-oxidase (CYP2A6). Pharmacogenetics 2004; 14:369-379.
23. Mwenifumbo JC, Lessov-Schlaggar CN, Zhou Q, Krasnow RE, Swan GE, Benowitz NL, et al. Identification of novel CYP2A6&z.ast;1B variants: the CYP2A6&z.ast;1B allele is associated with faster in vivo nicotine metabolism. Clin Pharmacol Ther 2008; 83:115-121.
24. Chang YF, Imam JS, Wilkinson MF. The nonsense-mediated decay RNA surveillance pathway. Annu Rev Biochem 2007; 76:51-74.
25. Fairbrother WG, Yeh RF, Sharp PA, Burge CB. Predictive identification of exonic splicing enhancers in human genes. Science 2002; 297: 1007-1013.
26. Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, Burge CB. Systematic identification and analysis of exonic splicing silencers. Cell 2004; 119: 831-845.
27. Hebsgaard SM, Korning PG, Tolstrup N, Engelbrecht J, Rouze P, Brunak S. Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Res 1996; 24:3439-3452.
28. Thorgeirsson TE, Gudbjartsson DF, Surakka I, Vink JM, Amin N, Geller F, et al. Sequence variants at CHRNB3-CHRNA6 and CYP2A6 affect smoking behavior. Nat Genet 2010; 42:448-453.
29. Tobacco and Genetics Consortium. Genome-wide meta-analyses identify multiple loci associated with smoking behavior. Nat Genet 2010; 42: 441-447.
30. Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB. Rare variants create synthetic genome-wide associations. PLoS Biol 2010; 8:e1000294.
31. Saccone NL, Culverhouse RC, Schwantes-An TH, Cannon DS, Chen X, Cichon S, et al. Multiple independent loci at chromosome 15q25.1 affect smoking quantity: a meta-analysis and comparison with lung cancer and COPD. PLoS Genet 2010; 6:e1001053.
32. Becker K, Braune M, Benderska N, Buratti E, Baralle F, Villmann C, et al. A retroelement modifies pre-mRNA splicing: the murine glrb(spa) allele is a splicing signal polymorphism amplified by long interspersed nuclear element insertion. J Biol Chem 2012; 287:31185-31194.