Alternative approach to a heavy weight problem

Genome Research

Volumn 18, Issue 2, 2008, Pages 214-220

  Goren, Amir ^a   Kim, Eddo ^a   Amit, Maayan ^a   Bochner, Ron ^a   Lev Maor, Galit ^a   Ahituv, Nadav ^b   Ast, Gil ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DIABETES MELLITUS; DISEASE PREDISPOSITION; DYSLIPIDEMIA; EXON; GENE MUTATION; GENE SEQUENCE; GENETIC VARIABILITY; HEART DISEASE; HUMAN; HYPERTENSION; NUCLEOTIDE SEQUENCE; OBESITY; PRIORITY JOURNAL; RISK FACTOR; RNA SPLICING; SINGLE NUCLEOTIDE POLYMORPHISM;

ALTERNATIVE SPLICING; BASE SEQUENCE; BODY MASS INDEX; COMPUTATIONAL BIOLOGY; DNA PRIMERS; EXONS; GENETIC VECTORS; HUMANS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; OBESITY; POLYMORPHISM, SINGLE NUCLEOTIDE; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 39049136572     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.6661308     Document Type: Article

References (42)

1. Ahituv, N., Kavaslar, N., Schackwitz, W., Ustaszewska, A., Martin, J., Hebert, S., Doelle, H., Ersoy, B., Kryukov, G., Schmidt, S., et al. 2007. Medical sequencing at the extremes of human body mass. Am. J. Hum. Genet. 80: 779-791.
2. Alberstein, M., Amit, M., Vaknin, K., O'Donnell, A., Farhy, C., Lerenthal, Y., Shomron, N., Shaham, O., Sharrocks, A.D., Ashery-Padan, R., et al. 2007. Regulation of transcription of the RNA splicing factor hSlu7 by Elk-1 and Sp1 affects alternative splicing. RNA 13: 1988-1999.
3. Allison, D.B., Kaprio, J., Korkeila, M., Koskenvuo, M., Neale, M.C., and Hayakawa, K. 1996. The heritability of body mass index among an international sample of monozygotic twins reared apart. Int. J. Obes. Relat. Metab. Disord. 20: 501-506.
4. Ast, G. 2004. How did alternative splicing evolve? Nat. Rev. Genet. 5: 773-782.
5. Bell, C.G., Walley, A.J., and Froguel, P. 2005. The genetics of human obesity. Nat. Rev. Genet. 6: 221-234.
6. Black, D.L. 2003. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72: 291-336.
7. Blencowe, B.J. 2000. Exonic splicing enhancers: Mechanism of action, diversity and role in human genetic diseases. Trends Biochem. Sci. 25: 106-110.
8. Cartegni, L. and Krainer, A.R. 2002. Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1. Nat. Genet. 30: 377-384.
9. Cartegni, L., Chew, S.L., and Krainer, A.R. 2002. Listening to silence and understanding nonsense: Exonic mutations that affect splicing. Nat. Rev. Genet. 3: 285-298.
10. Cartegni, L., Wang, J., Zhu, Z., Zhang, M.Q., and Krainer, A.R. 2003. ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res. 31: 3568-3571.
11. Chamary, J.V., Parmley, J.L., and Hurst, L.D. 2006. Hearing silence: Non-neutral evolution at synonymous sites in mammals. Nat. Rev. Genet. 7: 98-108.
12. Comuzzie, A.G. and Allison, D.B. 1998. The search for human obesity genes. Science 280: 1374-1377.
13. Cooper, T.A. and Mattox, W. 1997. The regulation of splice-site selection, and its role in human disease. Am. J. Hum. Genet. 61: 259-266.
14. Crawford, D.C., Akey, D.T., and Nickerson, D.A. 2005. The patterns of natural variation in human genes. Annu. Rev. Genomics Hum. Genet. 6: 287-312.
15. Fairbrother, W.G., Holste, D., Burge, C.B., and Sharp, P.A. 2004. Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol. 2: E268. doi: 10.1371/journal.pbio.0020268.
16. Flier, J.S. 2004. Obesity wars: Molecular progress confronts an expanding epidemic. Cell 116: 337-350.
17. Friedman, J.M. 2003. A war on obesity, not the obese. Science 299: 856-858.
18. Friedman, J.M. 2004. Modern science versus the stigma of obesity. Nat. Med. 10: 563-569.
19. Goren, A., Ram, O., Amit, M., Keren, H., Lev-Maor, G., Vig, I., Pupko, T., and Ast, G. 2006. Comparative analysis identifies exonic splicing regulatory sequences - The complex definition of enhancers and silencers. Mol. Cell 22: 769-781.
20. Graveley, B.R. 2000. Sorting out the complexity of SR protein functions. RNA 6: 1197-1211.
21. Graveley, B.R. 2001. Alternative splicing: Increasing diversity in the proteomic world. Trends Genet. 17: 100-107.
22. International HapMap Consortium. 2003. The International HapMap Project. Nature 426: 789-796.
23. Itoh, H., Washio, T., and Tomita, M. 2004. Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes. RNA 10: 1005-1018.
24. Karolchik, D., Hinrichs, A.S., Furey, T.S., Roskin, K.M., Sugnet, C.W., Haussler, D., and Kent, W.J. 2004. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 32: D493-D496.
25. Kashima, T. and Manley, J.L. 2003. A negative element in SMN2 exon 7 inhibits splicing in spinal muscular atrophy. Nat. Genet. 34: 460-463.
26. Kimchi-Sarfaty, C., Oh, J.M., Kim, I.W., Sauna, Z.E., Calcagno, A.M., Ambudkar, S.V., and Gottesman, M.M. 2007. A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science 315: 525-528.
27. Krawczak, M., Reiss, J., and Cooper, D.N. 1992. The mutational spectrum of single base-pair substitutions in mRNA splice junctions of human genes: Causes and consequences. Hum. Genet. 90: 41-54.
28. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
29. Lev-Maor, G., Goren, A., Sela, N., Kim, E., Kerem, H., Doron-Faigenboim, A., Leibman-Barak, S., Pupko, T., and Ast, G. 2007. The "alternative" choice of constitutive exons throughout evolution. PLoS Genet. 3: e203. doi: 10.1371/journal.pgen.0030203.
30. Liu, H.X., Cartegni, L., Zhang, M.Q., and Krainer, A.R. 2001. A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes. Nat. Genet. 27: 55-58.
31. Majewski, J. and Ott, J. 2002. Distribution and characterization of regulatory elements in the human genome. Genome Res. 12: 1827-1836.
32. Orban, T.I. and Olah, E. 2001. Purifying selection on silent sites - A constraint from splicing regulation? Trends Genet. 17: 252-253.
33. Parmley, J.L., Chamary, J.V., and Hurst, L.D. 2006. Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol. Biol. Evol. 23: 301-309.
34. Sanford, J.R., Ellis, J., and Caceres, J.F. 2005. Multiple roles of arginine/serine-rich splicing factors in RNA processing. Biochem. Soc. Trans. 33: 443-446.
35. Shapiro, M.B. and Senapathy, P. 1987. RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res. 15: 7155-7174.
36. Shen, L.X., Basilion, J.P., and Stanton Jr., V.P. 1999. Single-nucleotide polymorphisms can cause different structural folds of mRNA. Proc. Natl. Acad. Sci. 96: 7871-7876.
37. Sherry, S.T., Ward, M.H., Kholodov, M., Baker, J., Phan, L., Smigielski, E.M., and Sirotkin, K. 2001. dbSNP: The NCBI database of genetic variation. Nucleic Acids Res. 29: 308-311.
38. Sorek, R., Shemesh, R., Cohen, Y., Basechess, O., Ast, G., and Shamir, R. 2004. A non-EST-based method for exon-skipping prediction. Genome Res. 14: 1617-1623.
39. Steiner, B., Truninger, K., Sanz, J., Schaller, A., and Gallati, S. 2004. The role of common single-nucleotide polymorphisms on exon 9 and exon 12 skipping in nonmutated CFTR alleles. Hum. Mutat. 24: 120-129.
40. Stunkard, A.J., Foch, T.T., and Hrubec, Z. 1986. A twin study of human obesity. JAMA 256: 51-54.
41. Stunkard, A.J., Harris, J.R., Pedersen, N.L., and McClearn, G.E. 1990. The body-mass index of twins who have been reared apart. N. Engl. J. Med. 322: 1483-1487.
42. Zheng, C.L., Fu, X.D., and Gribskov, M. 2005. Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse. RNA 11: 1777-1787.