Alternative splicing of transcription factors' genes: Beyond the increase of proteome diversity

Comparative and Functional Genomics

Volumn 2009, Issue , 2009, Pages

  Talavera, David ^a,b,c   Orozco, Modesto ^a,d,e,f   de la Cruz, Xavier ^a,g,h  

^a INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

^d National Institute of Bioinformatics   (Spain)

^e UNIVERSITY OF BARCELONA   (Spain)

^f BARCELONA SUPERCOMPUTING CENTER   (Spain)

^g INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

^h INSTITUT DE BIOLOGIA MOLECULAR DE BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

HOX PROTEIN; PROTEOME; TRANSCRIPTION FACTOR;

ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; GENETIC VARIABILITY; HUMAN; MOUSE; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN MODIFICATION; SPECIES DIFFERENCE; TRANSCRIPTION REGULATION;

EID: 69249218018     PISSN: 15316912     EISSN: 15326268     Source Type: Journal    
DOI: 10.1155/2009/905894     Document Type: Article

References (61)

1. M. C. King and A. C. Wilson, "Evolution at two levels in humans and chimpanzees," Science, vol. 188, no. 4184, pp. 107-116, 1975.
2. S. B. Carroll, "Evolution at two levels: On genes and form," PLoS Biology, vol. 3, no. 7, article e245, 2005.
3. D. S. Latchman, "The Oct-2 transcription factor," International Journal of Biochemistry and Cell Biology, vol. 28, no. 10, pp. 1081-1083, 1996.
4. A. J. Lopez, "Developmental role of transcription factor isoforms generated by alternative splicing," Developmental Biology, vol. 172, no. 2, pp. 396-411, 1995.
5. A. J. Lopez, "Alternative splicing of pre-mRNA: Developmental consequences and mechanisms of regulation," Annual Review of Genetics, vol. 32, pp. 279-305, 1998.
6. T. Hsu, J. A. Gogos, S. A. Kirsh, and F. C. Kafatos, "Multiple zinc finger forms resulting from developmentally regulated alternative splicing of a transcription factor gene," Science, vol. 257, no. 5078, pp. 1946-1950, 1992.
7. B. M. Laoide, N. S. Foulkes, F. Schlotter, and P. Sassone- Corsi, "The functional versatility of CREM is determined by its modular structure," The EMBO Journal, vol. 12, no. 3, pp. 1179-1191, 1993.
8. D. Duma, C. M. Jewell, and J. A. Cidlowski, "Multiple glucocorticoid receptor isoforms and mechanisms of posttranslational modification," Journal of Steroid Biochemistry and Molecular Biology, vol. 102, no. 1-5, pp. 11-21, 2006.
9. M. Zou, Y. Guan, H. Ren, F. Zhang, and F. Chen, "Characterization of alternative splicing products of bZIP transcription factors OsABI5," Biochemical and Biophysical Research Communications, vol. 360, no. 2, pp. 307-313, 2007.
10. B. Taneri, B. Snyder, A. Novoradovsky, and T. Gaasterland, "Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific," Genome Biology, vol. 5, no. 10, article R75, 2004.
11. A. M. Cervera, N. Apostolova, F. Luna-Crespo, A. Sanjuan- Pla, R. Garcia-Bou, and K. J. McCreath, "An alternatively spliced transcript of the PHD3 gene retains prolyl hydroxylase activity," Cancer Letters, vol. 233, no. 1, pp. 131-138, 2006.
12. D. Ram, E. Ziv, F. Lantner, V. Lardans, and I. Schechter, "Stagespecific alternative splicing of the heat-shock transcription factor during the life-cycle of Schistosoma mansoni," Parasitology, vol. 129, no. 5, pp. 587-596, 2004.
13. E. Lamani, Y. Wu, J. Dong, M. S. Litaker, A. C. Acevedo, and M. MacDougall, "Tissue- and cell-specific alternative splicing of NFIC," Cells Tissues Organs, vol. 189, no. 1-4, pp. 105-110, 2008.
14. R. Caballero, F. Setien, L. Lopez-Serra, et al., "Combinatorial effects of splice variants modulate function of Aiolos," Journal of Cell Science, vol. 120, no. 15, pp. 2619-2630, 2007.
15. G. A. Robichaud, M. Nardini, M. Laflamme, M. Cuperlovic- Culf, and R. J. Ouellette, "Human Pax-5 C-terminal isoforms possess distinct transactivation properties and are differentially modulated in normal and malignant B cells," The Journal of Biological Chemistry, vol. 279, no. 48, pp. 49956-49963, 2004.
16. L. Waltzer, L. Bataille, S. Peyrefitte, and M. Haenlin, "Two isoforms of serpent containing either one or two GATA zinc fingers have different roles in Drosophila haematopoiesis," The EMBO Journal, vol. 21, no. 20, pp. 5477-5486, 2002.
17. H. L. Ford, "Homeobox genes: A link between development, cell cycle, and cancer?" Cell Biology International, vol. 22, no. 6, pp. 397-400, 1998.
18. R. P. Kuiper, M. Schepens, J. Thijssen, E. F. Schoenmakers, and A. G. van Kessel, "Regulation of the MiTF/TFE bHLHLZ transcription factors through restricted spatial expression and alternative splicing of functional domains," Nucleic Acids Research, vol. 32, no. 8, pp. 2315-2322, 2004.
19. H.-S. Choi, M. Chung, I. Tzameli, et al., "Differential transactivation by two isoforms of the orphan nuclear hormone receptor CAR," The Journal of Biological Chemistry, vol. 272, no. 38, pp. 23565-23571, 1997.
20. F. E. Chen, D.-B. Huang, Y.-Q. Chen, and G. Ghosh, "Crystal structure of p50/p65 heterodimer of transcription factor NF- ?B bound to DNA," Nature, vol. 391, no. 6665, pp. 410-412, 1998.
21. Q. Xu, B. Modrek, and C. Lee, "Genome-wide detection of tissue-specific alternative splicing in the human transcriptome," Nucleic Acids Research, vol. 30, no. 17, pp. 3754-3766, 2002.
22. A. R. R. Forrest, D. F. Taylor, M. L. Crowe, et al., "Genomewide review of transcriptional complexity in mouse protein kinases and phosphatases," Genome Biology, vol. 7, no. 1, article R5, 2006.
23. K. Yura, M. Shionyu, K. Hagino, et al., "Alternative splicing in human transcriptome: Functional and structural influence on proteins," Gene, vol. 380, no. 2, pp. 63-71, 2006.
24. A. Resch, Y. Xing, B. Modrek, M. Gorlick, R. Riley, and C. Lee, "Assessing the impact of alternative splicing on domain interactions in the human proteome," Journal of Proteome Research, vol. 3, no. 1, pp. 76-83, 2004.
25. S. Liu and R. B. Altman, "Large scale study of protein domain distribution in the context of alternative splicing," Nucleic Acids Research, vol. 31, no. 16, pp. 4828-4835, 2003.
26. D. Talavera, C. Vogel, M. Orozco, S. A. Teichmann, and X. de la Cruz, "The (in)dependence of alternative splicing and gene duplication," PLoS Computational Biology, vol. 3, no. 3, article e33, 2007.
27. A. Valenzuela, D. Talavera, M. Orozco, and X. de la Cruz, "Alternative splicing mechanisms for the modulation of protein function: Conservation between human and other species," Journal of Molecular Biology, vol. 335, no. 2, pp. 495- 502, 2004.
28. S. Lois, N. Blanco, M. Martínez-Balbás, and X. de la Cruz, "The functional modulation of epigenetic regulators by alternative splicing," BMC Genomics, vol. 8, article 252, 2007.
29. E. V. Kriventseva, I. Koch, R. Apweiler, et al., "Increase of functional diversity by alternative splicing," Trends in Genetics, vol. 19, no. 3, pp. 124-128, 2003.
30. P. Ferro, A. Forlani, M. Muselli, and U. Pfeffer, "Alternative splicing of the human estrogen receptor alpha primary transcript: mechanisms of exon skipping," International Journal of Molecular Medicine, vol. 12, no. 3, pp. 355-363, 2003.
31. K. Tajul-Arifin, R. Teasdale, T. Ravasi, et al., "Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome," Genome Research, vol. 13, no. 6, pp. 1416-1429, 2003.
32. B. Boeckmann, A. Bairoch, R. Apweiler, et al., "The SWISSPROT protein knowledgebase and its supplement TrEMBL in 2003," Nucleic Acids Research, vol. 31, no. 1, pp. 365-370, 2003.
33. G. A. Reeves, D. Talavera, and J. M. Thornton, "Genome and proteome annotation: Organization, interpretation and integration," Journal of the Royal Society Interface, vol. 6, no. 1, pp. 129-147, 2009.
34. L. Nagy, H. Hegyi, K. Farkas, et al., "Identification and correction of abnormal, incomplete and mispredicted proteins in public databases," BMC Bioinformatics, vol. 9, article 353, 2008.
35. W. Li, L. Jaroszewski, and A. Godzik, "Clustering of highly homologous sequences to reduce the size of large protein databases," Bioinformatics, vol. 17, no. 3, pp. 282-283, 2001.
36. I. Letunic, R. R. Copley, S. Schmidt, et al., "SMART 4.0: Towards genomic data integration," Nucleic Acids Research, vol. 32, pp. D142-D144, 2004.
37. A. Bateman, L. Coin, R. Durbin, et al., "The Pfam protein families database," Nucleic Acids Research, vol. 32, pp. D138- D141, 2004.
38. S. F. Altschul, T. L. Madden, A. A. Schaffer, et al., "Gapped BLAST and PSI-BLAST: A new generation of protein database search programs," Nucleic Acids Research, vol. 25, no. 17, pp. 3389-3402, 1997.
39. A. I. Su, T. Wiltshire, S. Batalov, et al., "A gene atlas of the mouse and human protein-encoding transcriptomes," Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 16, pp. 6062-6067, 2004.
40. L. Huminiecki and K. H. Wolfe, "Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse," Genome Research, vol. 14, no. 10, pp. 1870-1879, 2004.
41. I. Yanai, D. Graur, and R. Ophir, "Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control," OMICS, vol. 8, no. 1, pp. 15-24, 2004.
42. I. K. Jordan, L. Marino-Ramirez, and E. V. Koonin, "Evolutionary significance of gene expression divergence," Gene, vol. 345, pp. 119-126, 2005.
43. B.-Y. Liao and J. Zhang, "Evolutionary conservation of expression profiles between human and mouse orthologous genes,"Molecular Biology and Evolution, vol. 23, no. 3, pp. 530-540, 2006.
44. E. S. Lander, L. M. Linton, B. Birren, et al., "Initial sequencing and analysis of the human genome," Nature, vol. 409, no. 6822, pp. 860-921, 2001.
45. D. Brett, H. Pospisil, J. Valcárcel, J. Reich, and P. Bork, "Alternative splicing and genome complexity," Nature Genetics, vol. 30, no. 1, pp. 29-30, 2002.
46. H. Kim, R. Klein, J. Majewski, et al., "Estimating rates of alternative splicing in mammals and invertebrates," Nature Genetics, vol. 36, no. 9, pp. 915-917, 2004.
47. C. Chothia and A. M. Lesk, "The relation between the divergence of sequence and structure in proteins," The EMBO Journal, vol. 5, no. 4, pp. 823-826, 1986.
48. V. Daburon, S. Mella, J.-L. Plouhinec, S. Mazan, M. Crozatier, and A. Vincent, "The metazoan history of the COE transcription factors. Selection of a variant HLH motif by mandatory inclusion of a duplicated exon in vertebrates," BMC Evolutionary Biology, vol. 8, no. 1, article 131, 2008.
49. W. Tian and J. Skolnick, "How well is enzyme function conserved as a function of pairwise sequence identity?" Journal of Molecular Biology, vol. 333, no. 4, pp. 863-882, 2003.
50. T. A. Thanaraj, F. Clark, and J.Muilu, "Conservation of human alternative splice events in mouse," Nucleic Acids Research, vol. 31, no. 10, pp. 2544-2552, 2003.
51. R. H. Waterston, K. Lindblad-Toh, E. Birney, et al., "Initial sequencing and comparative analysis of the mouse genome," Nature, vol. 420, no. 6915, pp. 520-562, 2002.
52. J. Stetefeld and M. A. Ruegg, "Structural and functional diversity generated by alternative mRNA splicing," Trends in Biochemical Sciences, vol. 30, no. 9, pp. 515-521, 2005.
53. F. A. Kondrashov and E. V. Koonin, "Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences," Trends in Genetics, vol. 19, no. 3, pp. 115-119, 2003.
54. M. Hiller, K. Huse, M. Platzer, and R. Backofen, "Creation and disruption of protein features by alternative splicing-a novel mechanism tomodulate function," Genome Biology, vol. 6, no. 7, article R58, 2005.
55. K. Jackson Behan, J. Fair, S. Singh, et al., "Alternative splicing removes an Ets interaction domain from Lozenge during Drosophila eye development," Development Genes and Evolution, vol. 215, no. 8, pp. 423-435, 2005.
56. K. Homma, R. F. Kikuno, T. Nagase, O. Ohara, and K. Nishikawa, "Alternative splice variants encoding unstable protein domains exist in the human brain," Journal of Molecular Biology, vol. 343, no. 5, pp. 1207-1220, 2004.
57. M. Zavolan and E. van Nimwegen, "The types and prevalence of alternative splice forms," Current Opinion in Structural Biology, vol. 16, no. 3, pp. 362-367, 2006.
58. L. A. Goodman, "On simultaneous confidence intervals for multinomial proportions," Technometrics, vol. 7, pp. 247-254, 1965.
59. L. Chen and S. Zheng, "Studying alternative splicing regulatory networks through partial correlation analysis," Genome Biology, vol. 10, no. 1, article R3, 2009.
60. H. Vihma, P. Pruunsild, and T. Timmusk, "Alternative splicing and expression of human and mouse NFAT genes," Genomics, vol. 92, no. 5, pp. 279-291, 2008.
61. A. Nayak, J. Glockner-Pagel, M. Vaeth, et al., "SUMOylation of the transcription factor NFATc1 leads to its subnuclear relocalization and IL2 repression by HDAC," The Journal of Biological Chemistry, vol. 284, no. 16, pp. 10935-10946, 2009.