The multiassembly problems: Reconstructing multiple transcript isoforms from EST fragment mixtures

Genome Research

Volumn 14, Issue 3, 2004, Pages 426-441

  Xing, Yi ^a   Resch, Alissa ^a   Lee, Christopher ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL ADHESION MOLECULE; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; HAPTOCORRIN; HISTONE DEACETYLASE; ISOPROTEIN; MESSENGER RNA; TRANSCRIPTION FACTOR PAX6; WT1 PROTEIN; ZINC FINGER PROTEIN; TRANSCOBALAMIN;

ALGORITHM; ALTERNATIVE RNA SPLICING; ANALYTICAL ERROR; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENOMICS; HUMAN; INTRON; POLYADENYLATION; PRIORITY JOURNAL; PROTEIN DATABASE; RELIABILITY; REVIEW; SEQUENCE ANALYSIS; SEQUENCE DATABASE; STATISTICAL ANALYSIS; TRANSCRIPTION INITIATION; VALIDATION PROCESS; ARTICLE; BIOLOGY; COMPARATIVE STUDY; EXON; GENETIC DATABASE; GENETICS; HUMAN GENOME PROJECT; METHODOLOGY; PROTEIN SYNTHESIS; STATISTICS; VALIDATION STUDY;

ALGORITHMS; ALTERNATIVE SPLICING; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EXONS; EXPRESSED SEQUENCE TAGS; HUMAN GENOME PROJECT; HUMANS; PROTEIN BIOSYNTHESIS; PROTEIN ISOFORMS; TRANSCOBALAMINS; TRANSCRIPTION, GENETIC;

EID: 1542316923     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1304504     Document Type: Review

References (74)

1. Bairoch, A. and Apweiler, R. 1998. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res. 26: 38-42.
2. Baskin, D.G., Schwartz, M.W., Seeley, R.J., Woods, S.C., Porte Jr., D., Breininger, J.F., Jonak, Z., Schaefer, J., Krouse, M., Burghardt, C., et al. 1999. Leptin receptor long-form splice-variant protein expression in neuron cell bodies of the brain and co-localization with neuropeptide Y mRNA in the arcuate nucleus. J. Histochem. Cytochem. 47: 353-362.
3. Berkowitz, L.A. and Gilman, M.Z. 1990. Two distinct forms of active transcription factor CREB (cAMP response element binding protein). Proc. Natl. Acad. Sci. 87: 5258-5262.
4. Boman, A.L., Zhang, C., Zhu, X., and Kahn, R.A. 2000. A family of ADP-ribosylation factor effectors that can alter membrane transport through the trans-Golgi. Mol. Biol. Cell 11: 1241-1255.
5. Brett, D., Hanke, J., Lehmann, G., Haase, S., Delbruck, S., Krueger, S., Reich, J., and Bork, P. 2000. EST comparison indicates 38% of human mRNAs contain possible alternative splice forms. FEBS Lett. 474: 83-86.
6. Burke, J., Wang, H., Hide, W., and Davison, D.B. 1998. Alternative gene form discovery and candidate gene selection from gene indexing projects. Genorne Res. 8: 276-290.
7. Christoffels, A., van Gelder, A., Greyling, G., Miller, R., Hide, T., and Hide, W. 2001. STACK: Sequence Tag Alignment and Consensus Knowledgebase. Nucleic Acids Res. 29: 234-238.
8. Cobellis, L., Reis, F.M., Driul, L., Vultaggio, G., Ferretti, I., Villa, E., and Petraglia, F. 2002. Estrogen receptor a mRNA variant lacking exon 5 is co-expressed with the wild-type in endometrial adenocarcinoma. Eur. J. Obstet. Gynecol. Reprod. Biol. 102: 92-95.
9. Corti, O., DiDonato, S., and Finocchiaro, G. 1994a. Divergent sequences in the 5′ region of cDNA suggest alternative splicing as a mechanism for the generation of carnitine acetyltransferases with different subcellular localizations. Biochem. J. 303: 27-41.
10. Corti, O., Finocchiaro, G., Rossi, E., Zuffardi, O., and DiDonato, S. 1994b. Molecular cloning of cDNAs encoding human carnitine acetyltransferase and mapping of the corresponding gene to chromosome 9q34.1. Genomics 23: 94-99.
11. Croft, L., Schandorff, S., Clark, F., Burrage, K., Arctander, P., and Mattick, J.S. 2000. ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nat. Genet. 24: 340-341.
12. Davuluri, R.V., Grosse, I., and Zhang, M.Q. 2001. Computational identification of promoters and first exons in the human genome. Nat. Genet. 29: 412-417.
13. Dell'Angelica, E.C., Puertollano, R., Mullins, C., Aguilar, R.C., Vargas, J.D., Hartnell, L.M., and Bonifacino, J.S. 2000. GGAs: A family of ADP ribosylation factor-binding proteins related to adaptors and associated with the Golgi complex. J. Cell Biol. 149: 81-94.
14. Denger, S., Reid, G., Kos, M., Flouriot, G., Parsch, D., Brand, H., Korach, K.S., Sonntag-Buck, V., and Gannon, F. 2001. ERα gene expression in human primary osteoblasts: Evidence for the expression of two receptor proteins. Mol. Endocrinol. 15: 2064-2077.
15. Droin, N., Rebe, C., Bichat, F., Hammann, A., Bertrand, R., and Solary, E. 2001. Modulation of apoptosis by procaspase-2 short isoform: Selective inhibition of chromatin condensation, apoptotic body formation and phosphatidylserine externalization. Oncogene 20: 260-269.
16. D'Souza, I. and Schellenberg, G.D. 2000. Determinants of 4-repeat τ expression: Coordination between enhancing and inhibitory splicing sequences for exon 10 inclusion. J. Biol. Chem. 275: 17700-17709.
17. Epstein, J.A., Glaser, T., Cai, J., Jepeal, L., Walton, D.S., and Maas, R.L. 1994. Two independent and interactive DNA-binding subdomains of the Pax6 paired domain are regulated by alternative splicing. Genes & Dev. 8: 2022-2034.
18. Fairbrother, W.G., Yeh, R.F., Sharp, P.A., and Burge, C.B. 2002. Predictive identification of exonic splicing enhancers in human genes. Science 297: 1007-1013.
19. Fasulo, D., Halpern, A., Dew, I., and Mobarry, C. 2002. Efficiently detecting polymorphisms during the fragment assembly process. Bioinformatics 18 Suppl 1: S294-S302.
20. Figtree, G.A., McDonald, D., Watkins, H., and Channon, K.M. 2003. Truncated estrogen receptor α 46-kDa isoform in human endothelial cells: Relationship to acute activation of nitric oxide synthase. Circulation 107: 120-126.
21. Grozinger, C.M., Hassig, C.A., and Schreiber, S.L. 1999. Three proteins define a class of human histone deacetylases related to yeast Hda1p. Proc. Natl. Acad. Sci. 96: 4868-4873.
22. Haas, S.A., Beissbarth, T., Rivals, E., Krause, A., and Vingron, M. 2000. GeneNest: Automated generation and visualization of gene indices. Trends Genet. 16: 521-523.
23. Haber, D.A., Sohn, R.L., Buckler, A.J., Pelletier, J., Call, K.M., and Housman, D.E. 1991. Alternative splicing and genomic structure of the Wilms tumor gene WT1. Proc. Natl. Acad. Sci. 88: 9618-9622.
24. Harrison, P.M., Kumar, A., Lang, N., Snyder, M., and Gerstein, M. 2002. A question of size: The eukaryotic proteome and the problems in defining it. Nucleic Acids Res. 30: 1083-1090.
25. Heber, S., Alekseyev, M., Sze, S.H., Tang, H., and Pevzner, P.A. 2002. Splicing graphs and EST assembly problem. Bioinformatics 18 Suppl. 1: S181-S188.
26. Hide, W.A., Babenko, V.N., van Heusden, P.A., Seoighe, C., and Kelso, J.F. 2001. The contribution of exon-skipping events on chromosome 22 to protein coding diversity. Genome Res. 11: 1848-1853.
27. Hovanes, K., Li, T.W., Munguia, J.E., Truong, T., Milovanovic, T., Lawrence Marsh, J., Holcombe, R.F., and Waterman, M.L. 2001. β-Catenin-sensitive isoforms of lymphoid enhancer factor-1 are selectively expressed in colon cancer. Nat. Genet. 28: 53-57.
28. Hubbert, C., Guardiola, A., Shao, R., Kawaguchi, Y., Ito, A., Nixon, A., Yoshida, M., Wang, X.F., and Yao, T.P. 2002. HDAC6 is a microtubule-associated deacetylase. Nature 417: 455-458.
29. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
30. Irizarry, K., Kustanovich, V., Li, C., Brown, N., Nelson, S., Wong, W., and Lee, C. 2000. Genome-wide analysis of single-nucleotide polymorphisms in human expressed sequences. Nat. Genet. 26: 233-236.
31. Jacob, J., Haspel, J., Kane-Goldsmith, N., and Grumet, M. 2002. L1 mediated homophilic binding and neurite outgrowth are modulated by alternative splicing of exon 2. J. Neurobiol. 51:177-189.
32. Jazaeri, O., Shupnik, M.A., Jazaeri, A.A., and Rice, L.W. 1999. Expression of estrogen receptor α mRNA and protein variants in human endometrial carcinoma. Gynecol. Oncol. 74: 38-47.
33. Jouet, M., Rosenthal, A., and Kenwrick, S. 1995. Exon 2 of the gene for neural cell adhesion molecule L1 is alternatively spliced in B cells. Brain Res. Mol. Brain Res. 30: 378-380.
34. Kan, Z., Rouchka, E.C., Gish, W.R., and States, D.J. 2001. Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res. 11: 889-900.
35. Kan, Z., States, D., and Gish, W. 2002. Selecting for functional alternative splices in ESTs. Genome Res. 12: 1837-1845.
36. Kim, M., Tezuka, T., Suziki, Y., Sugano, S., Hirai, M., and Yamamoto, T. 1999. Molecular cloning and characterization of a novel cbl-family gene, cbl-c. Gene 239: 145-154.
37. Kirschner, R., Rosenberg, T., Schultz-Heienbrok, R., Lenzner, S., Fell, S., Roepman, R., Cremers, F.P., Ropers, H.H., and Berger, W. 1999. RPGR transcription studies in mouse and human tissues reveal a retina-specific isoform that is disrupted in a patient with X-linked retinitis pigmentosa. Hum. Mol. Genet. 8: 1571-1578.
38. Kozmik, Z., Czerny, T., and Busslinger, M. 1997. Alternatively spliced insertions in the paired domain restrict the DNA sequence specificity of Pax6 and Pax8. EMBO J. 16: 6793-803.
39. Lee, C. 2003. Generating consensus sequences from partial order multiple sequence alignment graphs. Bioinformatics 19: 999-1008.
40. Lee, C., Grasso, C., and Sharlow, M. 2002. Multiple sequence alignment using partial order graphs. Bioinformatics 18: 452-464.
41. Lewis, B.P., Green, R.E., and Brenner, S.E. 2003. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc. Natl. Acad. Sci. 100: 189-192.
42. Liang, F., Holt, I., Pertea, G., Karamycheva, S., Salzberg, S.L., and Quackenbush, J. 2000a. Gene Index analysis of the human genome estimates approximately 120,000 genes. Nat. Genet. 25: 239-240.
43. Liang, F., Holt, I., Pertea, G., Karamycheva, S., Salzberg, S.L., and Quackenbush, J. 2000b. An optimized protocol for analysis of EST sequences. Nucleic Acids Res. 28: 3657-3665.
44. Maquat, L.E. 2002. Nonsense-mediated mRNA decay. Curt. Biol. 12: R196-R197.
45. Maquat, L.E. and Carmichael, G.G. 2001. Quality control of mRNA function. Cell 104: 173-176.
46. Markovtsov, V., Nikolic, J.M., Goldman, J.A., Turck, C.W., Chou, M.Y., and Black, D.L. 2000. Cooperative assembly of an hnRNP complex induced by a tissue-specific homolog of polypyrimidine tract binding protein. Mol. Cell. Biol. 20: 7463-7479
47. Meindl, A., Dry, K., Herrmann, K., Manson, F., Ciccodicola, A., Edgar, A., Carvalho, M.R., Achatz, H., Hellebrand, H., Lennon, A., et al. 1996. A gene (RPGR) with homology to the RCC1 guanine nucleotide exchange factor is mutated in X-linked retinitis pigmentosa (RP3). Nat. Genet. 13: 35-42.
48. Mironov, A.A., Fickett, J.W., and Gelfand, M.S. 1999. Frequent alternative splicing of human genes. Genome Res. 9: 1288-1293.
49. Modrek, B. and Lee, C. 2002. A genomic view of alternative splicing. Nat. Genet. 30: 13-19.
50. Modrek, B., Resch, A., Grasso, C., and Lee, C. 2001. Genome-wide analysis of alternative splicing using human expressed sequence data. Nucleic Acids Res. 29: 2850-2859.
51. Muilu, J., Rodriguez-Tome, P., and Robinson, A. 2001. GBuilder - An application for the visualization and integration of EST cluster data. Genome Res. 11: 179-184.
52. Nakai, A., Tanabe, M., Kawazoe, Y., Inazawa, J., Morimoto, R.I., and Nagata, K. 1997. HSF4, a new member of the human heat shock factor family which lacks properties of a transcriptional activator. Mol. Cell. Biol. 17: 469-481.
53. Oshima, H., Szapary, D., and Simons Jr., S.S. 1995. The factor binding to the glucocorticoid modulatory element of the tyrosine aminotransferase gene is a novel and ubiquitous heteromeric complex. J. Biol. Chem. 270: 21893-21901.
54. Patek, C.E., Little, M.H., Fleming, S., Miles, C., Charlieu, J.P., Clarke, A.R., Miyagawa, K., Christie, S., Doig, J., Harrison, D.J., et al. 1999. A zinc finger truncation of murine WT1 results in the characteristic urogenital abnormalities of Denys-Drash syndrome. Proc. Natl. Acad. Sci. 96: 2931-2936.
55. Perez-Sanchez, C., Arias-de-la-Fuente, C., Gomez-Ferreria, M.A., Granadino, B., and Rey-Campos, J. 2000a. FHX.L and FHX.S, two isoforms of the human fork-head factor FHX (FOXJ2) with differential activity. J. Mol. Biol. 301: 795-806.
56. Perez-Sanchez, C., Gomez-Ferreria, M.A., de La Fuente, C.A., Granadino, B., Velasco, G., Esteban-Gamboa, A., and Rey-Campos, J. 2000b. FHX, a novel fork head factor with a dual DNA binding specificity. J. Biol. Chem. 275: 12909-12916.
57. Pruitt, K.D., Katz, K.S., Sicotte, H., and Maglott, D.R. 2000. Introducing RefSeq and LocusLink: Curated human genome resources at the NCBI. Trends Genet. 16: 44-47.
58. Pujols, L., Mullol, J., Perez, M., Roca-Ferrer, J., Juan, M., Xaubet, A., Cidlowski, J.A., and Picado, C. 2001. Expression of the human glucocorticoid receptor α and β isoforms in human respiratory epithelial cells and their regulation by dexamethasone. Am. J. Respir. Cell Mol. Biol. 24: 49-57.
59. Quackenbush, J., Liang, F., Holt, I., Pertea, G., and Upton, J. 2000. The TIGR Gene Indices: Reconstruction and representation of expressed gene sequences. Nucleic Acids Res. 28: 141-145.
60. Quackenbush, J., Cho, J., Lee, D., Liang, F., Holt, I., Karamycheva, S., Parvizi, B., Pertea, G., Sultana, R., and White, J. 2001. The TIGR Gene Indices: Analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res. 29: 159-164.
61. Rahman, L., Bliskovski, V., Reinhold, W., and Zajac-Kaye, M. 2002. Alternative splicing of brain-specific PTB defines a tissue-specific isoform pattern that predicts distinct functional roles. Genomics 80: 245-249.
62. Rice, P., Longden, I., and Bleasby, A. 2000. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16: 276-277.
63. Schuler, G. 1997. Pieces of the puzzle: Expressed sequence tags and the catalog of human genes. J. Mol. Med. 75: 694-698.
64. Skandalis, A., Ninniss, P.J., McCormac, D., and Newton, L. 2002. Spontaneous frequency of exon skipping in the human HPRT gene. Mut. Res. 501: 37-44.
65. Stimpfl, M., Tong, D., Fasching, B., Schuster, E., Obermair, A., Leodolter, S., and Zeillinger, R. 2002. Vascular endothelial growth factor splice variants and their prognostic value in breast and ovarian cancer. Clin. Cancer Res. 8: 2253-2259.
66. Strausberg, R.L., Feingold, E.A., Klausner, R.D., and Collins, F.S. 1999. The mammalian gene collection. Science 286: 455-457.
67. Tanabe, M., Sasai, N., Nagata, K., Liu, X.D., Liu, P.C., Thiele, D.J., and Nakai, A. 1999. The mammalian HSF4 gene generates both an activator and a repressor of heat shock genes by alternative splicing. J. Biol. Chem. 274: 27845-27856.
68. Theriault, J.R., Charette, S.J., Lambert, H., and Landry, J. 1999. Cloning and characterization of hGMEB1, a novel glucocorticoid modulatory element binding protein. FEBS Lett. 452: 170-176.
69. Uthoff, S.M., Duchrow, M., Schmidt, M.H., Broll, R., Bruch, H.P., Strik, M.W., and Galandiuk, S. 2002. VEGF isoforms and mutations in human colorectal cancer. Int. J. Cancer 101: 32-36.
70. Vervoort, R., Lennon, A., Bird, A.C., Tulloch, B., Axton, R., Miano, M.G., Meindl, A., Meitinger, T., Ciccodicola, A., and Wright, A.F. 2000. Mutational hot spot within a new RPGR exon in X-linked retinitis pigmentosa. Nat. Genet. 25: 462-466.
71. Wang, L., Miura, M., Bergeron, L., Zhu, H., and Yuan, J. 1994. Ich-1, an Ice/ced-3-related gene, encodes both positive and negative regulators of programmed cell death. Cell 78: 739-750.
72. Williams, A.J., Khachigian, L.M., Shows, T., and Collins, T. 1995. Isolation and characterization of a novel zinc-finger protein with transcription repressor activity. J. Biol. Chem. 270: 22143-22152.
73. Yamamoto, K.K., Gonzalez, G.A., Menzel, P., Rivier, J., and Montminy, M.R. 1990. Characterization of a bipartite activator domain in transcription factor CREB. Cell 60: 611-617.
74. Zhuo, D., Zhao, W.D., Wright, F.A., Yang, H.Y., Wang, J.P., Sears, R., Baer, T., Kwon, D.H., Gordon, D., Gibbs, S., et al. 2001. Assembly, annotation, and integration of UNIGENE clusters into the human genome draft. Genome Res. 11: 904-918.