Large-scale sequencing in human chromosome 12p13: Experimental and computational gene structure determination

Genome Research

Volumn 7, Issue 3, 1997, Pages 268-280

  Ansari Lari, M Ali ^a   Shen, Ying ^a   Muzny, Donna M ^a   Lee, William ^a   Gibbs, Richard A ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ARTICLE; CHROMOSOME 12P; CHROMOSOME MAP; COMPUTER PROGRAM; GENE STRUCTURE; GENETIC TRANSCRIPTION; HUMAN; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY;

EID: 0030895299     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.7.3.268     Document Type: Article

References (61)

1. Adams, S.M., N.R. Helps, M.G.F. Sharp, W.J. Brammar, R.A. Walker, and J.M. Varley. 1992. Isolation and characterization of a novel gene with differential expression in benign and malignant human breast tumors. Hum. Mol. Genet. 1: 91-96.
2. Altschul, S.F., W. Gish, W. Miller, E.W. Myers, and D.J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
3. Andersson, B., M.A. Wentland, J.Y. Ricafrente, W. Liu, and R.A. Gibbs. 1996a. A "double adaptor" method for improved shotgun library construction. Anal. Biochem. 236: 107-113.
4. Andersson, B., J. Lu, K.E. Edwards, D.M. Muzny, and R.A. Gibbs. 1996b. Method for 96-well M13 DNA template preparations for large-scale sequencing. BioTechniques 20: 1022-1027.
5. Andersson, B., J. Lu, Y. Shen, M. Wentland, and R.A. Gibbs. 1997. Simultaneous shotgun sequencing of multiple cDNA clones. DNA Sequence (in press).
6. Ansari-Lari, M.A., D.M. Muzny, J. Lu, F. Lu, C.E. Lilley, S. Spanos, T. Malley, and R.A. Gibbs. 1996a. A gene-rich cluster between the CD4 and triosephosphate isomerase genes at human chromosome 12p13. Genome Res. 6: 314-326.
7. Ansari-Lari, M.A., S.N. Jones, K.M. Timms, and R.A. Gibbs. 1996b. Improved ligation-anchored PCR strategy for identification of 5′ ends of transcripts. BioTechniques 21: 34-38.
8. Bairoch, A. 1993. The PROSITE dictionary of sites and patterns in proteins, its current status. Nucleic Acids Res. 21: 3097-3103.
9. Banville, D., R. Stocco, and S.-H. Shen. 1995. Human protein tyrosine phosphatase 1C (PTPN6) gene structure: alternate promoter usage and exon skipping generate multiple transcripts. Genomics 27: 165-173.
10. Boguski, M.S. and G.D. Schuler. 1995. ESTablishing a human transcript map. Nature Genet. 10: 369-371.
11. Bonfield, J.K., K.F. Smith, and R. Staden. 1995. A new DNA sequence assembly program. Nucleic Acids Res. 25: 4992-4999
12. Burset, M. and R. Guigo. 1996. Evaluation of gene structure prediction programs. Genomics 34: 353-367.
13. Cavalier-Smith, T. 1991. Intron phylogeny: A new hypothesis. Trends Genet. 7: 145-148.
14. Chelly, J. and A. Kahn. 1994. RT-PCR and mRNA quantitation. In The polymerase chain reaction (ed. K.B. Mullis, F. Ferre, and R.A. Gibbs), pp. 97-109. Birkhauser, Boston, MA.
15. Civitello, A.B., S. Richards, and R.A. Gibbs. 1993. A simple protocol for the automation of DNA cycle sequencing reactions and polymerase chain reactions. DNA Sequence 3: 17-23.
16. Eveleth, D.D.J. and J.L. Marsh. 1986. Sequence and expression of Cc gene, a member of the dopa decarboxylase gene cluster of Drosophila: Possible translational regulation. Nucleic Acids Res. 14: 6169-6183.
17. Gibbs, R.A. 1995. Pressing ahead with human genome sequencing. Nature Genet. 11: 121-125.
18. Gibbs, R.A. and M. Cockerill. 1995. Working on the assembly line. Trends Biochem. Sci. 20: 162-163.
19. Goeddel, D.V., D.W. Leung, T.J. Dull, M. Gross, R.M. Lawn, R. McCandliss, P.M. Seeburg, A. Ullrich, E. Yelverton, and P.W. Gray. 1981. The structure of eight distinct cloned human leukocyte interferon cDNAs. Nature 290: 20-26.
20. Guigo, R., S. Knudsen, N. Drake, and T.F. Smith. 1992. Prediction of gene structure. J. Mol. biol. 226: 141-157.
21. Hawkins, M., B. Pope, S.K. Maciver, and A.G. Weeds. 1993. Human actin depolymerizing factor mediates a pH-sensitive destruction of actin filaments. Biochemistry 32: 9985-9993.
22. Helps, N.R., S.M. Adams, W.J. Brammar, and J.M. Varley. 1995. The Drosophila melanogaster homologue of the human BBC1 gene is highly expressed during embryogenesis. Gene 162: 245-248.
23. Henikoff, S., J.G. Henikoff, W.J. Alford, and S. Pietrokovski. 1995. Automated construction and graphical presentation of protein blocks from unaligned sequences. Gene 163: GC17-26.
24. Hillier, L., G. Lennon, M. Becker, M.F. Bonaldo, B. Chiapelli, S. Chissoe, N. Dietrich, T. DuBuque, A. Favello, W. Gish, M. Hawkins, M. Hultman, T. Kucaba, M. Lacy, M. Le, N. Le, E. Mardis, B. Moore, M. Morris, J. Parsons, C. Prange, L. Rifkin, T. Rohlfing, K. Schellenberg, M.B. Soares, F. Tan, J. Thierry-Meg, E. Trevaski, K. Underwood, P. Wohldman, R. Waterston, R. Wilson, and M. Marra. 1996. Generation and analysis of 280,000 human expressed sequence tags. Genome Res. 6: 807-828.
25. Hofmann, K. and W. Stoffel. 1993. TMBASE - A database of membrane spanning protein segments. Biol. Chem. Hoppe-Seyler 374: 166.
26. Jurka, J., P. Klonowski, V. Dagman, and P. Pelton. 1995. CENSOR - A program for identification and elimination of repetitive elements from DNA sequences. Comput. & Chem. 20: 119-122.
27. Kwiatowski, J., M. Krawczyk, M. Kornacki, K. Bailey, and F.J. Ayala. 1995. Evidence against the exon theory of genes derived from the triose-phosphate isomerase gene. Proc. Natl. Acad. Sci. 92: 8503-8506.
28. Koide, R., T. Ikeuchi, O. Onodera, H. Tanaka, S. Igarashi, K. Endo, H. Takahashi, R. Kondo, A. Ishikawa, T. Hayashi, M. Saito, A. Tomoda, T. Miike, H. Natio, F. Ikuta, and S. Tsuji. 1994. Unstabel expansion of CAG repeat in hereditary dentatorubral-pallidoluysian atrophy (DRPLA). Nature Genet. 6: 9-13.
29. Koop, B.F. and L. Hood. 1994. Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA. Nature Genet. 7: 48-53.
30. Kulp, D., D. Haussler, M.G. Reese, and F.H. Eeckman. 1996. A generalized hidden Markov model for the recognition of human genes in DNA (ed. D.J. States, P. Agarwal, T. Gaasterland, L. Hunter, and R. Smith), pp. 134-142. AAAI Press, Menlo Park, CA.
31. Logsdon, J.M.J., M.G. Tyshenko, C. Dixon, J.D.-Jafari, V.K. Walker, and J.D. Palmer. 1995. Seven newly discovered intron positions in the triose-phosphate isomerase gene: Evidence for the introns-late theory. Proc. Natl. Acad. Sci. 92: 8507-8511.
32. Lowe, T.M. and S.R. Eddy. 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequences. Nucleic Acids Res. 25 (in press).
33. McCarrey, J.R. and K. Thomas. 1987. Human testis-specific PGK gene lacks introns and possesses characteristics of a processed gene. Nature 326: 501-505.
34. Moriyama, K., E. Nishida, N. Yonezawa, H. Sakai, S. Matsumoto, K. Iida, and I. Yahara. 1990. Destrin, a mammalian actin-depolymerizing protein is closely related to cofilin. J. Biol. Chem. 265: 5768-5773.
35. Mowry, K.L. and J.A. Steitz. 1987. Identification of the human U7 snRNP as one of several factors involved in the 3′ end maturation of histone premessenger RNA's. Science 238: 1682-1687.
36. Muzny, D.M., S. Richards, Y. Shen, and R.A. Gibbs. 1994. PCR based strategies for gap closure in large-scale sequencing projects. In Automated DNA sequencing and analysis (ed. M.D. Adams, C. Fields, and J.C. Venter), pp. 182-190. Academic Press, San Diego, CA.
37. Nagafuchi, S., H. Yanagisawa, E. Ohsaki, T. Shirayama, K. Tadokoro, T. Inoue, and M. Yamada. 1994. Structure and expression of the gene responsible for the triplet repeat disorder, dentatorubral and pallidoluysian atrophy (DRPLA). Nature Genet. 8: 177-182.
38. Nuell, M.J., D.A. Stewart, L. Walker, V. Friedman, C.M. Wood, G.A. Owens, J.R. Smith, E.L. Schneider, R. Dell'Orco, C.K. Lumpkin, D.B. Danner, and J.K. McClung. 1991. Prohibitin, an evolutionary conserved intracellular protein that blocks DNA synthesis in normal fibroblasts and Hela Cells. Mol. Cell. Biol. 11: 1372-1381.
39. Oeltjen, J.C., T.M. Malley, D.M. Muzny, W. Miller, R.A. Gibbs, and J.W. Belmont. 1997. Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains. Genome Res. 11: (in press).
40. Oliva, D., L. Cali, S. Feo, and A. Giallongo. 1991. Complete structure of the human gene encoding neuron-specific enolase. Genomics 10: 157-165.
41. Olvera, J. and I.G. Wool. 1994. The primary structure of rat ribosomal protein L13. Biochem. Biophys. Res. Common 201: 102-107.
42. Onodera, O., M. Oyake, H. Takano, T. Ikeuchi, S. Igarashi, and S. Tsuji. 1995. Molecular cloning of a full-length cDNA for dentatorubral-pallidoluysian atrophy and regional expressions of the expanded alleles in the CNS. Am. J. Hum. Genet. 57: 1050-1060.
43. Pearson, W.R. 1990. Rapid and sensitive sequence comparisons with FASTP and FASTA. Methods Enzymol. 183: 63-98.
44. Phillips, S.C. and P.C. Turner. 1991. Nucleotide sequence of the mouse U7 snRNA gene. Nucleic Acids Res. 19: 1344.
45. Plutzky, J., B.G. Neel, and R.D. Rosenberg. 1992. Isolation of a src homology 2-containing tyrosine phosphatase. Proc. Natl Acad. Sci 89: 1123-1127.
46. Sambrook, J., E.F. Fritsch, and T. Maniatis. 1989. Molecular cloning: A laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
47. Sato, T., H. Saito, J. Swensen, A. Olifant, C. Wood, D. Danner, T. Sakamoto, K. Takita, F. Kasumi, Y. Miki, M. Skolnick, and Y. Nakamura. 1992. The human prohibitin gene located on chromosome 17q21 is mutated in sporadic breast cancer. Cancer Res. 52: 1643-1646.
48. Sato, T., T. Sakamoto, K.-I. Takita, H. Saito, K. Okui, and Y. Nakamura. 1993. The human prohibitin (PHB) gene family and its somatic mutations in human tumors. Genomics 17: 762-764.
49. Shen, S.-H., L. Bastien, B.I. Posner, and P. Chretien. 1991. A protein-tyrosine phosphatase with sequence similarity to the SH2 domain of the protein-tyrosine kinases. Nature 352: 736-739.
50. Smith, R.F. and T.F. Smith. 1992. Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for comparative protein modelling. Protein Eng. 5: 35-41.
51. Smith, R.F., B.A. Wiese, M.K. Wojzynski, D.B. Davison, and K.C. Worley. 1996. BCM search launcher-an integrated interface to molecular biology data base search and analysis services available on the World Wide Web. Genome Res. 6: 454-462.
52. Snyder, E.E. and G.D. Stormo. 1995. Identification of protein coding regions in genomic DNA. J. Mol. Biol. 248: 1-18.
53. Soldati, D. and D. Schumperli. 1988. Structural and functional characterization of mouse U7 small nuclear RNA active in 3′ processing of histone pre-mRNA. Mol. Cell Biol. 8: 1518-1524.
54. Solovyev, V.V., A.A. Salamov, and C.B. Lawrence.1994. Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. Nucleic Acids Res. 22: 5156-5163.
55. _. 1995. Identification of human gene structure using linear discriminant functions and dynamic programming. In Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology (ed. C. Rawling, D. Clark, R. Altman, L. Hunter, T. Lengauer, and S. Wodak), pp. 367-375. AAAI Press, Cambridge, UK.
56. Sorge, J., E. Gross, C. West, and E. Beutler. 1990. High level transcription of the glucocerebrosidase pseudogene in normal subjects and patients with Gaucher disease. J. Clin. Invest. 86: 1137-1141.
57. Terashima, M., K.-M. Kim, T. Adachi, P.J. Nielsen, M. Reth, G. Kohler, and M.C. Lamers. 1994. The IgM antigen receptor of B lymphocytes is associated with prohibitin and a prohibitin-related protein. EMBO J. 13: 3782-3792.
58. Thompson, J.D., D.G. Higgins, and T.J. Gibson. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighing, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
59. Worley, K.C., B.A. Weise, and R.F. Smith. 1995. BEAUTY: An enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results. Genome Res. 5: 173-184.
60. Xu, Y., R.J. Mural, M.B. Shah, and E.C. Uberbacher. 1994. Recognizing exons in genomic sequence using GRAIL II. In Genetic engineering: Principles and methods (ed. J. Setlow), Vol. 16, pp. 241-253. Plenum Press, New York, NY.
61. Zhang, J. 1996. PowerBLAST: A new network BLAST application for genomic sequence analysis. In Genome mapping & sequencing, p. 19. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.