Model for a transcript map of human chromosome 21: Isolation of new coding sequences from exon and enriched cDNA libraries

Human Molecular Genetics

Volumn 4, Issue 8, 1995, Pages 1291-1304

  Yaspo, Marie Laure ^a   Gellen, Lisa ^a   Mott, Richard ^a   Korn, Bernhard ^a,b   Nizetic, Dean ^a   Poustka, Annemarie ^a,b   Lehrach, Hans ^a  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; CARRIER PROTEIN; COMPLEMENTARY DNA; DIHYDROOROTASE; NUCLEOTIDE; SYNTHETASE;

ANIMAL CELL; ARTICLE; AUTOIMMUNITY; CHROMOSOME 21; COMPARATIVE STUDY; CONTROLLED STUDY; COSMID; DATA BASE; DNA HYBRIDIZATION; DNA LIBRARY; DNA SEQUENCE; DNA TRANSCRIPTION; DOWN SYNDROME; EXON; GENE AMPLIFICATION; GENE ISOLATION; GENE MAPPING; HUMAN; HUMAN CELL; MOLECULAR CLONING; MYOCLONUS EPILEPSY; NONHUMAN; NORTHERN BLOTTING; PRIORITY JOURNAL; PROTEIN DOMAIN; SEQUENCE HOMOLOGY;

CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 21; COMPARATIVE STUDY; COSMIDS; DATABASES, FACTUAL; DNA, COMPLEMENTARY; EXONS; GENE AMPLIFICATION; GENE LIBRARY; HUMAN; MODELS, GENETIC; MOLECULAR PROBES; SUPPORT, NON-U.S. GOV'T; TRANSCRIPTION, GENETIC;

EID: 0029083423     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/4.8.1291     Document Type: Article

References (55)

1. Adams, M.D., Kelley, J.M., Gocayne, J.D., Dubnick, M., Polymeropoulos Xiao, H., Merril, C.R., Wu, M., Olde, B., Moreno, R.F., Kerlavage, A.R., McCombie, W.R., and Venter, J.C. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252, 1651-1656.
2. Adams, M.D., Kerlavage, A.R., Field, C. and Venter, J.C. (1993) 3,400 new expressed sequence tags identify diversity of transcripts in human brain. Nature Genet. 4, 256-267.
3. Okubo, K., Hori, N., Matoba, R., Niiyama, T., Fukushima, A., Kojima, Y., and Matsubara, K. (1993) Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression. Nature Genet. 2, 173-179.
4. Takeda, J., Yano, H., Eng, S., Zeng, Y., and Bell, G.I. (1993) A molecular inventory of human pancreatic islets: sequence analysis of 1000 clones. Hum. Mol. Genet. 2, 1793-1798.
5. Boguski, M.S., Lowe M.J. Todd, and Tolstoshev, C.M. (1993) dbEST- database for ‘expressed sequence tags’. Nature Genet. 4, 332-333.
6. Gardiner, K., Horisberger, M., Kraus, J., Tantravahi, U., Korenberg, J., Rao, V., Reddy, S., Patterson, D. (1990) Analysis of human chromosome 21: correlation of physical and cytogenetic maps; gene and CpG island distributions. EMBO J. 9, 25-34.
7. Crete, N., Delabar, J.M., Rahmani, Z., Yaspo, M.L., Kraus, J., Marks, A., Sinet, P.M., and Creau-Goldberg, N. (1993) Partial physical map of human chromosome 21 from fibroblast and lymphocyte DNA. Hum. Genet. 91, 245-253.
8. Ichikawa, H., Hosoda, F., Arai, Y., Shimizu, K., Ohira, M., Ohki, M. A Noll restriction map of the entire long arm of human chromosome 21. (1993) Nature Genet. 4, 361-366.
9. Delabar, J.M., Creau, N., Sinet, P.M., Ritter, O., Antonorakis, S.E., Burmeister, M., Chakravarti, A., Nizetic, D., Ohki, M., Patterson, D., Petersen, M.B., Reeves, R.H., and Van Broeckhoven, C. (1993) Report of the fourth international workshop on human chromosome 21. Genomics 18, 735-745.
10. Epstein, C.J., Korenberg, J.R., Anneren, G., Antonarakis, S.E., Ayme, S., Courchesne, E., Epstein, L.B., Fowler, A., Groner, Y., Huret, J.L., Kemper, T.L., Lott, I.T., Lubin, B.H., Magenis, E., Opitz, J.M., Patterson, D., Priest, J.H., Pueschel, S.M., Rapoport, S.I., Sinet, P.M., Tanzi, R.E., and de la Cruz, F. (1991) Protocols to establish genotype-phenotype correlations in Down syndrome. Am. J. Hum. Genet. 49, 207-235.
11. Rahmani, Z., Blouin, J.L., Creau-Goldberg, N., Watkins, P.C., Mattei, J.F., Poissonnier, M., Prieur, M., Chettouh, Z., Nicole, A., Aurias, A., Sinet, P.M., and Delabar, J.M. (1989) Critical role of the D21S55 region on chromosome 21 in the pathogenesis of Down syndrome. Proc. Natl. Acad. Sci. USA 86, 5958-5962.
12. Korenberg, J.R., Chen, X.N., Schipper, R., Sun, Z., Gonsky, R., Gerwehrcarpenter, N., Daumer, C., Dignan, P., Disteche, C., Graham, J.M., Hugdins, L., McGillivray, B., Miyazaki, K., Ogasawara, N., Park, J.P., Pagon, R., Pueschel, S., Sack, G., Say, B., Schuffenhauer, S., Soukup, and Yamanaka, T. (1994) Down syndrome phenotypes: the consequences of chromosomal imbalance. Proc. Natl. Acad. Sci. USA 91, 4997-5001.
13. Estabrooks, L.L., Rao, K.W., Donahue, R.P., and Aylsworth, A.S. (1990) Holoprosencephaly in an infant with a minute deletion of chromosome 21 (q22.3). Am. J. Med. Genet. 36, 306-309.
14. Aaltonen, J., Bjorses, P., Sandkuijl, L., Perheentupa, J., and Peltonen, L. (1994) An autosomal locus causing autoimmune disease: autoimmune polyglandular disease type I assigned to chromosome 21. Nature Genet. 8, 83-87.
15. Lehesjoki, A.E., Koskiniemi, M., Sistonen, P., Miao, J., Hastbacka, J., Norio, R., de la Chapelle, A. (1991) Localization of a gene for progressive myoclonus epilepsy to chromosome 21q22. Proc. Natl. Acad. Sci. USA 88, 3696-3699.
16. Kao, F.T., Yu, J., Tong, S., Qi, J., Patanjali, S.R., Weissman, S.M, and Patterson, D. (1994) Isolation and refined regional mapping of expressed sequences from human chromosome 21. Genomics 23, 700-703.
17. Cheng, J.F., Boyartchuk, V., and Zhu, Y. (1994) Isolation and mapping of human chromosome 21 cDNA: progress in constructing a chromosome 21 expression map. Genomics 23, 75-84.
18. Lindsay, S., and Bird, A.P. (1987) Use of restriction enzymes to detect potential gene sequences in mammalian DNA. Nature 327, 336-338.
19. Melmer, G., and Buchwald, M. (1992) Identification of genes using oligonucleotides corresponding to splice site consensus sequences. Hum. Mol Genet. 1, 433-438.
20. Snell, R.G., Doucette-Stamm, L.A., Gillepsie, K.M., Taylor, S.A.M., Ribabates, G.P., Altherr, M.R., MacDonald, M.E., Gusella, J.F., Wasmuth, J.J., Lehrach, H., Housman, D.E., Harper, P.S., Shaw, D.J. (1993) The isolation of cDNAs within the Huntington disease region by hybridisation of yeast artificial chromosomes to a cDNA library. Hum. Mol. Genet. 2, 305-309.
21. Claverie, J.M. (1994) A streamline random sequencing strategy for finding coding exons. Genomics 23, 575-581.
22. Auch, D., and Reth, M. (1991). Exon trap cloning: using PCR to rapidly detect and clone exons from genomic DNA fragments. Nucleic Acids Res. 18, 6743-6744.
23. Duyk, G.M., Kim, S., Myers, R.M., and Cox, D.R. (1990) Exon trapping: A genetic screen to identify candidate transcribed sequences in cloned mammalian genome DNA. Proc. Natl. Acad. Sci. USA 87, 8995-8999.
24. Buckler, A.J., Chang, D.D., Brook, J.D., Harber, D.A., Sharp, P.A., and Housman, D.E. (1991) Exon amplification: A stategy to isolate mammalian genes based on RNA splicing. Proc. Natl. Acad. Sci. USA 88, 4005-4009.
25. Church, D.M., Stotler, C.J., Rutter, J.L., Murrell, J.R., Trofatter, J.A., Buckler, A.J. (1994) Isolation of genes from complex sources of mammalian genomic DNA using exon amplification. Nature Genet. 6, 98-105.
26. Datsun, N.A., Duyk, G.M., Van Ommen, GJB., and Den Dunnen, J.T. (1994) Specific isolation of 3'-terminal exons of human genes by exon trapping. Nucleic Acids Res. 22, 4148-4153.
27. Nehls, M., Pfeifer, D., and Boehm, T. (1994) Exon amplification from complete libraries of genomic DNA using a novel phage vector with automatic plasmid excision facility: application to the mouse neurofibromatosis-1 locus. Oncogene 9, 2169-2175.
28. Parimoo, S., Patanjali, S.R., Shukla, H., Chaplin, D.D., and Weissman, S.M. (1991) cDNA selection: Efficient PCR approach for the selection of cDNAs encoded in large chromosomal DNA fragments. Proc. Natl. Acad. Sci. USA 88, 9623-9627.
29. Lovett, M., Kere, J., and Hinton, L. M. (1991) Direct selection: A method for the isolation of cDNAs encoded by large genomic regions. Proc. Nall. Acad. Sci. USA 88, 9628-9632.
30. Korn, B., Sedlacek, Z., Manca, A., Kioschis, P., Konecki, D., Lehrach, H. and Poutska, A.M. (1992) A strategy for the selection of transcribed sequences in the Xq28 region. Hum. Mol. Genet. 1, 235-242.
31. Tagle, D.A., Swaroop, M., Lovett, M., and Collins, F.S. (1993) Magnetic bead capture of expressed sequences encoded within large genomic segments. Nature 361. 751-753.
32. The Hungtington’s Disease Collaborative Research Group. (1993) A novel gene containing a trinucleotide repeat that is expanded and unstable on Hungtington’s disease chromosomes. Cell 72, 971-983.
33. Vulpe, C., Levinson, B., Whitney, S., Packman S., and Gitshier, J. (1993) Isolation of a candidate gene for Menkes disease and evidence that it encodes a copper-transporting ATPase. Nature Genet. 3, 7-13.
34. Rommens, J.M., Blin, B., Hutchinson, G.B., Andrew, S.E., Goldberg, Y.P., Glaves, M.L., Graham, R., Lai, V., Arthur, J.Mc., Nasir, J., Theilmann, J., McDonald, H., Kalchman, M., Clarke, L.A., Schapper, K., Haydn, M. R. (1993) A transcription map of the region containing the Hungtington disease gene. Hum. Mol. Genet. 2, 901-907.
35. Peterson, A., Patil, N., Robbins, C., Wang, L., Cox, D., Myers, R.M. (1994) A transcript map of the Down syndrome critical region on chromosome 21. Hum. Mol. Genet. 3, 1735-1742.
36. Brennan, M. B and Hochgeschwender, U. (1995) Commentary: so many needles, so much hay. Hum. Mol. Genet 4, 153-156.
37. Yaspo, M.L., Sanseau, P., Nizetic, D., Kom, B., Poutska, A.M., and Lehrach, H. (1994). Integrated transcriptional map of large DNA regions: towards a transcriptional map of human chromosome 21. In Hochgeschwender, U. and Gardiner, K. (ed.) Identification of transcribed sequences. (Third workshop on transcribed sequences; 1993). Plenum Press, New York, pp. 213-228.
38. Lehrach, H., Drmanac, R., Hoheisel, J., Larin, Z., Lennon, G., Monaco, A.P., Nizetic, D., Zehetner, G., and Poutska, A.M. (1990) In Davies (ed.) Hybridization fingerprinting in genome mapping and sequencing. Genome Analysis. Cold Spring Harbour Laboratory Press, Vol.1, pp 39-81.
39. Chumakov, I., Rigault, P., Guillou, S., Ougen, P., Billaut, A., Guasconi, G., Gervy, P., LeGall, I., Soularue, P., Grinas, L., Bougueleret, L., Bellane-Chantelot, C., Lacroix, B., Barillot, E., Gesnouin, P., Pook, S., Vaysseix, G., Frelat, G., Schmitz, A., Sambucy, J.L., Bosch, A., Estivill, X., Weissenbach, J., Vignal, A., Riethman, H., Cox, D., Patterson, D., Gardiner, K., Hattori, M., Sakaki, Y., Ichikawa, H., Ohki, M., LePaslier, D., Heilig, R., Antonorakis, S. E., and Cohen, D. (1992) Continuum of overlapping clones spanning the entire human chromosome 21 q. Nature 359, 380-386.
40. Nizetic, D., Gellen, L., Hamvas, R.M.J., Mott, R., Grigoriev, A., Vatcheva, R., Zehetner, G., Yaspo, M.L., Dutriaux, A., Lopes, C., Delabar, J., Van Broeckhoven, C., Potier, M.C., and Lehrach, H. (1994) An integrated YAC-overlap and ‘cosmid-pocket’ map of the human chromosome 21. Hum. Mol. Genet. 3, 759-770.
41. Nizetic, D., Zehetner, G., Monaco, A.P., Gellen, L., Young, B.D., and Lehrach, H. (1991) Construction, arraying and high-density screening of large insert libraries from human chromosomes X and 21: Their potential use as reference libraries. Proc. Natl. Acad. Sci. USA 88, 3233-3237.
42. Durbin, R., and Thierry Mieg, J. (1991) A C. elegans Database. Documentation, code and data available from anonymous ftp servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov.
43. Ross, M.T., Nizetic, D., Nguyen, C., Knights, C., Vatcheva, R., Burden, N., Douglas, C., Zehetner, G., Ward, D.C., Baldini, A., and Lehrach, H. (1992) Selection of a human chromosome 21 enriched YAC sub-library using a chromosome-specific composite probe. Nature Genet. 1, 284-290.
44. Makalowski, W., Mitchell, G.A., and Labuda, D. (1994) Alu sequences in the coding regions of mRNA: a source of protein variability. Trends Genet. 10, 188-193.
45. Suzuki, H., Ozawa, N., Taga, C., Kano, T., Hattori, M., and Sakaki Y. (1994) Genomic analysis of a NF1-related pseudogene on human chromosome 21. Gene 147, 277-280.
46. Saccone, S., De Sario, A., Della Valle, G., and Bemardi G. (1992) The highest gene concentrations in the human genome are in telomeric bands of metaphase chromosomes. Proc. Nad. Acad. Sci. USA 89. 4913-4917.
47. Chomczynski, P., and Sacchi, N. (1987) Anal. Biochem. 162, 156-159.
48. Meier-Ewert, S., Maier, E., Ahmadi, A., Curtis, J., and Lehrach, H. (1993) An automated approach to generating expressed sequence catalogues. Nature 361. 375-376.
49. Senger, G., Ragoussi, J., Trowsdale, J., and Sheer D. (1993) Fine mapping
50. of the MHC class II region within 6p2l and evaluation of probe ordering using the fluorescent in situ hybridisation. Cvtogenet. Cell. Genet. 64, 49-53.
51. Gardiner, K., Watkins, P., Munke, M., Drabkin, H., Jones K., and Patterson, D. (1988) Partial physical map of human chromosome 21. Som. Cell. Mol. Genet. 14, 623-638.
52. Mott, R., Grigoriev, A., Maier, E., Hoheisel, J., and Lehrach, H. (1993) Algorithms and software tools for ordering clone libraries: application to the mapping of the genome of Schizosaccharomyces pombe. Nucleic Acids Res. 21, 1965-1974.
53. Dear S., and Staden R. (1991) A sequence assembly and editing for efficient management of large projects. Nucleic Acids Res. 19,6481-6488.
54. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990) Basic local aligment search tool. J. Mol. Biol. 215, 403-410.
55. Claverie, J.M., and States, D. (1993) Information enhancement methods for large scale sequence analysis. Computers Chem. 17, 191-201.