Clonability and gene distribution on human chromosome 21: Reflections of junk DNA content?

Gene

Volumn 205, Issue 1-2, 1997, Pages 39-46

  Gardiner, Katheleen ^a  

^a UNIVERSITY OF DENVER   (United States)

Author keywords

cDNA selection; Chromosome bands; dbEST; Exon trapping; Transcriptional mapping

Indexed keywords

COMPLEMENTARY DNA; DNA;

CHROMOSOME 21; CHROMOSOME 21Q; CONFERENCE PAPER; GENE FUNCTION; GENE MAPPING; HUMAN; INTRON; MOLECULAR CLONING; PRIORITY JOURNAL;

ANIMALS; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 21; CLONING, MOLECULAR; DNA; DNA, COMPLEMENTARY; EXONS; FISHES, POISONOUS; HUMANS; PHENOTYPE; RESTRICTION MAPPING; SEQUENCE TAGGED SITES;

TAKIFUGU RUBRIPES;

EID: 0031593214     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(97)00481-2     Document Type: Conference Paper

References (37)

1. Baxendale, S., Abdulla, S., Elgar, G., Buck, D., Berks, M., Micklem, G., Durbin, R., Bates, G., Brenner, S., Beck, S., Lehrach, H., 1995. Comparative sequence analysis of the human and pufferfish Huntington's disease genes. Nature Genet. 10, 67-77.
2. Bernardi, G., 1995. The human genome: organization and evolutionary history. Annu. Rev. Genetics 29, 445-476.
3. Cheng, J.-F., Boyartchuk, V., Zhu, Y., 1994. Isolation and mapping of human chromosome 21 cDNA: progress in constructing a chromosome 21 expression map. Genomics 23, 75-84.
4. Chumakov, I., Rigault, P., Guillou, S., Ougen, P., Billaut, A., Guasconi, G. et al., 1992. A continuum of overlapping clones spanning the entire human chromosome 21q. Nature 359, 380-387.
5. Church, D.M., Stotler, C.J., Rutter, J.L., Murrell, J.R., Trofatter, J.A., Buckler, A.J., 1993. Isolation of genes from complex sources of mammalian genomic DNA using exon amplification. Nature Genet. 6, 98-105.
6. de Sario, A., Geigl, E., Palmieri, G., D'Urso, M., Bernardi, G., 1996. A compositional map of human chromosome band Xq28. Proc. Natl. Acad. Sci. USA 93, 1298-1302.
7. Duret, L., Mouchiroud, D., Gautier, C., 1995. Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J. Mol. Evol. 40, 308-317.
8. Elgar, G., Rattray, F., Greystrong, J., Brenner, S., 1995. Genomic structure and nucleotide sequence of the p55 gene of the puffer fish Fugu rubripes. Genomics 27, 442-446.
9. Elgar, G., Sandford, R., Aparicio, S., Macrae, A., Venkatesh, B., Brenner, S., 1996. Small is beautiful: comparative genomics with the pufferfish (Fugu rubripes). Trends Genet. 12, 145-150.
10. Fickett, J.W., 1996. Finding genes by computer: the state of the art. Trends Genet. 12, 316-320.
11. Francke, U., 1994. Digitized and differentially shaded human chromosome ideograms for genomic applications. Cytogenet. Cell Genet. 65, 206-219.
12. Gardiner, K., 1996. Base composition and gene distribution: critical patterns in mammalian genome organization. Trends Genet. 12, 519-524.
13. 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.
14. Gardiner, K., Ichikawa, H., Ohki, M., Patterson, D., Cheng, J.-F., 1995a. Localization of cDNAs to a region poorly represented in the CEPH chromosome 21 YAC contig: candidate genes for genetic diseases mapped to 21q22.3. Genomics 30, 376-379.
15. Gardiner, K., Graw, S., Ichikawa, H., Ohki, M., Joetham, A., Gervy, P., Chumakov, I., Patterson, D., 1995b. YAC analysis and minimal tiling path construction for chromosome 21q. Somat. Cell Mol. Genet. 21, 399-414.
16. Graw, S.L., Gardiner, K., Hall-Johnson, K., Hart, I., Joetham, A., Walton, K., Donaldson, D., Patterson, D., 1995. Molecular analysis and breakpoint definition of a set of human chromosome 21 somatic cell hybrids. Somat. Cell Mol. Genet. 21, 415-428.
17. Hattori, M., Tsukahara, F., Furuhata, Y., Tanahashi, H., Hirose, M., Saito, M., Tsukuni, S., Sakaki, Y., 1997. A novel method for making nested deletions and its application for sequencing of a 300 kb region of human APP locus. Nucleic Acids Res 25, 1802-1808.
18. Ichikawa, H., Hosoda, F., Arai, Y., Shimizu, K., Ohira, M., Ohki, M., 1993. A NotI restriction map of the entire long arm of human chromosome 21. Nature Genet. 4, 361-365.
19. Koop, B.G., Nadeau, J.H., 1996. Pufferfish and a new paradigm for comparative genome analysis. Proc. Natl. Acad. Sci. USA 93, 1363-1365.
20. Korenberg, J.R., Chen, X.-N., Schipper, R., Sun, Z., Gonsky, R., Gerwehr, S., Carpenter, N., Daumer, C., Dignan, P., Disteche, C., Graham Jr., J.M., Hugdins, L., McGillivray, B., Miyazaki, K., Ogasawara, N., Park, J.P., Pagon, R., Pueschel, S., Sack, G., Say, B., Schuffenhauer, S., Soukup, S., Yamanaka, T., 1994. Down syndrome phenotypes: the consequences of chromosomal imbalance. Proc. Natl. Acad. Sci. USA 91, 4997-5001.
21. Korenberg, J., Rykowski, M.C., 1988. Human genome organization: Alu, lines, and the molecular structure of metaphase chromosome bands. Cell 53, 391-400.
22. Lee, C.C., Yazdani, A., Wehnert, M., Zhao, Z.Y., Lindsay, E.A., Bailey, J., Coolbauch, M.I., Couch, L., Xiong, M., Chinault, A.C., Baldini, A., Caskey, C.T., 1995. Isolation of chromosome-specific genes by reciprocal probing of arrayed cDNA and cosmid libraries. Hum. Mol. Genet. 4, 1373-1380.
23. Lovett, M., 1994. Fishing for complements: finding genes by direct selection. Trends Genet. 10, 352-357.
24. Mason, P.J., Stevens, D.J., Luzzatto, L., Brenner, S., Aparicio, S., 1995. Genomic structure and sequence of the Fugu rubripes glucose-6-phosphate dehydrogenase gene (G6PD). Genomics 26, 587-591.
25. Mural, R.J., 1995. Identifying candidate genes in genomic DNA: gene discovery and sequence annotation in the GRAIL-genQuest environment. In: Current Protocols in Human Genetics, John Wiley, New York, NY, pp. 6.5.1-6.5.22.
26. Nizetic, D., Gellen, L., Hamvas, R.M., Mott, R., Grigoriev, A., Vatcheva, R., Zehetner, G., Yaspo, M.L., Dutriaux, A., Lopes, C. et al., 1994. An integrated YAC-overlap and 'cosmid-pocket' map of the human chromosome 21. Hum. Mol. Genet. 3, 759-770.
27. Pekarsky, Y., Zabarovsky, E., Kashuba, V., Drabkin, H., Sandberg, A., Morgan, R., Rynditch, A., Gardiner, K., 1995. Cloning of breakpoints in 3q21 associated with hematological malignancy. Can. Genet. Cytogenet. 80, 1-8.
28. Pilia, G., Little, R., Aissani, B., Bernardi, G., Schlessinger, D., 1993. Isochores and CpG islands in YAC contigs in human Xq26.1-qter. Genomics 17, 456-462.
29. Porta, G., Zucchi, I., Hillier, L., Green, P., Nowotny, V., D'Urso, M., Schlessinger, D., 1993. Alu and L1 sequence distribution in Xq24-q28 and their comparative utility in YAC contig assembly and verification. Genomics 16, 417-423.
30. Riboldi, G., Nyakatura, G., Taudien, S., Coutelle, O., Perret, X., Elgar, G., Brenner, S., Platzer, M., Drescher, B., Rosenthal, A., 1996. Comparative Sequencing in Human and the Pufferfish FUGU: Analysis of 17 FUGU Genes Including Homologues of Human L1CAM, G6PD and P55 Located in Xq28. Genome Mapping and Sequencing. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, p. 205.
31. Schuler, G.D., Boguski, M.S., Stewart, E.A., Stein, L.D., Gyapay, G., Rice, K. et al., 1996. A gene map of the human genome. Science 274, 547-562.
32. Shimizu, N., Antonarakis, S.E., Van Broeckhoven, C., Patterson, D., Gardiner, K., Nizetic, D., Créau, N., Delabar, J-M., Korenberg, J., Reeves, R., Doering, J., Chakravati, A., Minoshima, S., Ritter, O., Cuticchia, J., 1995. Report of the Fifth International Workshop on Human Chromosome 21 Mapping 1994. Cytogenet. Cell Genet. 70, 147-182.
33. Soeda, E., Hou, D-X., Osoegawa, K., Atsuchi, Y., Yamagata, T., Shimokawa, T., Kishida, H., Soeda, E., Okano, S., Chumakov, I., Cohen, D., Raff, M., Gardiner, K., Graw, S.L., Patterson, D., De Jong, P., Ashworth, L.K., Slezak, T., Carrano, A.V., 1995. Cosmid assembly and anchoring to human chromosome 21. Genomics 25, 7384
34. Tanzi, R.E., Gusella, J.R., Watkins, P.C., Bruns, G.A.P., St. George-Hyslop, P., Van Keuren, M.L., Patterson, D., Pagan, S., Kurnit, D.M., Neve, R.L., 1987. Amyloid β protein gene: cDNA, mRNA distribution, and genetic linkage near the Alzheimer locus. Science 235, 880-884.
35. Tassone, F., Xu, H., Burkin, H., Weissman, S., Gardiner, K., 1995. cDNA selection from 10 Mb of chromosome 21 DNA: efficiency in transcriptional mapping and reflections of genome organization. Hum. Mol. Genet. 4, 1509-1518.
36. Xu, H., Wei, H., Tassone, F., Graw, S., Gardiner, K., Weissman, S.M., 1995. A search for genes from the dark band regions of human chromosome 21. Genomics 27, 1-8.
37. Yaspo, M.-L., Gellen, L., Mott, R., Korn, B., Nizetic, D., Poustka, A., Lehrach, H., 1995. Model for a transcript map of human chromosome 21: isolation of new coding sequences from exon and enriched cDNA libraries. Hum. Mol. Genet 4, 1291-1304.