Transcriptional analysis of the candidate region for incontinentia pigmenti (IP2) in Xq28

Genome Research

Volumn 6, Issue 10, 1996, Pages 922-934

  Rogner, Ute C ^a   Heiss, Nina S ^a   Kioschis, Petra ^a   Wiemann, Stefan ^a   Korn, Bernhard ^a   Poustka, Annemarie ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BLOOD CLOTTING FACTOR 8; COMPLEMENTARY DNA;

AMINO ACID SEQUENCE; ARTICLE; CHROMOSOME XQ; COMPUTER ANALYSIS; CONTROLLED STUDY; COSMID; DNA LIBRARY; DNA TRANSCRIPTION; ECTODERM; EXON; FEMALE; FETUS; GENE FUNCTION; GENE SEQUENCE; GENE STRUCTURE; GENETIC LINKAGE; HUMAN; HUMAN CELL; HUMAN TISSUE; INCONTINENTIA PIGMENTI; INTRON; MALE; NEUROECTODERM; NORTHERN BLOTTING; OPEN READING FRAME; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TELOMERE; YEAST ARTIFICIAL CHROMOSOME;

EID: 0029909335     PISSN: 10549803     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.6.10.922     Document Type: Article

References (59)

1. Altschul, S.F., W. Gish, W. Miller, E.W. Meyers, and D.J. Lipman. 1990. Basic alignment search tool. J. Mol. Biol. 215:403-410.
2. Bione, S., F. Tamanini, E. Maestrini, C. Tribioli, A. Poustka, G. Torri, S. Rivella, and D. Toniolo. 1993. Transcriptional organization of a 450-kb region of the human X chromosome in Xq28. Proc. Natl. Acad. Sci. 90: 10977-10981.
3. Brennan, M.B. and U. Hochgeschwender. 1995. Commentary: So many needles, and so much hay. Hum. Mol. Genet. 4: 153-156.
4. Brown, W.R.A., P.J. Mackinnon, A. Villasante, N. Spurr, V.J. Buckle, and M.J. Dobson. 1990. Structure and polymorphism of human telomere-associated DNA. Cell 63: 119-132.
5. Buckler, A., D. Chang, S. Graw, D. Brook, D. Haber, P. Sharp, and D. Housman. 1991. Exon amplification: A strategy to isolate mammalian genes based on RNA splicing. Proc. Natl. Acad. Sci. 88: 4005-4009.
6. Carney, R.G. 1976. Incontinentia pigmenti: A world statistical analysis. Arch. Dermatol. 112: 535-542.
7. Church, D.M., C.J. Stotler, J.L. Rutter, J.R. Muriel, J.A. Troffatter, and A.J. Buckler. 1994. Isolation of genes from complex sources of mammalian genomic DNA using exon amplification. Nature Genet. 6: 98-105.
8. Coleman, R., S.A. Genet, J.I. Harper, and A.O. Wilkie. 1993. Interaction of incontinentia pigmenti and factor VIII mutations in a female with biased X inactivation, resulting in hemophilia. J. Med. Genet. 30: 497-500.
9. Dear, S. and R. Staden. 1991. A sequence assembly and editing program for efficient management of large projects. Nucleic Acids Res. 19: 3907-3911.
10. D'Esposito, M., A. Ciccodicola, F. Gianfrancesco, T. Esposito, L. Flagiello, and M. D'Urso. 1996. A novel gene in the Xq28 PAR. Nature Genet. 13: 227-229.
11. Dietrich, A., B. Korn, and A. Poustka. 1992. Completion of the physical map of Xq28: The location of the gene for L1CAM on the human X chromosome. Mamm. Genome 3: 168-172.
12. Duret, L., D. Mouchiroud, and C. Gautier. 1995. Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J. Mol. Evol. 40: 308-317.
13. Eksioglu, Y.Z., I.E. Scheffer, P. Caedenas, J. Knoll, F. DiMario, G. Rambsy, M. Berg, K. Kamuro, S.F. Berkovic, G.M. Duyk, J. Parisi, P.R. Huttenlocher, and C.A. Walsh. 1996. Periventricular heterotopia: An X-linked dominant epilepsy locus causing aberrant cerebral cortical development. Neuron 16: 77-87.
14. Fisch, P., A. Forster, P.D. Sherrington, M.J. Dyer, and T.H. Rabbitts. 1993. The chromosomal translocation t(X;14)(q28;q11) in T-cell pro-lymphocytic leukemia breaks with one gene and activates another. Oncogene 8: 3271-3276.
15. Freije, D. and D. Schlessinger. 1992. A 1.6-Mb contig of Yeast Artificial Chromosomes around human factor VIII gene reveals three regions homologous to probes DXS115 and two for the DXYS64 locus. Am. J. Hum. Genet. 51: 66-80.
16. Gitschier, J., T.M. Goralka, K.L. Wion, E.Y. Chen, D.H. Eaton, G.A. Vehar, D.J. Capon, and R.M. Lawn. 1984. Characterization of the human factor VIII gene. Nature 312: 326-330.
17. Gorski, J.L., E.N. Burright, C.E. Harden, C.K. Stein, T.W. Glover, and E.L. Reyner. 1991. Localization of DNA sequences to a region within Xp11.21 between incontinentia pigment! (IP1) X-chromosomal translocation breakpoints. Am. J. Hum. Genet. 48: 63-64.
18. Gregg, R.G., A.B. Metzenberg, K. Hogan, G. Sekhon, and R. Laxova. 1991. Waisman syndrome, a human X-linked recessive basal ganglia disorder with mental retardation: Localization to Xq27.3-qter. Genomics 9: 701-706.
19. Heiss, N.S., B. Korn, U.C. Rogner, and A. Poustka. 1996a. Generation of specific exon trap probes from YACs by using AIu long-range PCR products. Methods Mol. Cell Biol. (in press).
20. Heiss, N.S., U.C. Rogner, P. Kioschis, B. Korn, and A. Poustka. 1996b. Transcriptional mapping in a 700 kb region around the DXS52 locus in Xq28: Isolation of six novel transcripts and a novel ATPase isoform (hPMCA5). Genome Res. 6: 478-491.
21. Isselbacher, K.J., E. Braunwals, J.D. Wilson, J.B. Martin, A.S. Fauci, and D.L. Kasper. 1994. Hnrrison's principles of internal medicine, 13th edition. McGraw-Hill Inc., New York, NY.
22. Kenwrick, S., B. Levinson, S. Taylor, A. Shapiro, and J. Gitschier. 1992. Isolation and sequence of two genes associated with a CpG island 5′ of the factor VIII gene. Hum. Mol. Genet. 1: 179-186.
23. Kermouni, A., E. Van Roost, K.C. Arden, J.R. Vermeesch, S. Weiss, D. Godelaine, J. Flint, C. Lurquin, J.-P. Szikora, D.R. Higgs, P. Marynen, and J.-C. Renauld. 1995. The IL-9 receptor gene (IL9R): Genomic structure, chromosomal localization in the pseudoautosomal region of the long arm of the sex chromosomes, and identification of IL9R pseudogenes at 9qter, 10pter, 16pter, and 18pter. Genomics 29: 371-382.
24. Kioschis, P., B. Gross, D. Nizetic, G. Zehetner, H. Lehrach, and A. Poustka. 1991. Molecular analysis of the Xq28 region. Cytogenet. Cell. Genet. 58: 2070.
25. Kioschis, P., U.C. Rogner, E. Pick, S.M. Klauck, N. Heiss, R. Siebenhaar, B. Korn, J.F. Coy, J. Laporte, S. Liechti-Gallati, and A. Poustka. 1996. A 900 kb contig and ten new transcripts within the candidate region for myotubular myopathy (MTM1). Genomics 33: 365-373.
26. Korn, B., Z. Sedlacek, A. Manca, P. Kioschis, D. Konecki, H. Lehrach, and A. Poustka. 1992. A strategy for the selection of transcribed sequences in Xq28 region. Hum. Mol. Genet. 4: 235-242.
27. Kvaloy, K., F. Galvagni, and W.R.A. Brown. 1994. The sequence organization of the long arm pseudoautosomal region of the human sex chromosomes. Hum. Mol. Genet. 3: 771-778.
28. Lakich, D., H.H. Kazazian, S.E. Antonarakis, and J. Gitschier. 1993. Inversions disrupting the factor VIII gene are a common cause of severe haemophilia A. Nature Genetics 5: 236-241.
29. Landry, D., S. Sullivan, M. Nicolaides, C. Redhead, A. Edelman, M. Field, Q. Al-Awqati, and J. Edwards. 1993. Molecular cloning and characterization of p64, a chloride channel protein from kidney microsomes. J. Biol. Chem. 268: 14989-14955.
30. Levinson, B., S. Kenwrick, D. Lakish, G. Hammonds, and J. Gitschier. 1990. A transcribed gene in an intron of the human factor VIII gene. Genomics 7: 1-11.
31. Levinson, B., S. Kenwrick, P. Gamel, K. Fisher, and J. Gitschier. 1992. Evidence for a third transcript from the human factor VIII gene. Genomics 14: 585-589.
32. Li, L. and D. Hamer. 1995. Recombination and allelic association in the Xq/Yq homology region. Hum. Mol. Genet. 4: 2013-2016.
33. Lovett, M., J. Kere, and L.M. Hinton. 1991. Direct selection: A method for the isolation of cDNAs encoded by large genomic regions. Proc. Natl. Acad. Sci. 88: 9628-9632.
34. Maestrini, E., F. Tamanini, P. Kioschis, E. Gimbo, P. Marinelli, C. Tribioli, M. d'Urso, G. Palmieri, A. Poustka, and D. Toniolo. 1992. An archipelago of CpG islands in Xq28: Identification and fine mapping of 20 new CpG islands of the human X chromosome. Hum. Mol. Genet. 1: 275-280.
35. McMahon, H.T., Y.A. Ushkaryov, L. Edelmann, E. Link, T. Binz, H. Niemann, R. Jahn, and T.C. Südhof. 1993. Cellubrevin is a ubiquitous tetanus-toxin substrate homologous to a putative synaptic vesicle fusion protein. Nature 364: 346-349.
36. Migeon, B.R., J. Axelman, S. de Beur, D. Valle, G.A. Mitchell, and K.N. Rosenbaum. 1989. Selection against lethal alleles in females heterozygous for incontinentia pigmenti. Am. J. Hum. Genet. 44: 100-106.
37. Naylor, J., A. Brinke, S. Hassock, P.M. Green, and F. Giannelli. 1993. Characteristic mRNA abnormality found in half the patients with severe haemophila A is due to large DNA inversions. Hum. Mol. Genet. 2: 1773-1778.
38. Naylor, J.A., D. Buck, P. Green, H. Williamson, D. Bentley, and F. Giannelli. 1995. Investigation of the factor VIII intron 22 repeated region (int22h) and the associated inversion junctions. Hum. Mol. Genet. 4: 1217-1224.
39. Nizetic, D., G. Zehetner, A.P. Monaco, L. Gellen, B.D. Young, and H. Lehrach. 1991. Construction, arraying, and high density screening of large insert libraries of human chromosomes X and 21; Their potential use as reference libraries. Proc. Natl. Acad. Sci. 88: 3233-3237.
40. Palmieri, G., G. Romano, A. Ciccodicola, A. Casamassimi, C. Campanile, T. Esposito, V. Cappa, A. Lania, S. Johnson, R. Reinbold, A. Poustka, D. Schlessinger, and M. d'Urso. 1994. YAC contig organization and CpG island analysis in Xq28. Genomics 24: 149-158.
41. Parimoo, S., S.R. Patanjali, H. Shukla, D.D. Chaplin, and S.M. Weissman. 1991. cDNA selection: Efficient PCR approach for the selection of cDNAs encoded in large chromosomal DNA fragments. Proc. Acad. Natl. Sci. 88: 9623-9627.
42. Parrish, J. and D. Nelson. 1994. Practical aspects of fingerprinting human DNA using Alu polymerase chain reaction. Methods Mol. Cell Biol. 5: 74-77.
43. Perlino, E., G. Paonessa, and G. Ciliberto. 1985. Alu sequences transcription in X. laevis oocytes: Nuclear-cytoplasmic partitioning and evidence for 3′ end processing reactions. Nucleic Acids Res. 13: 8359-8377.
44. Poustka, A. .1990. Physical mapping by PFGE. Methods: A Companion to Methods in Enzymology 1: 204-211.
45. Poustka, A., A. Dietrich, G. Langenstein, D. Toniolo, S.T. Warren, and H. Lehrach. 1991. Physical map of human Xq27-qter: Localizing the region of the fragile X mutation. Proc. Natl. Acad. Sci. 88: 8302-8306.
46. Reed, V., S. Rider, G.L. Maslen, E. Hatchwell, H.J. Blair, I.C. Uwechue, I.W. Craig, S.H. Laval, A.P. Monaco, and Y. Boyd. 1994. A 2-Mb YAC contig encompassing three loci (DXF34, DXS14, and DXS390) that lie between Xp11.2 translocation breakpoints associated with incontinentia pigmenti type 1. Cenomics 20: 341-346.
47. Rogner, U.C., P. Kioschis, K. Wilke, W. Gong, E. Pick, A. Dietrich, U. Zechner, H. Hameister, A. Pragliola, G.E. Herman, J.R.W. Yates, H. Lehrach, and A. Poustka. 1994. A YAC clone map spanning 7.5 megabases of human chromosome band Xq28. Hum. Mol. Genet. 3: 2137-2146.
48. Rogner, U.C., K. Wilke, E. Steck, B. Korn, and A. Poustka. 1995. The melanoma antigen (MAGE) family is clustered in the chromosomal band Xq28. Genomics 29: 725-731.
49. Sedlacek, Z., B. Korn, D.S. Konecki, R. Siebenhaar, J.F. Coy, P. Kioschis, and A. Poustka. 1993. Construction of a transcription map of a 300 kb region around the human G6PD locus by direct cDNA selection. Hum. Mol. Genet. 11: 1865-1869.
50. Sefiani, A., R. M'rad, L. Simard, A. Vincent, C. Julier, L. Holvoet-Vermaut, S. Heuertz, N. Dahl, J.F. Stadler, M.O. Peter, C. Moraine, J. Maleville, J. Boyer, I. Oberlé, D. Labuda, and M.C. Hors-Cayla. 1991. Linkage relationship between incontinentia pigmenti (IP2) and nine terminal X long arm markers. Hum. Genet. 86: 297-299.
51. Shafit-Zagardo, B., J.J. Maio, and F.L. Brown. 1982. KpnI families of long interspersed repetitive DNAs in human and other primate genomes. Nucleic Acids Res. 10: 3175-3193.
52. Smahi, A., C. Hyden-Granskog, B. Peterlin, P. Vabres, S. Heuertz, M.C. Fulchignoni-Lataud, N. Dahl, P. Labrune, B. Le Marec, C. Piussan, A. Taieb, H. von Koskull, and M.C. Hors-Cayla. 1994. The gene for the familial form of incontinentia pigmenti (IP2) maps to the distal part of Xq28. Hum. Mol. Genet. 3: 273-278.
53. Tagle, D.A. and F.S. Collins. 1992. An optimized Alu-PCR primer pair for human-specific amplification of YACs and somatic hybrids. Hum. Mol. Genet. 1: 121-122.
54. Thick, J., Y.F. Mak, J. Metcalfe, D. Beatty, and A.M. Taylor. 1994. A gene on chromosome Xq28 associated with T-cell prolymphocytic leukemia in two patients with ataxia telangiectasia. Leukemia 8: 564-573.
55. Warren, S.T., S.L. Knight, J.F. Peters, C.L. Stayton, G.G. Consalez, and F. Zhang. 1990. Isolation of the human chromosomal band Xq28 within somatic cell hybrids by fragile site breakage. Proc. Natl. Acad. Sci. 87: 3856-3860.
56. Wilgenbus, K.K., A. Mincheva, B. Korn, P. Lichter, and A. Poustka. 1995. IRS-long range (LR) PCR: A simple method for efficient amplification of human genomic DNA from complex sources. Methods Mol. Cell Biol. 5: 214-221.
57. Wood, W.I., D.J. Capon, C.C. Simonsen, D.L. Eaton, J. Gitschier, B. Keyt, P.H. Seeburg, D.H. Smith, P. Hollingshead, K.L. Wion, E. Delwart, E.G.D. Tuddenham, G.A., Vehar, and R.M. Lawn. 1984. Expression of active human factor VIII from recombinant clones. Nature 312: 330-337.
58. Yokoi, H., S. Hadana, H. Kogi, X. Kang, K. Wakasa, and J.-E Ikeda. 1994. Isolation of expressed sequences encoded by the human Xq terminal portion using microclone probes generated by laser microdissection. Genomics 20: 404-411.
59. Zuffardi, O. and M. Fraccaro. 1982. Gene mapping and serendipity. The locus for Torticollis, Keloids, Crytorchidism and Renal Dysplasia (31430, McKusick) is at Xq28, distal to the G6PD locus. Hum. Genet. 62: 280-281.