Isolation and mapping of novel candidate genes for retinal disorders using suppression subtractive hybridization

Genomics

Volumn 58, Issue 3, 1999, Pages 240-249

  Den Hollander, Anneke I ^a   Van Driel, Marc A ^a   De Kok, Yvette J M ^a   Van De Pol, Dorien J R ^a   Hoyng, Carel B ^a   Brunner, Han G ^a   Deutman, August F ^a   Cremers, Frans P M ^a  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

Retina; Retinal pigment epithelium; RP12; RP17; Suppression subtractive hybridization

Indexed keywords

COMPLEMENTARY DNA;

ARTICLE; BARDET BIEDL SYNDROME; CHOROID; DNA HYBRIDIZATION; GENE CONSTRUCT; GENE EXPRESSION; GENE ISOLATION; GENE LIBRARY; GENE LOCATION; GENE MAPPING; HUMAN; HUMAN TISSUE; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; PIGMENT EPITHELIUM; PRIORITY JOURNAL; RETINA; RETINA DISEASE; RETINITIS PIGMENTOSA;

EID: 0033564935     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1006/geno.1999.5823     Document Type: Article

References (60)

1. Abe T., Nakabayashi H., Tamada H., Takagi T., Sakuragi S., Yamaki K., Shinohara T. Analysis of the human, bovine and rat 33-kDa proteins and cDNA in retina and pineal gland. Gene. 91:1990;209-215.
2. Agarwal N., Swaroop A., Zheng K., Liou J.-d., O'Rourke K., Graves K. A., Gieser L., Del Monte M., Yang-Feng T. L. Expression and chromosomal localization of cDNA clones from an enriched human retinal pigment epithelial (RPE) cell line library: Identification of two RPE-specific genes. Cytogenet. Cell Genet. 69:1995;71-74.
3. Allikmets R., Singh N., Sun H., Shroyer N. F., Hutchinson A., Chidambaram A., Gerrard B., Baird L., Stauffer D., Peiffer A., Rattner A., Smallwood P., Li Y., Anderson K. L., Lewis R. A., Nathans J., Leppert M., Dean M., Lupski J. R. A photoreceptor cell-specific ATP-binding transporter gene (ABCR) is mutated in recessive Stargardt macular dystrophy. Nature Genet. 15:1997;236-246.
4. Banerjee P., Kleyn P. W., Knowles J. A., Lewis C. A., Ross B. M., Parano E., Kovats S. G., Lee J. J., Penchazadeh G. K., Ott J., Jacobson S. G., Gilliam T. C. TULP1 mutation in two extended Dominican kindreds with autosomal recessive retinitis pigmentosa. Nature Genet. 18:1998;177-179.
5. Bardien S., Ebenezer N., Greenberg J., Inglehearn C. F., Bartmann L., Goliath R., Beighton P., Ramesar R., Bhattacharya S. S. An eighth locus for autosomal dominant retinitis pigmentosa is linked to chromosome 17q. Hum. Mol. Genet. 4:1995;1459-1462.
6. Bardien S., Ramesar R., Bhattacharya S., Greenberg J. Retinitis pigmentosa locus on 17q (RP17): Fine localization to 17q22 and exclusion of the PDEG and TIMP2 genes. Hum. Genet. 101:1997;13-17.
7. Bascom R. A., Manara S., Collins L., Molday R. S., Kalnins V. I., McInnes R. R. Cloning of the cDNA for a novel photoreceptor membrane protein (rom-1) identifies a disk rim protein family implicated in human retinopathies. Neuron. 8:1992;1171-1184.
8. Bech-Hansen N. T., Naylor M. J., Maybaum T. A., Pearce W. G., Koop B., Fishman G. A., Mets M., Musarella M. A., Boycott K. M. Loss-of-function mutations in a calcium-channel subunit gene in Xp11.23 cause incomplete X-linked congenital stationary nightblindness. Nature Genet. 19:1998;264-267.
9. Bernstein S. L., Borst D. E., Wong P. W. Isolation of differentially expressed human fovea genes: Candidates for macular disease. Mol. Vis. 1:1995.
10. Bernstein S. L., Borst D. E., Neuder M. E., Wong P. Characterization of a human fovea cDNA library and regional differential gene expression in the human retina. Genomics. 32:1996;301-308.
11. Bunt-Milam A. H., Saari J. C. Immunocytochemical localization of two retinoid-binding proteins in vertebrate retina. J. Cell Biol. 97:1983;703-712.
12. Carmi R., Rokhlina T., Kwitek-Black A. E., Elbedour K., Nishimura D., Stone E. M., Sheffield V. C. Use of a DNA pooling strategy to identify a human obesity syndrome locus on chromosome 15. Hum. Mol. Genet. 4:1995;9-13.
13. Cremers F. P. M., van de Pol T. J. R., van Kerkhoff E. P. M., Wieringa B., Ropers H-H. Cloning of a gene that is rearranged in patients with choroideraemia. Nature. 347:1990;674-677.
14. Davis A. A., Bernstein P. S., Bok D., Turner J., Nachtigal M., Hunt R. C. A human retinal pigment epithelial cell line that retains epithelial characteristics after prolonged culture. Invest. Ophthalmol. Vis. Sci. 36:1995;955-964.
15. Den Hollander A. I., van der Velde-Visser S. D., Pinckers A. J. L. G., Hoyng C. B., Brunner H. G., Cremers F. P. M. Refined mapping of the gene for autosomal dominant retinitis pigmentosa (RP17) on chromosome 17q22. Hum. Genet. 104:1999;73-76.
16. Diatchenko L., Lau Y.-F. C., Campbell A. P., Chenchik A., Moqadam F., Huang B., Lukyanov S., Lukyanov K., Gurskaya N., Sverdlov E. D., Siebert P. D. Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. USA. 93:1996;6025-6030.
17. Dryja T. P. Deficiencies in sight with the candidate gene approach. Nature. 347:1990;614.
18. Dryja T. P. Gene-based approach to human gene-phenotype correlations. Proc. Natl. Acad. Sci. USA. 94:1997;12117-12121.
19. Dryja T. P., Li T. Molecular genetics of retinitis pigmentosa. Hum. Mol. Genet. 4:1995;1739-1743.
20. Dunn K. C., Aotaki-Keen A. E., Putkey F. R., Hjelmeland L. M. ARPE-19, a human retinal pigment epithelial cell line with differentiated properties. Invest. Ophthalmol. Vis. Sci. 36:1995;S766.
21. Freund C. L., Gregory-Evans C. Y., Furukawa T., Papaioannou M., Looser J., Ploder L., Bellingham J., Ng D., Herbrick J-A. S., Duncan A., Scherer S. W., Tsui L-C., Loutradis-Anagnostou A., Jacobson S. G., Cepko C. L., Bhattacharya S. S., McInnes R. R. Cone-rod dystrophy due to mutations in a novel photoreceptor-specific homeobox gene (CRX) essential for maintenance of the photoreceptor. Cell. 91:1997;543-553.
22. Gieser L., Swaroop A. Expressed sequence tags and chromosomal localization of cDNA clones from a subtracted retinal pigment epithelium library. Genomics. 13:1992;873-876.
23. Gu S-m., Thompson D. A., Srikumari C. R. S., Lorenz B., Finckh U., Nicoletti A., Murthy K. R., Rathmann M., Kumaramanickavel G., Denton M. J., Gal A. Mutations in RPE65 cause autosomal recessive childhood-onset severe retinal dystrophy. Nature Genet. 17:1997;194-197.
24. Hagstrom S. A., North M. A., Nishina P. M., Berson E. L., Dryja T. P. Recessive mutations in the gene encoding the tubby-like protein TULP1 in patients with retinitis pigmentosa. Nature Genet. 18:1998;174-176.
25. Higashide T., Murakami A., McLaren M. J., Inana G. Cloning of the cDNA for a novel photoreceptor protein. J. Biol. Chem. 271:1996;1797-1804.
26. Imamura Y., Kubota R., Wang Y., Asakawa S., Kudoh J., Mashima Y., Oguchi Y., Shimizu N. Human retina-specific amine oxidase (RAO): cDNA cloning, tissue expression, and chromosomal mapping. Genomics. 40:1997;277-283.
27. Klein M. L., Schultz D. W., Edwards A., Matise T. C., Rust K., Berselli C. B., Trzupek K., Weleber R. G., Ott J., Wirtz M. K., Acott T. S. Age-related macular degeneration: Clinical features in a large family and linkage to chromosome 1q. Arch. Ophthalmol. 116:1998;1082-1088.
28. Kwitek-Black A. E., Carmi R., Duyk G. M., Buetow K. H., Elbedour K., Parvari R., Naidu Yandava C., Stone E. M., Sheffield V. C. Linkage of Bardet-Biedl syndrome to chromosome 16q and evidence for non-allelic genetic heterogeneity. Nature Genet. 5:1993;392-396.
29. Kylstra J. A., Aylsworth A. S. Cone-rod retinal dystrophy in a patient with neurofibromatosis type 1. Can. J. Ophthalmol. 28:1993;79-80.
30. Leppert M., Baird L., Anderson K. L., Otterud B., Lupski J. R., Lewis R. A. Bardet-Biedl syndrome is linked to DNA markers on chromosome 11q and is genetically heterogeneous. Nature Genet. 7:1994;108-112.
31. MacDonald I. M., Haney P. M., Musarella M. A. Summary of ocular genetic disorders and inherited systemic conditions with eye findings. Ophthalmic Genet. 19:1998;1-17.
32. Marlhens F., Bareil C., Griffoin J-M., Zrenner E., Amalric P., Eliaou C., Liu S-Y., Harris E., Redmond T. M., Arnaud B., Claustres M., Hamel C. P. Mutations in RPE65 cause Leber's congenital amaurosis. Nature Genet. 17:1997;139-141.
33. Maw M. A., Kennedy B., Knight A., Bridges R., Roth K. E., Mani E. J., Mukkadan J. K., Nancarrow D., Crabb J. W., Denton M. J. Mutation of the gene encoding cellular retinaldehyde-binding protein in autosomal recessive retinitis pigmentosa. Nature Genet. 17:1997;198-200.
34. Meindl A., Dry K., Herrmann K., Manson F., Ciccodicola A., Edgar A., Carvalho M. R. S., Achatz H., Hellebrand H., Lennon A., Migliaccio C., Porter K., Zrenner E., Bird A., Jay M., Lorenz B., Wittwer B., D'Urso M., Meitinger T., Wright A. A gene (RPGR) with homology to the RCC1 guanine nucleotide exchange factor is mutated in X-linked retinitis pigmentosa (RP3). Nature Genet. 13:1996;35-42.
35. Murakami A., Yajima T., Sakuma H., McLaren M. J., Inana G. X-arrestin: A new retinal arrestin mapping to the X chromosome. FEBS Lett. 334:1993;203-209.
36. Nystuen A., Costeff H., Elpeleg O. N., Apter N., Bonné-Tamir B., Mohrenweiser H., Haider N., Stone E. M., Sheffield V. C. Iraqi-Jewish kindreds with optic atrophy plus (3-methylglutaconic aciduria type 3) demonstrate linkage disequilibrium with the CTG repeat in the 3′ untranslated region of the myotonic dystrophy protein kinase gene. Hum. Mol. Genet. 6:1997;563-569.
37. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA. 85:1988;2444-2448.
38. Pentao L., Lewis R. A., Ledbetter D. H., Patel P. I., Lupski J. R. Maternal uniparental isodisomy of chromosome 14: Association with autosomal recessive rod monochromacy. Am. J. Hum. Genet. 50:1992;690-699.
39. Petrukhin K., Koisti M. J., Bakall B., Li W., Xie G., Marknell T., Sandgren O., Forsman K., Holmgren G., Andreasson S., Vujic M., Bergen A. A. B., McGarty-Dugan V., Figueroa D., Austin C. P., Metzker M. L., Caskey C. T., Wadelius C. Identification of the gene responsible for Best macular dystrophy. Nature Genet. 19:1998;241-247.
40. Redmond T. M., Yu S., Lee E., Bok D., Hamasaki D., Chen N., Goletz P., Ma J.-X., Crouch R. K., Pfeifer K. Rpe65 is necessary for production of 11-cis-vitamin A in the retinal visual cycle. Nature Genet. 20:1998;344-351.
41. Roepman R., Bauer D., Rosenberg T., van Duynhoven G., van de Vosse E., Platzer M., Rosenthal A., Ropers H-H., Cremers F. P. M., Berger W. Identification of a gene disrupted by a microdeletion in a patient with X-linked retinitis pigmentosa. Hum. Mol. Genet. 5:1996;827-833.
42. Rosenfeld P. J., McKusick V. A., Amberger J. S., Dryja T. P. Recent advances in the gene map of inherited eye disorders: Primary hereditary disease of the retina, choroid, and vitreous. J. Med. Genet. 31:1994;903-915.
43. Saari J. C., Bredberg D. L., Noy N. Control of substrate flow at a branch in the visual cycle. Biochemistry. 33:1994;3106-3112.
44. Sauer C. G., Gehrig A., Warneke-Wittstock R., Marquardt A., Ewing C. C., Gibson A., Lorenz B., Jurklies B., Weber B. H. F. Positional cloning of the gene associated with X-linked juvenile retinoschisis. Nature Genet. 17:1997;164-170.
45. Schwahn U., Lenzner S., Dong J., Feil S., Hinzmann B., van Duijnhoven G., Kirschner R., Hemberger M., Bergen A. A. B., Rosenberg T., Pinckers A. J. L. G., Fundele R., Rosenthal A., Cremers F. P. M., Ropers H-H., Berger W. Positional cloning of the gene for X-linked retinitis pigmentosa 2. Nature Genet. 19:1998;327-332.
46. Sheffield V. C., Carmi R., Kwitek-Black A., Rokhlina T., Nishimura D., Duyk G. M., Elbedour K., Sunden S. L., Stone E. M. Identification of a Bardet-Biedl syndrome locus on chromosome 3 and evaluation of an efficient approach to homozygosity mapping. Hum. Mol. Genet. 3:1994;1331-1335.
47. Shimizu-Matsumoto A., Adachi W., Mizuno K., Inazawa J., Nishida K., Kinoshita S., Matsubara K., Okubo K. An expression profile of genes in human retina and isolation of a complementary DNA for a novel rod photoreceptor protein. Invest. Ophthalmol. Vis. Sci. 38:1997;2576-2585.
48. Simunovic M. P., Moore A. T. The cone dystrophies. Eye. 12:1998;553-565.
49. Strom T. M., Nyakatura G., Apfelstedt-Sylla E., Hellebrand H., Lorenz B., Weber B. H. F., Wutz K., Gutwillinger N., Rüther K., Drescher B., Sauer C., Zrenner E., Meitinger T., Rosenthal A., Meindl A. An L-type calcium-channel gene mutated in incomplete X-linked congenital stationary nightblindness. Nature Genet. 19:1998;260-263.
50. Stryer L. Visual excitation and recovery. J. Biol. Chem. 266:1991;10711-10714.
51. Sullivan L. S., Daiger S. P. Inherited retinal degeneration: exceptional genetic and clinical heterogeneity. Mol. Med. Today. 2:1996;380-386.
52. Swanson D. A., Freund C. L., Steel J. M., Xu S., Ploder L., McInnes R. R., Valle D. A differential hybridization scheme to identify photoreceptor-specific genes. Genome Res. 7:1997;513-521.
53. Swaroop A., Xu J., Agarwal N., Weissman S. M. A simple and efficient cDNA library subtraction procedure: Isolation of human retina-specific cDNA clones. Nucleic Acids Res. 19:1991;1954.
54. Swaroop A., Xu J., Pawar H., Jackson A., Skolnick C., Agarwal N. A conserved retina-specific gene encodes a basic motif/leucine zipper domain. Proc. Natl. Acad. Sci. USA. 89:1992;266-270.
55. Travis G. H., Christerson L., Danielson P. E., Klisak I., Sparkes R. S., Hahn L. B., Dryja T. P., Sutcliffe J. G. The human retinal degeneration slow (RDS) gene: Chromosome assignment and structure of the mRNA. Genomics. 10:1991;733-739.
56. Valle D., Simell O. The hyperornithinemias. Scriver C. R., Beaudet A. L., Sly W. S., Valle D. The Metabolic Basis of Inherited Disease I. 1989;599-627 McGraw-Hill, New York.
57. Van Soest S., Te Nijenhuis S., van den Born L. I., Bleeker-Wagemakers E. M., Sharp E., Sandkuijl L. A., Westerveld A., Bergen A. A. B. Fine mapping of the autosomal recessive retinitis pigmentosa locus (RP12) on chromosome 1q: Exclusion of the phosducin gene (PDC). Cytogenet. Cell Genet. 73:1996;81-85.
58. Van Soest S., Van Rossem M. J., Heckenlively J. R., van den Born L. I., De Meulemeester T. M. A. M. O., Vliex S., de Jong P. T. V. M., Bleeker-Wagemakers E. M., Westerveld A., Bergen A. A. B. Integrated genetic and physical map of the 1q31-q32.1 region, encompassing the RP12 locus, the F13B and HF1 genes and the EEF1AL11 and rpL30 pseudogenes. Cytogenet. Cell Genet. 1999.
59. Weber B. H. F., Vogt G., Pruett R. C., Stöhr H., Felbor U. Mutations in the tissue inhibitor of metalloproteinases-3 (TIMP3) in patients with Sorsby's fundus dystrophy. Nature Genet. 8:1994;352-356.
60. Young T.-L., Penney L., Woods M. O., Parfrey P. S., Green J. S., Hefferton D., Davidson W. S. A fifth locus for Bardet-Biedl syndrome maps to chromosome 2q31. Am. J. Hum. Genet. 64:1999;900-904.