Defining the human macula transcriptome and candidate retinal disease genes using EyeSAGE

Investigative Ophthalmology and Visual Science

Volumn 47, Issue 6, 2006, Pages 2305-2316

  Rickman, Catherine Bowes ^a   Ebright, Jessica N ^a   Zavodni, Zachary J ^a   Yu, Ling ^a   Wang, Tianyuan ^a   Daiger, Stephen P ^b   Wistow, Graeme ^c   Boon, Kathy ^d   Hauser, Michael A ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

^b UNIVERSITY OF TEXAS   (United States)

^c NATIONAL EYE INSTITUTE   (United States)

^d NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME; MESSENGER RNA;

ADULT; AGED; ARTICLE; BARDET BIEDL SYNDROME; BBS5 GENE; FEMALE; GENE; GENE EXPRESSION PROFILING; GENE MAPPING; GENETIC ASSOCIATION; GENETIC DATABASE; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN TISSUE; MALE; MICROARRAY ANALYSIS; PHOTORECEPTOR; PIGMENT EPITHELIUM; PRIORITY JOURNAL; QUANTITATIVE GENETICS; RETINA; RETINA DISEASE; RETINA DYSTROPHY; RETINA MACULA LUTEA; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SPLICING; SERIAL ANALYSIS OF GENE EXPRESSION; DNA MICROARRAY; FACTUAL DATABASE; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MIDDLE AGED; PHYSIOLOGY; RETINA DEGENERATION;

ADULT; AGED; DATABASES, FACTUAL; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; HUMANS; MACULA LUTEA; MALE; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHOTORECEPTORS, VERTEBRATE; PIGMENT EPITHELIUM OF EYE; RETINAL DEGENERATION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

EID: 33745660391     PISSN: 01460404     EISSN: None     Source Type: Journal    
DOI: 10.1167/iovs.05-1437     Document Type: Article

References (59)

1. Klein R, Klein BE, Linton KL. Prevalence of age-related maculopathy. The Beaver Dam Eye Study. Ophthalmology. 1992;99:933-943.
2. Mitchell P, Smith W, Attebo K, Wang JJ. Prevalence of age-related maculopathy in Australia. The Blue Mountains Eye Study. Ophthalmology. 1995;102:1450-1460.
3. Vingerling JR, Dielemans I, Bots ML, Hofman A, Grobbee DE, de Jong PT. Age-related macular degeneration is associated with atherosclerosis. The Rotterdam Study. Am J Epidemiol. 1995;142:404-409.
4. Curcio CA. Photoreceptor topography in ageing and age-related maculopathy. Eye. 2001;15:376-383.
5. Curcio CA, Medeiros NE, Millican CL. Photoreceptor loss in age-related macular degeneration. Invest Ophthalmol Vis Sci. 1996;37:1236-1249.
6. Curcio CA, Millican CL, Allen KA, Kalina RE. Aging of the human photoreceptor mosaic: evidence for selective vulnerability of rods in central retina. Invest Ophthalmol Vis Sci. 1993;34:3278-3296.
7. Jackson GR, Owsley C, Curcio CA. Photoreceptor degeneration and dysfunction in aging and age-related maculopathy. Ageing Res Rev. 2002;1:381-396.
8. Chowers I, Esumi N, Campochiaro P, Zack DJ. Studies on retinal and retinal pigment epithelial gene expression. Novartis Found Symp. 2004;255:131-145; discussion 2004;6:177-8.
9. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression. Science. 1995;270:484-487.
10. Saha S, Sparks AB, Rago C, et al. Using the transcriptome to annotate the genome. Nat Biotechnol. 2002;20:508-512.
11. Wahl MB, Heinzmann U, Imai K. LongSAGE analysis significantly improves genome annotation: identifications of novel genes and alternative transcripts in the mouse. Bioinformatics. 2005;21:1393-1400.
12. Schulz HL, Rahman FA, Fadl El Moula FM, Stojic J, Gehrig A, Weber BH. Identifying differentially expressed genes in the mammalian retina and the retinal pigment epithelium by suppression subtractive hybridization. Cytogenet Genome Res. 2004;106:74-81.
13. Swaroop A, Zack DJ. Transcriptome analysis of the retina. Genome Biol. 2002;3:REVIEWS1022.
14. Sharon D, Blackshaw S, Cepko CL, Dryja TP. Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE). Proc Natl Acad Sci USA. 2002;99:315-320.
15. Chowers I, Gunatilaka TL, Farkas RH, et al. Identification of novel genes preferentially expressed in the retina using a custom human retina cDNA microarray. Invest Ophthalmol Vis Sci. 2003;44:3732-3741.
16. Chowers I, Liu D, Farkas RH, et al. Gene expression variation in the adult human retina. Hum Mol Genet. 2003;12:2881-2893.
17. Yoshida S, Yashar BM, Hiriyanna S, Swaroop A. Microarray analysis of gene expression in the aging human retina. Invest Ophthalmol Vis Sci. 2002;43:2554-2560.
18. Johnston NL, Cervenak J, Shore AD, Torrey EF, Yolken RH. Multi-variate analysis of RNA levels from postmortem human brains as measured by three different methods of RT-PCR. Stanley Neuropathology Consortium. J Neurosci Methods. 1997;77:83-92.
19. Ebright JN, Bowes Rickman C. Rapid, reproducible real-time quantitative RT-PCR using the iCycler iQ real-time PCR detection system and iQ supermix. Bioradiations. 2003;110:32-35.
20. Yang P, Wiser JL, Peairs JJ, et al. Human RPE expression of cell survival factors. Invest Ophthalmol Vis Sci. 2005;46:1755-1764.
21. Thompson CL, Rickman CB, Shaw SJ, et al. Expression of the blue-light receptor cryptochrome in the human retina. Invest Ophthalmol Vis Sci. 2003;44:4515-521.
22. St Croix B, Rago C, Velculescu V, et al. Genes expressed in human tumor endothelium. Science. 2000;289:1197-1202.
23. Boon K, Osorio EC, Greenhut SF, et al. An anatomy of normal and malignant gene expression. Proc Natl Acad Sci USA. 2002;99:11287-11292.
24. Hauser MA, Li YJ, Takeuchi S, et al. Genomic convergence: identifying candidate genes for Parkinson's disease by combining serial analysis of gene expression and genetic linkage. Hum Mol Genet. 2003;12:671-677.
25. Vandesompele J, De Preter K, Pattyn F, et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002;3:RESEARCH0034.
26. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001;25:402-408.
27. Nishizawa Y, Komori N, Usukura J, Jackson KW, Tobin SL, Matsumoto H. Initiating ocular proteomics for cataloging bovine retinal proteins: microanalytical techniques permit the identification of proteins derived from a novel photoreceptor preparation. Exp Eye Res. 1999;69:195-212.
28. Yuodelis C, Hendrickson A. A qualitative and quantitative analysis of the human fovea during development. Vision Res. 1986;26:847-855.
29. McHeyzer-Williams LJ, Panus JF, Mikszta JA, McHeyzer-Williams MG. Evolution of antigen-specific T cell receptors in vivo: preimmune and antigen-driven selection of preferred complementarity-determining region 3 (CDR3) motifs. J Exp Med. 1999;189:1823-1838.
30. Blackshaw S, Kuo WP, Park PJ, et al. MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues. Genome Biol. 2003;4:R17.
31. Chen J, Sun M, Lee S, Zhou G, Rowley JD, Wang SM. Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc Natl Acad Sci USA. 2002;99:12257-12262.
32. Schein SJ. Anatomy of macaque fovea and spatial densities of neurons in foveal representation. J Comp Neurol. 1988;269:479-505.
33. Ishibashi K, Tian J, Handa JT. Similarity of mRNA phenotypes of morphologically normal macular and peripheral retinal pigment epithelial cells in older human eyes. Invest Ophthalmol Vis Sci. 2004;45:3291-3301.
34. Xu Q, Modrek B, Lee C. Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res. 2002;30:3754-3766.
35. Yelin R, Dahary D, Sorek R, et al. Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol. 2003;21:379-386.
36. Beales PL, Katsanis N, Lewis RA, et al. Genetic and mutational analyses of a large multiethnic Bardet-Biedl cohort reveal a minor involvement of BBS6 and delineate the critical intervals of other loci. Am J Hum Genet. 2001;68:606-616.
37. Li JB, Gerdes JM, Haycraft CJ, et al. Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene. Cell. 2004;117:541-552.
38. Allingham RR, Wiggs JL, Hauser ER, et al. Early adult-onset POAG linked to 15q11-13 using ordered subset analysis. Invest Ophthalmol Vis Sci. 2005;46:2002-2005.
39. Nemesure B, Jiao X, He Q, et al. A genome-wide scan for primary open-angle glaucoma (POAG): the Barbados Family Study of Open-Angle Glaucoma. Hum Genet. 2003;112:600-609.
40. Samples JR, Kitsos G, Economou-Petersen E, et al. Refining the primary open-angle glaucoma GLC1C region on chromosome 3 by haplotype analysis. Clin Genet. 2004;65:40-44.
41. Stoilova D, Child A, Trifan OC, Crick RP, Coakes RL, Sarfarazi M. Localization of a locus (GLC1B) for adult-onset primary open angle glaucoma to the 2cen-q13 region. Genomics. 1996;36:142-150.
42. Trifan OC, Traboulsi EI, Stoilova D, et al. A third locus (GLC1D) for adult-onset primary open-angle glaucoma maps to the 8q23 region. Am J Ophthalmol. 1998;126:17-28.
43. Wiggs JL, Allingham RR, Hossain A, et al. Genome-wide scan for adult onset primary open angle glaucoma. Hum Mol Genet. 2000;9:1109-1117.
44. Wirtz MK, Samples JR, Rust K, et al. GLC1F, a new primary open-angle glaucoma locus, maps to 7q35-q36. Arch Ophthalmol. 1999;117:237-241.
45. Wistow G, Bernstein SL, Touchman JW, et al. Grouping and identification of sequence tags (GRIST): bioinformatics tools for the NEIBank database. Mol Vis. 2002;8:164-170.
46. Bernstein SL, Borst DE, Neuder ME, Wong P. Characterization of a human fovea cDNA library and regional differential gene expression in the human retina. Genomics. 1996;32:301-308.
47. Bernstein SL, Borst DE, Wong PW. Isolation of differentially expressed human fovea genes: candidates for macular disease. Mol Vis. 1995;1:4.
48. Malone K, Sohocki MM, Sullivan LS, Daiger SP. Identifying and mapping novel retinal-expressed ESTs from humans. Mol Vis. 1999;5:5.
49. Sinha S, Sharma A, Agarwal N, Swaroop A, Yang-Feng TL. Expression profile and chromosomal location of cDNA clones, identified from an enriched adult retina library. Invest Ophthalmol Vis Sci. 2000;41:24-28.
50. Sohocki MM, Malone KA, Sullivan LS, Daiger SP. Localization of retina/pineal-expressed sequences: identification of novel candidate genes for inherited retinal disorders. Genomics. 1999;58:29-33.
51. Wistow G, Bernstein SL, Wyatt MK, et al. Expressed sequence tag analysis of human RPE/choroid for the NEIBank Project: over 6000 non-redundant transcripts, novel genes and splice variants. Mol Vis. 2002;8:205-220.
52. Wistow G, Bernstein SL, Wyatt MK, et al. Expressed sequence tag analysis of human retina for the NEIBank Project: retbindin, an abundant, novel retinal cDNA and alternative splicing of other retina-preferred gene transcripts. Mol Vis. 2002;8:196-204.
53. Rodieck RW. The First Steps of Seeing. Sunderland, MA: Sinauer; 1998.
54. Michaelides M, Johnson S, Poulson A, et al. An autosomal dominant bull's-eye macular dystrophy (MCDR2) that maps to the short arm of chromosome 4. Invest Ophthalmol Vis Sci. 2003;44:1657-1662.
55. Alfano G, Vitiello C, Caccioppoli C, et al. Natural antisense transcripts associated with genes involved in eye development. Hum Mol Genet. 2005;14:913-923.
56. Imanishi Y, Li N, Sokal I, et al. Characterization of retinal guanylate cyclase-activating protein 3 (GCAP3) from zebrafish to man. Eur J Neurosci. 2002;15:63-78.
57. Warburg M, Sjo O, Tranebjaerg L, Fledelius HC. Deletion mapping of a retinal cone-rod dystrophy: assignment to 18q211. Am J Med Genet. 1991;39:288-293.
58. Reim K, Wegmeyer H, Brandstatter JH, et al. Structurally and functionally unique complexins at retinal ribbon synapses. J Cell Biol. 2005;169:669-680.
59. Johnson S, Halford S, Morris AG, et al. Genomic organisation and alternative splicing of human RIM1, a gene implicated in autosomal dominant cone-rod dystrophy (CORD7). Genomics. 2003;81:304-314.