Development and characterization of a normalized canine retinal cDNA library for genomic and expression studies

Investigative Ophthalmology and Visual Science

Volumn 47, Issue 6, 2006, Pages 2632-2638

  Zangerl, Barbara ^a   Sun, Qi ^b   Pillardy, Jarek ^b   Johnson, Jennifer L ^b   Schweitzer, Peter A ^b   Hernandez, Alvaro G ^c   Liu, Lei ^c   Acland, Gregory M ^b   Aguirre, Gustavo D ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b Department of Obstetrics Gynecology   (United States)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; EYE PROTEIN;

ALGORITHM; ANIMAL TISSUE; ARTICLE; CHROMOSOMAL LOCALIZATION; CLONE; CONTROLLED STUDY; DATA BASE; DNA LIBRARY; DOG; EXPRESSED SEQUENCE TAG; EYE; EYE DEVELOPMENT; GENE; GENOME; GENOMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RETINA; UNINDEXED SEQUENCE; ANIMAL; FACTUAL DATABASE; GENE EXPRESSION; GENE LIBRARY; GENETICS; METABOLISM;

ANIMALS; DATABASES, FACTUAL; DNA, COMPLEMENTARY; DOGS; EXPRESSED SEQUENCE TAGS; EYE PROTEINS; GENE EXPRESSION; GENE LIBRARY; GENOMICS; RETINA;

EID: 33745653707     PISSN: 01460404     EISSN: None     Source Type: Journal    
DOI: 10.1167/iovs.05-1463     Document Type: Article

References (46)

1. Ostrander EA, Galibert F, Patterson DF. Canine genetics comes of age. Trends Genet. 2000;16:117-124.
2. Patterson DF, Haskins ME, Jezyk PF, et al. Research on genetic diseases: reciprocal benefits to animals and man. J Am Vet Med Assoc. 1988;193:1131-1144.
3. Patterson DF. Canine Genetic Disease Information System. St. Louis, MO; Mosby International; 2002:888.
4. Suber ML, Pittler SJ, Qin N, et al. Irish setter dogs affected with rod/cone dysplasia contain a nonsense mutation in the rod cGMP phosphodiesterase beta-subunit gene. Proc Natl Acad Sci USA. 1993;90:3968-3972.
5. Aguirre GD, Baldwin V, Pearce-Kelling S, et al. Congenital stationary night blindness in the dog: common mutation in the RPE65 gene indicates founder effect. Mol Vis. 1998;4:23.
6. Petersen-Jones SM, Entz DD, Sargan DR. cGMP phosphodiesterase-alpha mutation causes progressive retinal atrophy in the Cardigan Welsh corgi dog. Invest Ophthalmol Vis Sci. 1999;40:1637-1644.
7. Dekomien G, Runte M, Godde R, Epplen JT. Generalized progressive retinal atrophy of Sloughi dogs is due to an 8-bp insertion in exon 21 of the PDE6B gene. Cytogenet Cell Genet. 2000;90:261-267.
8. Kijas JW, Cideciyan AV, Aleman TS, et al. Naturally occurring rhodopsin mutation in the dog causes retinal dysfunction and degeneration mimicking human dominant retinitis pigmentosa. Proc Natl Acad Sci USA. 2002;99:6328-6333.
9. Sidjanin DJ, Lowe JK, McElwee JL, et al. Canine CNGB3 mutations establish cone degeneration as orthologous to the human achromatopsia locus ACHM3. Hum Mol Genet. 2002;11:1823-1833.
10. Zhang Q, Acland GM, Wu WX, et al. Different RPGR exon ORF15 mutations in Canids provide insights into photoreceptor cell degeneration. Hum Mol Genet. 2002;11:993-1003.
11. Aguirre-Hernandez J, Sargan DR. Evaluation of candidate genes in the absence of positional information: a poor bet on a blind dog! J Hered. 2005;96:475-484.
12. Sargan DR. IDID inherited diseases in dogs: web-based information for canine inherited disease genetics. Mamm Genome. 2004;15:503-506.
13. Portera-Cailliau C, Sung CH, Nathans J, Adler R. Apoptotic photoreceptor cell death in mouse models of retinitis pigmentosa. Proc Natl Acad Sci USA. 1994;91:974-978.
14. van Soest S, Westerveld A, de Jong PT, Bleeker-Wagemakers EM, Bergen AA. Retinitis pigmentosa: defined from a molecular point of view. Surv Ophthalmol. 1999;43:321-334.
15. Lindblad-Toh K, Wade CM, Mikkelsen TS, et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 2005;438:803-819.
16. Kirkness EF, Bafna V, Halpern AL, et al. The dog genome: survey sequencing and comparative analysis. Science. 2003;301:1898-1903.
17. Consortium HGS. Finishing the euchromatic sequence of the human genome. Nature. 2004;431:931-945.
18. Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM. Expression profiling using cDNA microarrays. Nat Genet. 1999;21:10-14.
19. Adams MD, Kelley JM, Gocayne JD, et al. Complementary DNA sequencing: expressed sequence tags and human genome project. Science. 1991;252:1651-1656.
20. Strachan T, Abitbol M, Davidson D, Beckmann JS. A new dimension for the human genome project: towards comprehensive expression maps. Nat Genet. 1997;16:126-132.
21. Kennan A, Aherne A, Palfi A, et al. Identification of an IMPDH1 mutation in autosomal dominant retinitis pigmentosa (RP10) revealed following comparative microarray analysis of transcripts derived from retinas of wild-type and Rho(-/-) mice. Hum Mol Genet. 2002;11:547-557.
22. Yoshida S, Mears AJ, Friedman JS, et al. Expression profiling of the developing and mature Nrl-/- mouse retina: identification of retinal disease candidates and transcriptional regulatory targets of Nrl. Hum Mol Genet. 2004;13:1487-1503.
23. 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.
24. Ida H, Boylan SA, Weigel AL, et al. EST analysis of mouse retina and RPE/choroid cDNA libraries. Mol Vis. 2004;10:439-444.
25. Roberts MC, Hitte CC, Hendrickson JA, et al. Characterization and radiation hybrid mapping of expressed sequence tags from the canine brain. Mamm Genome. 2003;14:203-213.
26. Lin CT, Sargan DR. Generation and analysis of canine retinal ESTs: isolation and expression of retina-specific gene transcripts. Biochem Biophys Res Commun. 2001;282:394-403.
27. Aguirre GD, Acland GM. Variation in retinal degeneration phenotype inherited at the prcd locus. Exp Eye Res. 1988;46:663-687.
28. Sidjanin DJ, Miller B, Kijas J, et al. Radiation hybrid map, physical map, and low-pass genomic sequence of the canine prcd region on CFA9 and comparative mapping with the syntenic region on human chromosome 17. Genomics. 2003;81:138-148.
29. Parkes JH, Aguirre G, Rockey JH, Liebman PA. Progressive rodcone degeneration in the dog: characterization of the visual pigment. Invest Ophthalmol Vis Sci. 1982;23:674-678.
30. Aguirre G, Alligood J, O'Brien P, Buyukmihci N. Pathogenesis of progressive rod-cone degeneration in miniature poodles. Invest Ophthalmol Vis Sci. 1982;23:610-630.
31. Aguirre G, O'Brien P. Morphological and biochemical studies of canine progressive rod-cone degeneration. 3H-fucose autoradiography. Invest Ophthalmol Vis Sci. 1986;27:635-655.
32. Aguirre G, Andrews L. Nomarski evaluation of rod outer segment renewal in a hereditary retinal degeneration: comparison with autoradiographic evaluation. Invest Ophthalmol Vis Sci. 1987;28:1049-1058.
33. Mieziewska K, van Veen T, Aguirre GD. Structural changes of the interphotoreceptor matrix in an inherited retinal degeneration: a lectin cytochemical study of progressive rod-cone degeneration. Invest Ophthalmol Vis Sci. 1993;34:3056-3067.
34. Bonaldo MF, Lennon G, Soares MB. Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res. 1996;6:791-806.
35. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998;8:175-185.
36. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998;8:186-194.
37. Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25-29.
38. Schulz HL, Goetz T, Kaschkoetoe J, Weber BH. The Retinome: defining a reference transcriptome of the adult mammalian retina/retinal pigment epithelium. BMC Genomics. 2004;5:50.
39. Bavik CO, Eriksson U, Allen RA, Peterson PA. Identification and partial characterization of a retinal pigment epithelial membrane receptor for plasma retinol-binding protein. J Biol Chem. 1991;266:14978-14985.
40. Hamel CP, Tsilou E, Harris E, et al. A developmentally regulated microsomal protein specific for the pigment epithelium of the vertebrate retina. J Neurosci Res. 1993;34:414-425.
41. Acland GM, Aguirre GD, Bennett J, et al. Long-term restoration of rod and cone vision by single dose rAAV-mediated gene transfer to the retina in a canine model of childhood blindness. Mol Ther. 2005;12:1072-1082
42. Pang JJ, Chang B, Kumar A, et al. Gene therapy restores vision-dependent behavior as well as retinal structure and function in a mouse model of RPE65 Leber congenital amaurosis. Mol Ther. 2006;13;565-572.
43. Whitfield CW, Band MR, Bonaldo MF, et al. Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee. Genome Res. 2002;12:555-566.
44. Fondon JW 3rd, Garner HR. Molecular origins of rapid and continuous morphological evolution. Proc Natl Acad Sci USA. 2004;101:18058-18063.
45. Guyon R, Lorentzen TD, Hitte C, et al. A 1-Mb resolution radiation hybrid map of the canine genome. Proc Natl Acad Sci USA. 2003;100:5296-5301.
46. Acland GM, Ray K, Mellersh CS, et al. Linkage analysis and comparative mapping of canine progressive rod-cone degeneration (prcd) establishes potential locus homology with retinitis pigmentosa (RP17) in humans. Proc Natl Acad Sci USA. 1998;95:3048-3053.