Full-Length Transcriptome Analysis of Human Retina-Derived Cell Lines ARPE-19 and Y79 Using the Vector-Capping Method

Investigative Ophthalmology and Visual Science

Volumn 52, Issue 9, 2011, Pages 6662-6670

  Oshikawa, Mio ^a   Tsutsui, Chihiro ^a,b   Ikegami, Tomoko ^a,b   Fuchida, Yuki ^a,b   Matsubara, Maki ^a   Toyama, Shigeru ^a   Usami, Ron ^b   Ohtoko, Kuniyo ^c   Kato, Seishi ^a  

^a NATIONAL REHABILITATION CENTER FOR PERSONS WITH DISABILITIES   (Japan)

^b TOYO UNIVERSITY   (Japan)

^c HITACHI HIGH TECHNOLOGIES CORPORATION   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE CITRATE LYASE; ALPHA CRYSTALLIN; ARGININOSUCCINATE SYNTHASE; BETA1 INTEGRIN; CALCIUM BINDING PROTEIN; CONNECTIVE TISSUE GROWTH FACTOR; CREATINE KINASE; CYSTEINE RICH PROTEIN 61; CYTOKERATIN 18; CYTOKERATIN 7; CYTOKERATIN 8; EOTAXIN 3; GUANINE NUCLEOTIDE BINDING PROTEIN BETA SUBUNIT; HIPPOCALCIN; INTERLEUKIN 18; LIPOCORTIN 2; MARCKS PROTEIN; METALLOTHIONEIN II; MYOSIN; PHOSPHOPROTEIN PHOSPHATASE 2; PROLINE RICH PROTEIN; RECOVERIN; RETINOIC ACID RECEPTOR; SECRETED FRIZZLED RELATED PROTEIN 2; SOMATOMEDIN BINDING PROTEIN; TRANSCRIPTOME; TRANSFORMING GROWTH FACTOR BETA; TRANSGELIN; UNINDEXED DRUG; XRCC4 PROTEIN; CAPPED RNA; MESSENGER RNA;

ARTICLE; DNA LIBRARY; DNA SEQUENCE; GENE EXPRESSION; GENE MAPPING; HUMAN; HUMAN CELL; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RETINA CELL; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENE VECTOR; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; METHODOLOGY; MOLECULAR CLONING; PHYSIOLOGY; PIGMENT EPITHELIUM; PLASMID; RETINA TUMOR; RETINOBLASTOMA; TUMOR CELL LINE; TUMOR GENE;

CELL LINE, TUMOR; CLONING, MOLECULAR; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE LIBRARY; GENES, NEOPLASM; GENETIC VECTORS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLASMIDS; RETINAL NEOPLASMS; RETINAL PIGMENT EPITHELIUM; RETINOBLASTOMA; RNA CAPS; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

EID: 80054790789     PISSN: 01460404     EISSN: 15525783     Source Type: Journal    
DOI: 10.1167/iovs.11-7479     Document Type: Article

References (65)

1. Dowling JE. The Retina: An Approachable Part of the Brain. Cambridge, MA: Belknap Press; 1987.
2. Luo DG, Xue T, Yau KW. How vision begins: an odyssey. Proc Natl Acad Sci U S A. 2008;105:9855-9862.
3. Marmor MF, Wolfensberger TJ. The Retinal Pigment Epithelium. Oxford, UK: Oxford University Press; 1998.
4. Strauss O. The retinal pigment epithelium in visual function. Physiol Rev. 2005;85:845-881.
5. Rattner A, Sun H, Nathans J. Molecular genetics of human retinal disease. Annu Rev Genet. 1999;33:89-131.
6. Phelan JK, Bok D. A brief review of retinitis pigmentosa and the identified retinitis pigmentosa genes. Mol Vis. 2000;6:116-124.
7. Pacione LR, Szego MJ, Ikeda S, Nishina PM, McInnes RR. Progress toward understanding the genetic and biochemical mechanisms of inherited photoreceptor degenerations. Annu Rev Neurosci. 2003; 26:657-700.
8. Coleman HR, Chan CC, Ferris FL 3rd, Chew EY. Age-related macular degeneration. Lancet. 2008;372:1835-1845.
9. Hennig AK, Peng GH, Chen S. Regulation of photoreceptor gene expression by Crx-associated transcription factor network. Brain Res. 2008;1192:114-133.
10. Swaroop A, Zack DJ. Transcriptome analysis of the retina. Genome Biol. 2002;3:REVIEWS1022.
11. Bortoluzzi S, d'Alessi F, Danieli GA. A novel resource for the study of genes expressed in the adult human retina. Invest Ophthalmol Vis Sci. 2000;41:3305-3308.
12. 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.
13. 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 U S A. 2002;99:315-320.
14. Kimura K, Wakamatsu A, Suzuki Y, et al. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res. 2006;16:55-65.
15. Modrek B, Resch A, Grasso C, Lee C. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res. 2001;29:2850-2859.
16. Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D. Patterns of variant polyadenylation signal usage in human genes. Genome Res. 2000;10:1001-1010.
17. Masland RH. The fundamental plan of the retina. Nat Neurosci. 2001;4:877-886.
18. Wahlin KJ, Lim L, Grice EA, Campochiaro PA, Zack DJ, Adler R. A method for analysis of gene expression in isolated mouse photoreceptor and Müller cells. Mol Vis. 2004;10:366-375.
19. Dunn KC, Aotaki-Keen AE, Putkey FR, Hjelmeland LM. ARPE-19, a human retinal pigment epithelial cell line with differentiated properties. Exp Eye Res. 1996;62:155-169.
20. Dunn KC, Marmorstein AD, Bonilha VL, Rodriguez-Boulan E, Giordano F, Hjelmeland LM. Use of the ARPE-19 cell line as a model of RPE polarity: basolateral secretion of FGF5. Invest Ophthalmol Vis Sci. 1998;39:2744-2749.
21. Tian J, Ishibashi K, Handa JT. The expression of native and cultured RPE grown on different matrices. Physiol Genomics. 2004; 17:170-182.
22. Chowers I, Kim Y, Farkas RH, et al. Changes in retinal pigment epithelial gene expression induced by rod outer segment uptake. Invest Ophthalmol Vis Sci. 2004;45:2098-2106.
23. Cai H, Del Priore LV. Gene expression profile of cultured adult compared to immortalized human RPE. Mol Vis. 2006;12:1-14.
24. Tian J, Ishibashi K, Honda S, Boylan SA, Hjelmeland LM, Handa JT. The expression of native and cultured human retinal pigment epithelial cells grown in different culture conditions. Br J Ophthalmol. 2005;89:1510-1517.
25. Bogenmann E, Lochrie MA, Simon MI. Cone cell-specific genes expressed in retinoblastoma. Science. 1988;240:76-78.
26. Xu XL, Fang Y, Lee TC, et al. Retinoblastoma has properties of a cone precursor tumor and depends upon cone-specific MDM2 signaling. Cell. 2009;137:1018-1031.
27. Kato S, Ohtoko K, Ohtake H, Kimura T. Vector-capping: a simple method for preparing a high-quality full-length cDNA library. DNA Res. 2005;12:53-62.
28. Oshikawa M, Sugai Y, Usami R, Ohtoko K, Toyama S, Kato S. Fine expression profiling of full-length transcripts using a size-unbiased cDNA library prepared with the vector-capping method. DNA Res. 2008;15:123-136.
29. Kato S, Sekine S, Oh SW, et al. Construction of a human full-length cDNA bank. Gene. 1994;150:243-250.
30. Chao A. Species richness estimation. In: Balakrishnan, N, Read CB, Vidakovic B, eds. Species Estimation and Applications: Encyclopedia of Statistical Sciences. New York: Wiley; 2005:7907-7916.
31. Godbout R, Bisgrove DA, Honoré LH, Day RS 3rd. Amplification of the gene encoding the alpha-subunit of the mitochondrial ATP synthase complex in a human retinoblastoma cell line. Gene. 1993;123:195-201.
32. Godbout R, Pandita A, Beatty B, Bie W, Squire JA. Comparative genomic hybridization analysis of Y79 and FISH mapping indicate the amplified human mitochondrial ATP synthase alpha-subunit gene (ATP5A) maps to chromosome 18q123q21. Cytogenet Cell Genet. 1997;77:253-256.
33. Godbout R, Squire J. Amplification of a DEAD box protein gene in retinoblastoma cell lines. Proc Natl Acad Sci U S A. 1993;90:7578-7582.
34. Manohar CF, Salwen HR, Brodeur GM, Cohn SL. Co-amplification and concomitant high levels of expression of a DEAD box gene with MYCN in human neuroblastoma. Genes Chromosomes Cancer. 1995;14:196-203.
35. Dou D, Joseph R. Structure and organization of the human neuronatin gene. Genomics. 1996;33:292-297.
36. Usui H, Morii K, Tanaka R, et al. cDNA cloning and mRNA expression analysis of the human neuronatin: high level expression in human pituitary gland and pituitary adenomas. J Mol Neurosci. 1997;9:55-60.
37. Bovolenta P, Esteve P, Ruiz JM, Cisneros E, Lopez-Rios J. Beyond Wnt inhibition: new functions of secreted Frizzled-related proteins in development and disease. J Cell Sci. 2008;121:737-746.
38. Melkonyan HS, Chang WC, Shapiro JP, et al. SARPs: a family of secreted apoptosis-related proteins. Proc Natl Acad Sci U S A. 1997;94:13636-13641.
39. Wakaguri H, Yamashita R, Suzuki Y, Sugano S, Nakai K. DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res. 2008;36:D97-D101.
40. Maeda N, Kim HS, Azen EA, Smithies O. Differential RNA splicing and post-translational cleavages in the human salivary proline-rich protein gene system. J Biol Chem. 1985;260:11123-11130.
41. Margolis RL, Stine OC, McInnis MG, et al. cDNA cloning of a human homologue of the Caenorhabditis elegans cell fate-determining gene mab-21: expression, chromosomal localization and analysis of a highly polymorphic (CAG)n trinucleotide repeat. Hum Mol Genet. 1996;5:607-616.
42. Peek R, Kammerer RA, Frank S, Otte-Höller I, Westphal JR. The angiopoietin-like factor cornea-derived transcript 6 is a putative morphogen for human cornea. J Biol Chem. 2002;277:686-693.
43. Oliver G, Mailhos A, Wehr R, Copeland NG, Jenkins NA, Gruss P. Six3, a murine homologue of the sine oculis gene, demarcates the most anterior border of the developing neural plate and is expressed during eye development. Development. 1995;121:4045-4055.
44. Ton CC, Hirvonen H, Miwa H, et al. Positional cloning and characterization of a paired box-and homeobox-containing gene from the aniridia region. Cell. 1991;67:1059-1074.
45. Iwasaki K, Bajenova E, Somogyi-Ganss E, et al. Amelotin-novel secreted, ameloblast-specific protein. J Dent Res. 2005;84:1127-1132.
46. Shinkai A, Yoshisue H, Koike M, et al. A novel human CC chemokine, eotaxin-3, which is expressed in IL-4-stimulated vascular endothelial cells, exhibits potent activity toward eosinophils. J Immunol. 1999;163:1602-1610.
47. 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.
48. Roberts MR, Hendrickson A, McGuire CR, Reh TA. Retinoid X receptor (gamma) is necessary to establish the S-opsin gradient in cone photoreceptors of the developing mouse retina. Invest Ophthalmol Vis Sci. 2005;46:2897-2904.
49. Lee RH, Lieberman BS, Yamane HK, Bok D, Fung BK. A third form of the G protein beta subunit, 1: immunochemical identification and localization to cone photoreceptors. J Biol Chem. 1992;267: 24776-24781.
50. Hagstrom SA, North MA, Nishina PL, Berson EL, Dryja TP. Recessive mutations in the gene encoding the tubby-like protein TULP1 in patients with retinitis pigmentosa. Nat Genet. 1998;18:174-176.
51. Banerjee P, Kleyn PW, Knowles JA, et al. TULP1 mutation in two extended Dominican kindreds with autosomal recessive retinitis pigmentosa. Nat Genet. 1998;18:177-179.
52. Gonzalez-Fernandez F. Evolution of the visual cycle: the role of retinoid-binding proteins. J Endocrinol. 2002;175:75-88.
53. Arriza JL, Eliasof S, Kavanaugh MP, Amara SG. Excitatory amino acid transporter 5, a retinal glutamate transporter coupled to a chloride conductance. Proc Natl Acad Sci U S A. 1997;94:4155-4160.
54. 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.
55. Stöhr H, Heisig JB, Benz PM, et al. TMEM16B, a novel protein with calcium-dependent chloride channel activity, associates with a presynaptic protein complex in photoreceptor terminals. J Neurosci. 2009;29:6809-6818.
56. Hurle B, Ignatova E, Massironi SM, et al. Non-syndromic vestibular disorder with otoconial agenesis in tilted/mergulhador mice caused by mutations in otopetrin 1. Hum Mol Genet. 2003;12: 777-789.
57. Acharya S, Foletta VC, Lee JW, et al. SPACRCAN, a novel human interphotoreceptor matrix hyaluronan-binding proteoglycan synthesized by photoreceptors and pinealocytes. J Biol Chem. 2000; 275:6945-6955.
58. Rattner A, Smallwood PM, Williams J, et al. A photoreceptorspecific cadherin is essential for the structural integrity of the outer segment and for photoreceptor survival. Neuron. 2001;32: 775-786.
59. Hutchins JB. Acetylcholine as a neurotransmitter in the vertebrate retina. Exp Eye Res. 1987;45:1-38.
60. Liu X, Bulgakov OV, Wen XH, et al. AIPL1, the protein that is defective in Leber congenital amaurosis, is essential for the biosynthesis of retinal rod cGMP phosphodiesterase. Proc Natl Acad Sci U S A. 2004;101:13903-13908.
61. Reim K, Wegmeyer H, Brandstätter JH, et al. Structurally and functionally unique complexins at retinal ribbon synapses. J Cell Biol. 2005;169:669-680.
62. Klein DC. Arylalkylamine N-acetyltransferase: the 'Timezyme.' J Biol Chem. 2007;282:4233-4237.
63. Kraemer C, Enklaar T, Zabel B, Schmidt ER. Mapping and structure of DMXL1, a human homologue of the DmX gene from Drosophila melanogaster coding for a WD repeat protein. Genomics. 2000; 64:97-101.
64. Abd El-Aziz MM, Barragan I, O'Driscoll CA, et al. EYS, encoding an ortholog of Drosophila spacemaker, is mutated in autosomal recessive retinitis pigmentosa. Nat Genet. 2008;40:1285-1287.
65. Collin RW, Littink KW, Klevering BJ, et al. Identification of a 2 Mb human ortholog of Drosophila eyes shut/spacemaker that is mutated in patients with retinitis pigmentosa. Am J Hum Genet. 2008;83:594-603.