A biphasic pattern of gene expression during mouse retina development

BMC Developmental Biology

Volumn 6, Issue , 2006, Pages

  Zhang, Samuel Shao Min ^a,d   Xu, Xuming ^a   Liu, Mu Gen ^a   Zhao, Hongyu ^a   Soares, Marcelo Bento ^b   Barnstable, Colin J ^a,d   Fu, Xin Yuan ^c  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

^c INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d PENN STATE COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; RNA; EYE PROTEIN;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CELL DIFFERENTIATION; CELL TYPE; CORRELATION COEFFICIENT; DEVELOPMENTAL STAGE; DNA MICROARRAY; EMBRYO DEVELOPMENT; GENE CLUSTER; GENE EXPRESSION; GENE IDENTIFICATION; MOUSE; NONHUMAN; PHOTORECEPTOR; POSTNATAL DEVELOPMENT; RETINA DEVELOPMENT; RNA ISOLATION; SERIAL ANALYSIS OF GENE EXPRESSION; TISSUE MICROARRAY; ANIMAL; ANTIBODY SPECIFICITY; C57BL MOUSE; CLASSIFICATION; COMPARATIVE STUDY; EMBRYOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GROWTH, DEVELOPMENT AND AGING; METABOLISM; NEWBORN; PROCEDURES; RETINA; RETINA ROD;

ANIMALS; ANIMALS, NEWBORN; EMBRYONIC DEVELOPMENT; EYE PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; MICE; MICE, INBRED C57BL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORGAN SPECIFICITY; RETINA; RETINAL ROD PHOTORECEPTOR CELLS;

EID: 33750633646     PISSN: 1471213X     EISSN: 1471213X     Source Type: Journal    
DOI: 10.1186/1471-213X-6-48     Document Type: Article

References (69)

1. Barnstable CJ: A molecular view of vertebrate retinal development. Mol Neurobiol 1987, l(l-2):9-46.
2. Cepko CL: The patterning and onset of opsin expression in vertebrate retinae. Curr Opin Neurobiol 1996, 6(4):542-546.
3. Cepko CL: The roles of intrinsic and extrinsic cues and bHLH genes in the determination of retinal cell fates. Curr Opin Neurobiol 1999, 9(1):37-46.
4. Zhang SS, Fu XY, Barnstable CJ: Molecular aspects of vertebrate retinal development. Mol Neurobiol 2002, 26(2-3):137-152.
5. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM: Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 1996, 14(4):457-460.
6. Coller HA, Grandori C, Tamayo P, Colbert T, Lander ES, Eisenman RN, Golub TR: Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion. Proc Natl Acad Sci USA 2000, 97(7):3260-3265.
7. Hedenfalk I, Duggan D, Chen Y, Radmacher M, Bittner M, Simon R, Meltzer P, Gusterson B, Esteller M, Kallioniemi OP, et al.: Gene-expression profiles in hereditary breast cancer. N Engl J Med 2001, 344(8):539-548.
8. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998, 9(12):3273-3297.
9. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95(25):14863-14868.
10. Sudarsanam P, Iyer VR, Brown PO, Winston F: Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2000, 97(7):3364-3369.
11. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, et al.: Genome-wide location and function of DNA binding proteins. Science 2000, 290(5500):2306-2309.
12. Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, et al.: Global analysis of protein activities using proteome chips. Science 2001, 293(5537):2101-2105.
13. Peng WT, Robinson MD, Mnaimneh S, Krogan NJ, Cagney G, Morris Q, Davierwala AP, Grigull J, Yang X, Zhang W, et al.: A panoramic view of yeast noncoding RNA processing. Cell 2003, 113(7):919-933.
14. Livesey FJ, Furukawa T, Steffen MA, Church GM, Cepko CL: Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. CurrBiol 2000, 10(6):301-310.
15. Farjo R, Yu J, Othman MI, Yoshida S, Sheth S, Glaser T, Baehr W, Swaroop A: Mouse eye gene microarrays for investigating ocular development and disease. Vision Res 2002, 42(4):463-470.
16. Diaz E, Yang YH, Ferreira T, Loh KC, Okazaki Y, Hayashizaki Y, Tessier-Lavigne M, Speed TP, Ngai J: Analysis of gene expression in the developing mouse retina. Proc Natl Acad Sci USA 2003, 100(9):5491-5496.
17. Dorrell MI, Aguilar E, Weber C, Friedlander M: Global gene expression analysis of the developing postnatal mouse retina. Invest Ophthalmol Vis Sci 2004, 45(3):1009-1019.
18. Gustincich S, Contini M, Gariboldi M, Puopolo M, Kadota K, Bono H, LeMieux J, Walsh P, Carninci P, Hayashizaki Y, et al.: Gene discovery in genetically labeled single dopaminergic neurons of the retina. Proc Natl Acad Sci USA 2004, 101(14):5069-5074.
19. Farkas RH, Qian J, Goldberg JL, Quigley HA, Zack DJ: Gene expression profiling of purified rat retinal ganglion cells. Invest Ophthalmol Vis Sci 2004, 45(8):2503-2513.
20. Mu X, Beremand PD, Zhao S, Pershad R, Sun H, Scarpa A, Liang S, Thomas TL, Klein WH: Discrete gene sets depend on POU domain transcription factor Brn3b/Brn-3.2/POU4f2 for their expression in the mouse embryonic retina. Development 2004, 131(6):1197-1210.
21. Zhang SS, Xu X, Li J, Liu MG, Zhao H, Soares MB, Barnstable CJ, Fu XY: Comprehensive in silico functional specification of mouse retina transcripts. BMC Genomics 2005, 6(1):40.
22. Corbo JC, Cepko CL: A Hybrid Photoreceptor Expressing Both Rod and Cone Genes in a Mouse Model of Enhanced SCone Syndrome. PLoS Genet 2005, I(2):e11.
23. Znoiko SL, Rohrer B, Lu K, Lohr HR, Crouch RK, Ma JX: Downregulation of cone-specific gene expression and degeneration of cone photoreceptors in the Rpe65-/- mouse at early ages. Invest Ophthalmol Vis Sci 2005, 46(4):1473-1479.
24. Smith L, Greenfield A: DNA microarrays and development. Hum Mol Genet 2003, 12(Suppl l):Rl-8.
25. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, et al.: Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 2002, 420(6915):563-573.
26. Mody M, Cao Y, Cui Z, Tay KY, Shyong A, Shimizu E, Pham K, Schultz P, Welsh D, Tsien JZ: Genome-wide gene expression profiles of the developing mouse hippocampus. Proc Natl Acad Sci USA 2001, 98(15):8862-8867.
27. Diaz E, Ge Y, Yang YH, Loh KC, Serafini TA, Okazaki Y, Hayashizaki Y, Speed TP, Ngai J, Scheiffele P: Molecular analysis of gene expression in the developing pontocerebellar projection system. Neuron 2002, 36(3):417-434.
28. Mariani TJ, Reed JJ, Shapiro SD: Expression profiling of the developing mouse lung: insights into the establishment of the extracellular matrix. Am J Respir Cell Mol Biol 2002, 26(5):541-548.
29. White KP, Rifkin SA, Hurban P, Hogness DS: Microarray analysis of Drosophila development during metamorphosis. Science 1999, 286(5447):2179-2184.
30. Reinke V, Smith HE, Nance J, Wang J, Van Doren C, Begley R, Jones SJ, Davis EB, Scherer S, Ward S, et al.: A global profile of germline gene expression in C. elegans. Mol Cell 2000, 6(3):605-616.
31. Li M, Zhang SS, Barnstable CJ: Developmental and tissue expression patterns of mouse Mpp4 gene. Biochem Biophys Res Commun 2003, 307(2):229-235.
32. Sharma RK, O'Leary TE, Fields CM, Johnson DA: Development of the outer retina in the mouse. Brain Res Dev Brain Res 2003, 145(1):93-105.
33. Gene Ontology (GO) database [http://www.godatabase.org/dev/database/]
34. Sheng HZ, Zhadanov AB, Mosinger B Jr, Fujii T, Bertuzzi S, Grinberg A, Lee EJ, Huang SP, Mahon KA, Westphal H: Specification of pituitary cell lineages by the LIM homeobox gene Lhx3. Science 1996, 272(5264):1004-1007.
35. Sharma K, Sheng HZ, Lettieri K, Li H, Karavanov A, Potter S, Westphal H, Pfaff SL: LIM homeodomain factors Lhx3 and Lhx4 assign subtype identities for motor neurons. Cell 1998, 95(6):817-828.
36. Thor S, Andersson SG, Tomlinson A, Thomas JB: A LIM-homeodomain combinatorial code for motor-neuron pathway selection. Nature 1999, 397(6714):76-80.
37. Mitsumoto Y, Oka S, Sakuma H, Inazawa J, Kawasaki T: Cloning and chromosomal mapping of human glucuronyltransferase involved in biosynthesis of the HNK-1 carbohydrate epitope. Genomics 2000, 65(2):166-173.
38. Naegele JR, Barnstable CJ, Wahle PR: Expression of a unique 56-kDa polypeptide by neurons in the subplate zone of the developing cerebral cortex. Proc Natl Acad Sci USA 1991, 88(2):330-334.
39. Uusitalo M, Schlotzer-Schrehardt U, Kivela T: Ultrastructural localization of the HNK-1 carbohydrate epitope to glial and neuronal cells of the human retina. Invest Ophthalmol Vis Sci 2003, 44(3):961-964.
40. Moreira EF, Jaworski C, Li A, Rodriguez IR: Molecular and biochemical characterization of a novel oxysterol-binding protein (OSBP2) highly expressed in retina. J Biol Chem 2001, 276(21):18570-18578.
41. Horne MC, Donaldson KL, Goolsby GL, Tran D, Mulheisen M, Hell JW, Wahl AF: Cyclin G2 is up-regulated during growth inhibition and B cell antigen receptor-mediated cell cycle arrest. J Biol Chem 1997, 272(19):12650-12661.
42. Altieri DC: Survivin in apoptosis control and cell cycle regulation in cancer. Prog Cell Cycle Res 2003, 5:447-452.
43. Pennartz S, Belvindrah R, Tomiuk S, Zimmer C, Hofmann K, Conradt M, Bosio A, Cremer H: Purification of neuronal precursors from the adult mouse brain: comprehensive gene expression analysis provides new insights into the control of cell migration, differentiation, and homeostasis. Mol Cell Neurosci 2004, 25(4):692-706.
44. Duncan PI, Stojdl DF, Marius RM, Bell JC: In vivo regulation of alternative pre-mRNA splicing by the Clkl protein kinase. Mol Cell Biol 1997, 17(10):5996-6001.
45. Ohkawara B, Shirakabe K, Hyodo-Miura J, Matsuo R, Ueno N, Matsumoto K, Shibuya H: Role of the TAK1-NLK-STAT3 pathway in TGF-beta-mediated mesoderm induction. Genes Dev 2004, 18(4):381-386.
46. Ham J, Eilers A, Whitfield J, Neame SJ, Shah B: c-Jun and the transcriptional control of neuronal apoptosis. Biochem Pharmacol 2000, 60(8):1015-1021.
47. Blackshaw S, Fraioli RE, Furukawa T, Cepko CL: Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes. Cell 2001, 107(5):579-589.
48. Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP, Weber G, Lee K, Fraioli RE, Cho SH, et al.: Genomic analysis of mouse retinal development. PLoS Biol 2004, 2(9):E247.
49. Lee JS, von der Hardt S, Rusch MA, Stringer SE, Stickney HL, Talbot WS, Geisler R, Nusslein-Volhard C, Selleck SB, Chien CB, et al.: Axon sorting in the optic tract requires HSPG synthesis by ext2 (dackel) and extl3 (boxer). Neuron 2004, 44(6):947-960.
50. Morris TA, Fong SL: Characterization of the gene encoding human cone transducin alpha-subunit (GNAT2). Genomics 1993, 17(2):442-448.
51. Yu YC, Cao LH, Yang XL: Modulation by brain natriuretic peptide of GABA receptors on rat retinal ON-type bipolar cells. J Neurosci 2006, 26(2):696-707.
52. Biedermann B, Bringmann A, Franze K, Faude F, Wiedemann P, Reichenbach A: GABA(A) receptors in Muller glial cells of the human retina. Glia 2004, 46(3):302-310.
53. Mitchell CK, Huang B, Redburn-Johnson DA: GABA(A) receptor immunoreactivity is transiently expressed in the developing outer retina. Vis Neurosci 1999, 16(6):1083-1088.
54. Swanson DA, Steel JM, Valle D: Identification and characterization of the human ortholog of rat STXBP1, a protein implicated in vesicle trafficking and neurotransmitter release. Genomics 1998, 48(3):373-376.
55. Albig W, Bramlage B, Gruber K, Klobeck HG, Kunz J, Doenecke D: The human replacement histone H3.3B gene (H3F3B). Genomics 1995, 30(2):264-272.
56. Okano M, Xie S, Li E: Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases. Nat Genet 1998, 19(3):219-220.
57. Krupnik VE, Sharp JD, Jiang C, Robison K, Chickering TW, Amaravadi L, Brown DE, Guyot D, Mays G, Leiby K, et al.: Functional and structural diversity of the human Dickkopf gene family. Gene 1999, 238(2):301-313.
58. Hackam AS, Strom R, Liu D, Qian J, Wang C, Otteson D, Gunatilaka T, Farkas RH, Chowers I, Kageyama M, et al.: Identification of gene expression changes associated with the progression of retinal degeneration in the rdl mouse. Invest Ophthalmol Vis Sci 2004, 45(9):2929-2942.
59. Kobayashi K, Ouchida M, Tsuji T, Hanafusa H, Miyazaki M, Namba M, Shimizu N, Shimizu K: Reduced expression of the REIC/Dkk-3 gene by promoter- hypermethylation in human tumor cells. Gene 2002, 282(1-2):151-158.
60. Mu X, Zhao S, Pershad R, Hsieh TF, Scarpa A, Wang SW, White RA, Beremand PD, Thomas TL, Gan L, et al.: Gene expression in the developing mouse retina by EST sequencing and microarray analysis. Nucleic Acids Res 2001, 29(24):4983-4993.
61. Chowers I, Gunatilaka TL, Farkas RH, Qian J, Hackam AS, Duh E, Kageyama M, Wang C, Vora A, Campochiaro PA, et al.: Identification of novel genes preferentially expressed in the retina using a custom human retina cDNA microarray. Invest Ophthalmol Vis Sci 2003, 44(9):3732-3741.
62. Farjo R, Yu J, Othman MI, Yoshida S, Sheth S, Glaser T, Baehr W, Swaroop A: Mouse eye gene microarrays for investigating ocular development and disease. Vision Res 2002, 42(4):463-470.
63. Young RW: Cell proliferation during postnatal development of the retina in the mouse. Brain Res 1985, 353(2):229-239.
64. Barnstable CJ: Monoclonal antibodies which recognize different cell types in the rat retina. Nature 1980, 286(5770):231-235.
65. Yale University Microarray Core [http://info.med.yale.edu/wmkeck/ dna_arrays.htm]
66. Cluster analysis software [http://rana.lbl.gov/EisenSoftware.htm]
67. Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP, Weber G, Lee K, Fraioli RE, Cho SH, Yung R, Asch E, Ohno-Machado L, Wong WH, Cepko CL: Genomic analysis of mouse retinal development. PLoS Biol 2004, 2(9):E247. Table S2
68. Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP, Weber G, Lee K, Fraioli RE, Cho SH, Yung R, Asch E, Ohno-Machado L, Wong WH, Cepko CL: Genomic analysis of mouse retinal development. PLoS Biol 2004, 2(9):E247. Table S5
69. Li TR, White KP: Tissue-specific gene expression and ecdysone-regulated genomic networks in Drosophila. Dev Cell 2003, 5(1):59-72.