Genomics

doi:10.1017/CBO9780511541629.018

16 - Genomics

Published online by Cambridge University Press: 22 August 2009

Edited by

Bill Harris and

Seth Blackshaw: Affiliation:
Department of Neuroscience and Center for High-Throughput Biology, Johns Hopkins University School of Medicine, BRB 329, 773 N. Broadway Avenue, Baltimore, MD 21287, USA
Evelyne Sernagor: Affiliation:
University of Newcastle upon Tyne
Stephen Eglen: Affiliation:
University of Cambridge
Bill Harris: Affiliation:
University of Cambridge
Rachel Wong: Affiliation:
Washington University, St Louis

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Summary

Introduction

Many distinct processes occur during the course of retinal development. These range from regulation of mitosis and cell fate specification to axon outgrowth and targeting, dendritogenesis and terminal differentiation of different cell types. Since all of these events require changes in gene expression, it follows that global analysis of changes in transcription during development should reveal the identity of many of the genes that mediate these processes. This has been the logic underlying genomic studies of the developing retina, which have so far been undertaken by a number of groups.

The retina has many features that make it well suited to genomic studies. In both invertebrates and vertebrates, the major cell subtypes in the retina are easily distinguished by both molecular and morphological criteria. Compared with other parts of the nervous system, the number of distinct retinal cell subtypes is quite limited and, in both rodents and flies, photoreceptors make up the majority of retinal cells. The birth order of each major cell type is known, and in vertebrates these generation times are distinct and only partially overlapping. Cell types are readily identified by spatial position, which renders in situ hybridization-based verification of primary expression data relatively straightforward. Interpretation of expression data in model organisms is also aided by previous work that has already identified large numbers of genes that are selectively expressed in specific cell types of the mature and differentiating retina. Finally, a wealth of mutations that disrupt different aspects of retinal development are available.

Information

Type: Chapter
Information: Retinal Development , pp. 325 - 341

DOI: https://doi.org/10.1017/CBO9780511541629.018 [Opens in a new window]

Publisher: Cambridge University Press

Print publication year: 2006

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References

Berns, K., Hijmans, E. M., Mullenders, J.et al. (2004). A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature, 428, 431–7CrossRef Google Scholar PubMed

Blackshaw, S., Fraioli, R. E., Furukawa, T. and Cepko, C. L. (2001). Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes. Cell, 107, 579–89CrossRef Google Scholar PubMed

Blackshaw, S., Kuo, W. P., Park, P. J.et al. (2003). MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues. Genome Biol., 4, R17CrossRef Google Scholar PubMed

Blackshaw, S., Harpavat, S., Trimarchi, J.et al. (2004). Genomic analysis of mouse retinal development. PLoS Biol, 2, E247CrossRef Google Scholar PubMed

Boutros, M., Kiger, A. A., Armknecht, S.et al. (2004). Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science, 303, 832–5CrossRef Google Scholar PubMed

Bowne, S. J., Sullivan, L. S., Blanton, S. H.et al. (2002). Mutations in the inosine monophosphate dehydrogenase 1 gene (IMPDH1) cause the RP10 form of autosomal dominant retinitis pigmentosa. Hum. Mol. Genet., 11, 559–68CrossRef Google Scholar PubMed

Brenner, S., Johnson, M., Bridgham, J.et al. (2000). Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol., 18, 630–4CrossRef Google Scholar PubMed

Cepko, C. L., Austin, C. P., Yang, X., Alexiades, M. and Ezzeddine, D. (1996). Cell fate determination in the vertebrate retina. Proc. Natl. Acad. Sci. U. S. A., 93, 589–95CrossRef Google Scholar PubMed

Cheng, J., Kapranov, P., Drenkow, J.et al. (2005). Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science, 308, 1149–54CrossRef Google Scholar PubMed

Chowers, I., Liu, D., Farkas, R. H.et al. (2003). Gene expression variation in the adult human retina. Hum. Mol. Genet., 12, 2881–93CrossRef Google Scholar PubMed

Diaz, E., Yang, Y. H., Ferreira, T.et al. (2003). Analysis of gene expression in the developing mouse retina. Proc. Natl. Acad. Sci. U. S. A., 100, 5491–6CrossRef Google Scholar PubMed

Dorrell, M. I., Aguilar, E., Weber, C. and Friedlander, M. (2004). Global gene expression analysis of the developing postnatal mouse retina. Invest. Ophthalmol. Vis. Sci., 45, 1009–19CrossRef Google Scholar PubMed

Evans, S. J., Datson, N. A., Kabbaj, M. (2002). Evaluation of Affymetrix Gene Chip sensitivity in rat hippocampal tissue using SAGE analysis. Serial Analysis of Gene Expression. Eur. J. Neurosci., 16, 409–13CrossRef Google Scholar PubMed

Gawantka, V., Pollet, N., Delius, H.et al. (1998). Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning. Mech. Dev., 77, 95–141CrossRef Google Scholar PubMed

Gong, S., Zheng, C., Doughty, M. L.et al. (2003). A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature, 425, 917–25CrossRef Google Scholar PubMed

Gustincich, S., Contini, M., Gariboldi, M.et al. (2004). Gene discovery in genetically labeled single dopaminergic neurons of the retina. Proc. Natl. Acad. Sci. U. S. A., 101, 5069–74CrossRef Google Scholar PubMed

Hackam, A. S., Bradford, R. L., Bakhru, R. N.et al. (2003). Gene discovery in the embryonic chick retina. Mol. Vis., 9, 262–76Google Scholar PubMed

Haeseleer, F., Jang, G. F., Imanishi, Y.et al. (2002). Dual-substrate specificity short chain retinol dehydrogenases from the vertebrate retina. J. Biol. Chem., 277, 45 537–46CrossRef Google Scholar PubMed

Irizarry, R. A., Warren, D., Spencer, F.et al. (2005). Multiple-laboratory comparison of microarray platforms. Nat. Methods, 2, 345–50CrossRef Google Scholar PubMed

Janecke, A. R., Thompson, D. A., Utermann, G.et al. (2004). Mutations in RDH12 encoding a photoreceptor cell retinol dehydrogenase cause childhood-onset severe retinal dystrophy. Nat. Genet., 36, 850–4CrossRef Google Scholar PubMed

Katsanis, N., Worley, K. C., Gonzalez, G., Ansley, S. J. and Lupski, J. R. (2002). A computational/functional genomics approach for the enrichment of the retinal transcriptome and the identification of positional candidate retinopathy genes. Proc. Natl. Acad. Sci. U. S. A., 99, 14 326–31CrossRef Google Scholar PubMed

Kennan, A., Aherne, A., Palfi, A.et al. (2002). Identification of an IMPDH1 mutation in autosomal dominant retinitis pigmentosa (RP10) revealed following comparative microarray analysis of transcripts derived from retinae of wild-type and Rho(−/−) mice. Hum. Mol. Genet., 11, 547–57CrossRef Google Scholar

Leveillard, T., Mohand-Said, S., Lorentz, O.et al. (2004). Identification and characterization of rod-derived cone viability factor. Nat. Genet., 36, 755–9CrossRef Google Scholar PubMed

Li, J. B., Gerdes, J. M., Haycraft, C. J.et al. (2004). Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene. Cell, 117, 541–52CrossRef Google Scholar PubMed

Livesey, F. J., Furukawa, T., Steffen, M. A., Church, G. M. and Cepko, C. L. (2000). Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. Curr. Biol., 10, 301–10CrossRef Google Scholar PubMed

Livesey, F. J., Young, T. L. and Cepko, C. L. (2004). An analysis of the gene expression program of mammalian neural progenitor cells. Proc. Natl. Acad. Sci. U. S. A., 101, 1374–9CrossRef Google Scholar PubMed

MacNeil, M. A. and Masland, R. H. (1998). Extreme diversity among amacrine cells: implications for function. Neuron, 20, 971–82CrossRef Google Scholar PubMed

Margulies, M., Egholm, M., Altman, W. E.et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376–80CrossRef Google Scholar PubMed

Mears, A. J., Kondo, M. and Swain, P. K. (2001). Nrl is required for rod photoreceptor development. Nat. Genet., 29, 447–52CrossRef Google Scholar PubMed

Mecham, B. H., Klus, G. T., Strovel, J.et al. (2004). Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res., 32, e74CrossRef Google Scholar PubMed

Mu, X., Beremand, P. D., Zhao, S.et al. (2004). Discrete gene sets depend on POU domain transcription factor Brn3b/Brn-3.2/POU4f2 for their expression in the mouse embryonic retina. Development, 131, 1197–210CrossRef Google Scholar PubMed

Neidhardt, L., Gasca, S., Wertz, K.et al. (2000). Large-scale screen for genes controlling mammalian embryogenesis, using high-throughput gene expression analysis in mouse embryos. Mech. Dev., 98, 77–94CrossRef Google Scholar PubMed

Pacione, L. R., Szego, M. J., Ikeda, S., Nishina, P. M. and McInnes, R. R. (2003). Progress toward understanding the genetic and biochemical mechanisms of inherited photoreceptor degenerations. Annu. Rev. Neurosci., 26, 657–700CrossRef Google Scholar PubMed

Paddison, P. J., Silva, J. M., Conklin, D. S.et al. (2004). A resource for large-scale RNA-interference-based screens in mammals. Nature, 428, 427–31CrossRef Google Scholar PubMed

Pritchard, C. C., Hsu, L., Delrow, J. and Nelson, P. S. (2001). Project normal: defining normal variance in mouse gene expression. Proc. Natl. Acad. Sci. U. S. A., 98, 13 266–71CrossRef Google Scholar PubMed

Shendure, J., Porreca, G. J., Reppas, N. B.et al. (2005). Accurate multiplex polony sequencing of an evolved bacterial genome. Science, 309(5741), 1728–32CrossRef Google Scholar PubMed

Thut, C. J., Rountree, R. B., Hwa, M. and Kingsley, D. M. (2001). A large-scale in situ screen provides molecular evidence for the induction of eye anterior segment structures by the developing lens. Dev. Biol., 231, 63–76CrossRef Google Scholar PubMed

Tietjen, I., Rihel, J. M., Cao, Y.et al. (2003). Single-cell transcriptional analysis of neuronal progenitors. Neuron, 38, 161–75CrossRef Google Scholar PubMed

Tomancak, P., Beaton, A., Weiszmann, R.et al. (2002). Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol, 3, RESEARCH0088CrossRef Google Scholar PubMed

Velculescu, V. E., Zhang, L., Vogelstein, B. and Kinzler, K. W. (1995). Serial analysis of gene expression. Science, 270, 484–7CrossRef Google Scholar PubMed

Yoshida, S., Yashar, B. M., Hiriyanna, S. and Swaroop, A. (2002). Microarray analysis of gene expression in the aging human retina. Invest. Ophthalmol. Vis. Sci., 43, 2554–60Google Scholar PubMed

Yoshida, S., Mears, A. J., Friedman, J. S.et al. (2004). Expression profiling of the developing and mature Nrl−/− mouse retina: identification of retinal disease candidates and transcriptional regulatory targets of Nrl. Hum. Mol. Genet., 13, 1487–503CrossRef Google Scholar PubMed

Yu, J., He, S., Friedman, J. S.et al. (2004a). Altered expression of genes of the Bmp/Smad and Wnt/calcium signaling pathways in the cone-only Nrl−/− mouse retina, revealed by gene profiling using custom cDNA microarrays. J. Biol. Chem., 279, 42 211–20CrossRef Google Scholar

Yu, J., Mears, A. J., Yoshida, S.et al. (2004b). From disease genes to cellular pathways: a progress report. Novartis Found. Symp., 255, 147–60; discussion 160–4, 177–8Google Scholar

Zhang, J., Gray, J., Wu, L.et al. (2004). Rb regulates proliferation and rod photoreceptor development in the mouse retina. Nat. Genet., 36, 351–60CrossRef Google Scholar PubMed

Zheng, L., Liu, J., Batalov, S.et al. (2004). An approach to genomewide screens of expressed small interfering RNAs in mammalian cells. Proc. Natl. Acad. Sci. U. S. A., 101, 135–40CrossRef Google Scholar PubMed