Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-6bf8c574d5-n2sc8 Total loading time: 0 Render date: 2025-03-09T15:21:09.345Z Has data issue: false hasContentIssue false

16 - Genomics

Published online by Cambridge University Press:  22 August 2009

By
Seth Blackshaw
Edited by
Evelyne Sernagor ,
Stephen Eglen ,
Bill Harris  and
Rachel Wong
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
Get access

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.

Type
Chapter
Information
Retinal Development , pp. 325 - 341
Publisher: Cambridge University Press
Print publication year: 2006

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

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, 431–7CrossRefGoogle ScholarPubMed
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, 579–89CrossRefGoogle ScholarPubMed
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, R17CrossRefGoogle ScholarPubMed
Blackshaw, S., Harpavat, S., Trimarchi, J.et al. (2004). Genomic analysis of mouse retinal development. PLoS Biol, 2, E247CrossRefGoogle ScholarPubMed
Boutros, M., Kiger, A. A., Armknecht, S.et al. (2004). Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science, 303, 832–5CrossRefGoogle ScholarPubMed
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, 559–68CrossRefGoogle ScholarPubMed
Brenner, S., Johnson, M., Bridgham, J.et al. (2000). Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol., 18, 630–4CrossRefGoogle ScholarPubMed
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, 589–95CrossRefGoogle ScholarPubMed
Cheng, J., Kapranov, P., Drenkow, J.et al. (2005). Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science, 308, 1149–54CrossRefGoogle ScholarPubMed
Chowers, I., Liu, D., Farkas, R. H.et al. (2003). Gene expression variation in the adult human retina. Hum. Mol. Genet., 12, 2881–93CrossRefGoogle ScholarPubMed
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, 5491–6CrossRefGoogle ScholarPubMed
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, 1009–19CrossRefGoogle ScholarPubMed
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, 409–13CrossRefGoogle ScholarPubMed
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, 95–141CrossRefGoogle ScholarPubMed
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, 917–25CrossRefGoogle ScholarPubMed
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, 5069–74CrossRefGoogle ScholarPubMed
Hackam, A. S., Bradford, R. L., Bakhru, R. N.et al. (2003). Gene discovery in the embryonic chick retina. Mol. Vis., 9, 262–76Google ScholarPubMed
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, 45 537–46CrossRefGoogle ScholarPubMed
Irizarry, R. A., Warren, D., Spencer, F.et al. (2005). Multiple-laboratory comparison of microarray platforms. Nat. Methods, 2, 345–50CrossRefGoogle ScholarPubMed
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, 850–4CrossRefGoogle ScholarPubMed
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, 14 326–31CrossRefGoogle ScholarPubMed
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, 547–57CrossRefGoogle Scholar
Leveillard, T., Mohand-Said, S., Lorentz, O.et al. (2004). Identification and characterization of rod-derived cone viability factor. Nat. Genet., 36, 755–9CrossRefGoogle ScholarPubMed
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, 541–52CrossRefGoogle ScholarPubMed
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, 301–10CrossRefGoogle ScholarPubMed
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, 1374–9CrossRefGoogle ScholarPubMed
MacNeil, M. A. and Masland, R. H. (1998). Extreme diversity among amacrine cells: implications for function. Neuron, 20, 971–82CrossRefGoogle ScholarPubMed
Margulies, M., Egholm, M., Altman, W. E.et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376–80CrossRefGoogle ScholarPubMed
Mears, A. J., Kondo, M. and Swain, P. K. (2001). Nrl is required for rod photoreceptor development. Nat. Genet., 29, 447–52CrossRefGoogle ScholarPubMed
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, e74CrossRefGoogle ScholarPubMed
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, 1197–210CrossRefGoogle ScholarPubMed
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, 77–94CrossRefGoogle ScholarPubMed
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, 657–700CrossRefGoogle ScholarPubMed
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, 427–31CrossRefGoogle ScholarPubMed
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, 13 266–71CrossRefGoogle ScholarPubMed
Shendure, J., Porreca, G. J., Reppas, N. B.et al. (2005). Accurate multiplex polony sequencing of an evolved bacterial genome. Science, 309(5741), 1728–32CrossRefGoogle ScholarPubMed
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, 63–76CrossRefGoogle ScholarPubMed
Tietjen, I., Rihel, J. M., Cao, Y.et al. (2003). Single-cell transcriptional analysis of neuronal progenitors. Neuron, 38, 161–75CrossRefGoogle ScholarPubMed
Tomancak, P., Beaton, A., Weiszmann, R.et al. (2002). Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol, 3, RESEARCH0088CrossRefGoogle ScholarPubMed
Velculescu, V. E., Zhang, L., Vogelstein, B. and Kinzler, K. W. (1995). Serial analysis of gene expression. Science, 270, 484–7CrossRefGoogle ScholarPubMed
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 ScholarPubMed
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, 1487–503CrossRefGoogle ScholarPubMed
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, 42 211–20CrossRefGoogle 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, 351–60CrossRefGoogle ScholarPubMed
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, 135–40CrossRefGoogle ScholarPubMed

Save book to Kindle

To save this book to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

  • Genomics
    • By Seth Blackshaw, 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
  • Edited by Evelyne Sernagor, University of Newcastle upon Tyne, Stephen Eglen, University of Cambridge, Bill Harris, University of Cambridge, Rachel Wong, Washington University, St Louis
  • Book: Retinal Development
  • Online publication: 22 August 2009
  • Chapter DOI: https://doi.org/10.1017/CBO9780511541629.018
Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

  • Genomics
    • By Seth Blackshaw, 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
  • Edited by Evelyne Sernagor, University of Newcastle upon Tyne, Stephen Eglen, University of Cambridge, Bill Harris, University of Cambridge, Rachel Wong, Washington University, St Louis
  • Book: Retinal Development
  • Online publication: 22 August 2009
  • Chapter DOI: https://doi.org/10.1017/CBO9780511541629.018
Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

  • Genomics
    • By Seth Blackshaw, 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
  • Edited by Evelyne Sernagor, University of Newcastle upon Tyne, Stephen Eglen, University of Cambridge, Bill Harris, University of Cambridge, Rachel Wong, Washington University, St Louis
  • Book: Retinal Development
  • Online publication: 22 August 2009
  • Chapter DOI: https://doi.org/10.1017/CBO9780511541629.018
Available formats
×