May 2007
Volume 48, Issue 13
ARVO Annual Meeting Abstract  |   May 2007
Gene Profiling and Patterning in the Developing Mouse Retina: Microarray, Q-PCR and Bioinformatics
Author Affiliations & Notes
  • W. Xiao
    University of Houston, Houston, Texas
  • A. Giddabasappa CS
    University of Houston, Houston, Texas
  • B. Xu
    University of Houston, Houston, Texas
  • S. Mukherjee
    University of Houston, Houston, Texas
  • S. Chaney
    University of Houston, Houston, Texas
  • M. Brooks
    University of Michigan, Ann Arbor, Michigan
  • A. Swaroop
    University of Michigan, Ann Arbor, Michigan
  • D. A. Fox
    University of Houston, Houston, Texas
  • Footnotes
    Commercial Relationships W. Xiao, None; A. Giddabasappa CS, None; B. Xu, None; S. Mukherjee, None; S. Chaney, None; M. Brooks, None; A. Swaroop, None; D.A. Fox, None.
  • Footnotes
    Support NIH Grants ES012482, EY007551, EY11115 and Sramek Foundation.
Investigative Ophthalmology & Visual Science May 2007, Vol.48, 3783. doi:
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    • Get Citation

      W. Xiao, A. Giddabasappa CS, B. Xu, S. Mukherjee, S. Chaney, M. Brooks, A. Swaroop, D. A. Fox; Gene Profiling and Patterning in the Developing Mouse Retina: Microarray, Q-PCR and Bioinformatics. Invest. Ophthalmol. Vis. Sci. 2007;48(13):3783.

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      © ARVO (1962-2015); The Authors (2016-present)

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Purpose:: During the late embryonic (E) and early postnatal (PN) period of mouse retinal development, late-born retinal progenitor cells (RPCs: rods, bipolar cells and Müller glial cells) proliferate, differentiate and migrate and retinal synaptic connections are initiated. This study determined the pattern of gene expression and signaling pathways that contribute to retinal development during this period.

Methods:: Retinal RNA from four independent replicates of E16.5, E18.5, PN2, PN6 and PN10 C57BL/6 mice was isolated. Gene expression was analyzed by Affymetrix GeneChip® Mouse Genome 430 2.0 Array and validated by quantitative real-time PCR (qPCR). Following a stringent threshold procedure and statistical analyses (ANOVA), genes with significant changes in expression were identified. These genes were sorted into clusters based on their differential pattern and level of expression during development using K-means clustering analysis. For Gene Ontology (GO) analysis, NIH DAVID was used.

Results:: Using these techniques, we identified 4,899 differentially expressed genes. Five distinct cluster patterns were obtained. Clusters 1, 2 and 3 contained ~85% of the genes. Genes in clusters 2, 3 and 5 were up-regulated and those in clusters 1 and 4 were down-regulated from E16.5 to PN10. Clusters 3 and 5 contained genes and transcription factors specific for late-born rod photoreceptors and bipolar cells, whereas cluster 1 contained genes presumed to be selective for Müller glial cells. The expression level of 22 genes, selected from these five clusters, was confirmed at each age by qPCR. GO analysis showed that the majority of genes regulating the cell cycle were dramatically down-regulated from E16.5 to PN10, whereas those regulating cell growth, cell metabolism and visual function were significantly up-regulated from E16.5 to PN10.

Conclusions:: These results provide additional insight into the differential regulation of mouse gene expression during development and particularly those of late-born RPCs. Some novel genes and molecular pathways involved in the regulation of cell cycle, cell fate and visual function also were identified during this period of retinal development. Moreover, this data will be used to determine the molecular mechanisms underlying the proliferation and increase of late-born rod and bipolar cells observed in the adult retina of gestationally lead-exposed mice (Giddabasappa et al., ARVO 2006, 2007).

Keywords: retina: distal (photoreceptors, horizontal cells, bipolar cells) • development • gene/expression 

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