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Y.F. Leung, P. Ma, F. Emran, P. Grosu, B.A. Link, J.E. Dowling; A Genomic View Of Retinal Development And Differentiation In Zebrafish . Invest. Ophthalmol. Vis. Sci. 2006;47(13):2785.
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© ARVO (1962-2015); The Authors (2016-present)
A number of retinal development genes have been identified in zebrafish by forward and reverse genetic approaches. However, large–scale genomic research on zebrafish retinal development has been difficult because the embryos are so small. Methodology has been developed in our laboratory for isolating pure retinal tissue and extracting its total RNA from zebrafish embryos. The goal of the present study was to apply this methodology for the study of retinal development and differentiation in zebrafish using microarray analysis.
Embryonic retinas at 36 and 52 hours post–fertilization (hpf) were microdissected from wild type zebrafish and homozygous mutants of young (yng) in which retinal lamination, a terminal differentiation process, is disrupted due to a point mutation in a brahma–related gene (brg1). Stage–matched whole embryos were collected as a control. Gene expression levels in these samples were evaluated using an Affymetrix Zebrafish Genome Array with approximately 15,000 genes. A three–factor factorial design was utilized to investigate the effect of the mutation, change of time, change of tissue, and their interactions on gene expression. A gene was regarded as related to retinal differentiation or retinal development if the factorial analysis contrast’s q–value was significant and the fold change was greater than two. Selected candidate genes were validated with in situ hybridization data from wild–type embryos at the same developmental stage (zfin database – http://www.zfin.org).
Eight hundred and seventy seven genes were found to be significantly related to retinal differentiation. Among the retinal development genes, 823 genes were found to change in a time–dependent manner, and 2064 genes were differentially expressed in the retina. The temporal change of 28 out of 30 genes that were significantly related to retinal development and differentiation, and 13 out of 13 genes that were significantly suppressed in the retina matched in situ hybridization data.
This study has successfully identified a number of candidate genes that are potentially important for retinal development and differentiation. Further in situ hybridization on both wild–type and yng embryos, and gene knock–down experiments will provide functional insights on these candidate genes.
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