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L. Hackler, Jr., H. Huang, Y. Yang, J. Qian, V. M. Canto-Soler, M. Mcnall, K. J. Wahlin, R. Adler, D. J. Zack; Transcription Factor Profiling of Individual Chick Embryo Photoreceptor Cells. Invest. Ophthalmol. Vis. Sci. 2008;49(13):4423. doi: https://doi.org/.
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© ARVO (1962-2015); The Authors (2016-present)
To assess how transcription factor (TF) regulatory networks differ between different photoreceptor subtypes, we have profiled individual chicken photoreceptors cells with a custom-made TF microarray.
750 candidate chicken TFs were identified by searching databases including TIGR and NCBI, and by homology comparison with mammalian TFs of interest. Due to the 3` bias of the generated single cell cDNA samples, array probes for the TFs were designed within 400 bp of the 3` end of the corresponding mRNAs. Individual cells were microcaptured from dissociated ED20 chicken retinas and processed as described by Wahlin et al (Mol Vis. 2004; J Comp Neurol, in press). 18 cells (6 rods, 6 red and 6 green cones) have been analyzed to date.
In general, each photoreceptor was found to express an individual visual pigment. Some TF genes showed expression exclusively in one or another subtype, while others were detected in several or all three subtypes. There was also significant variation in expression even among cells of the same subtype. Cluster analysis identified several groups of genes whose expression pattern tended to be specific for certain cellular subtypes. As expected, factors thought to be involved in rod-differentiation, such as Nr2e3 and MafA, were detected mostly in rods, albeit with cell to cell variation. Some TFs were preferentially expressed in cones in general, or in specific cone subtypes, but so far few if any genes have been identified that are specific for green cones. Homeobox genes seem to be over-represented among the differentially expressed TF genes. Among the genes with particularly interesting expression patterns were Baz1B, Ldb1, Islet-2, Brachyury and Lbh. 26 candidate genes were selected for further analysis by real time PCR and in situ hybridization, and this analysis is underway.
These studies demonstrate that photoreceptor TF transcriptome can be analyzed at the single cell level, and the specific results are providing insights into the combinatorial networks of TFs that determine patterns of photoreceptor gene expression.
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