Retinal stem cell differentiation is orchestrated by transcription cascades, and is prone to be influenced by stress factors. While threshold radiation dose for human mental retardation is reported, the effects on retinal transcription factors are unknown. To elucidate the effects of low-dose radiation on retinal differentiation, stem cells were irradiated. Genome-wide gene expression and histone modification were observed. After a month, the expression of PAX6, an essential transcription factor for retinal ganglion cell, was increased by 30 mGy but decreased by 180 mGy. POU5F1, POU2F1, SOX2, and PAX6 were predicted to be involved in regulation of PAX6. Further, upstream of POU5F1/POU2F1/ SOX2 was detected. Altered Rho family could be responsible for activity of SRF/STAT3/RELA, which were upstream of POU2F1/SOX2. These cascades could contribute to the regulation of PAX6 and unstable retinal development under stressful environment. Identification of the hierarchical regulations in the differentiation will help elucidate the retinal cell maintenance.