Synapsin I and synaptophysin are major proteins of small synaptic vesicles. In neurons the transcriptional repressor REST is a major regulator of synapsin I and synaptophysin gene transcription. Gene regulation by REST is influenced by the configuration of the chromatin and cell type specific variations have been observed. Here, we have investigated the regulation of the synapsin I and synaptophysin genes in R28 retinal precursor cells. Chromatin immunoprecipitation experiments revealed that both genes are embedded in open chromatin in R28 retinal precursor cells. In contrast, in fibroblasts the synapsin I and synaptophysin genes are found in nucleosomes that carried an epigenetic marker that is linked to a condensed form of chromatin and gene silencing. Synapsin I and synaptophysin gene expression in retinal precursor cells was enhanced following inhibition of histone deacetylase activity, indicating that these genes are regulated via histone acetylation/deacetylation in R28 cells. Inhibition of histone deacetylase activity did not induce synapsin I and synaptophysin expression in fibroblasts, indicating that these genes are silenced in this cell type in a histone acetylation/deacetylation-independent manner. Moreover, elevated levels of synapsin I and synaptophysin mRNA were found in retinal precursor cells that expressed a mutant of REST that activated gene transcription. In contrast, the ribeye gene, encoding a major structural protein of synaptic ribbons, was neither regulated by histone acetylation/deacetylation nor by the REST mutant in retinal precursor cells. These data reveal that the synapsin I and synaptophysin genes are bona fide target genes for REST in R28 retinal precursor cells.