Gene Regulation by ATF3 in response to serine deprivation

The goal of this study is to identify genes that are regulated by activiating transcription factor (ATF3) in the cellular response to serine deprivation. Serine biosynthesis is crucial for cancer cells to proliferate and survival under serine-limiting conditions. We found that ATF3 expression induced by serine deprivation supports cancer cell growth. This RNA-seq study is thus designed to understand how ATF3 regulates serine biosynthesis in cells. The results indicate that ATF3 regulates the genes involved in the serine synthesis pathway. Overall design: ATF3-wildtype (wt) or -knockout (Ko) hTERT-RPE1 cells were cultured in the completed medium or serine/glycine-free medium for 8 h. Total RNAs were prepared from the cells and subjected to RNA-seq. There are 4 samples, each with a biological replicate. Therefore, Samples Wt0h1, Wt8h1, Ko0h1, and KO8h1 were from the same batch of treated cells, while Samples Wt0h2, Wt8h2, Ko0h2, and Ko8h2 were from a second batch of treated cells. These two batches of samples were from independent experiments carried out one week apart.