The effect of doxycycline-induced expression of host-cell-factor 2 (HCF-2) proteins on the global gene expression in HEK-293 cells

Here we study the effect of doxycycline induced expression of HCF-2 (the host-cell-factor 2) proteins - HCF-2WT and its mutant HCF-2Fn3nc* on the global gene expression in HEK-293 cells. We identified 7175 genes that were differentially expressed after day 1 in any of the HCF-2WT or HCF-2Fn3nc* samples (log2 (fold change) > 0.5 or < -0.5 and FDR < 0.05). The maximal gene-expression changes over time were on day 6 in each case, with more genes up-regulated (2199 vs. 1241) in the HCF-2WT samples and more genes down-regulated (2513 vs. 1555) in the HCF-2Fn3nc* samples after six days compared to day 1. Notably, there was little overlap between the genes affected by the induced synthesis of HCF-2WT or HCF-2Fn3nc* indicating that the HCF-2Fn3nc* mutation seriously disrupts HCF-2 function. In total, we found that up-regulated genes in HCF-2WT were associated with developmental and morphogenesis programs induction, whereas down-regulated genes were linked to the inhibition of cellular metabolism and proliferation. Overall design: Flag-Cherry-HCF-2-encoding Flp-In T-Rex-HEK-293 cells were induced in duplicates with doxycycline (1ul/ml) and samples were collected 1, 2, 4, and 6 days post induction (16 samples in total).