RNA-seq analysis of FTO depletion effect on gene expression during the type I IFN response

FTO is an m6A and m6Am demethylase protein that regulates many biological processes through modulation of RNA biology. The goal of this experiment was to determine the role of FTO in regulation of gene expressoin during the type I interferon response. We found that FTO suppresses the expression of a subset of interferon-stimulated genes at the mRNA level. In follow-up experiment, we determined that FTO regulates the transcription of these ISGs through suppression of activation of the transcription factor STAT3. Overall design: Huh7 cells were seeded in 10-cm plates and treated with siRNAs (non-targeting control; CTRL or FTO) for 36 hours, followed by IFN-b treatment at 50 units/mL or mock treatment for 8 hours. RNA was extracted and RNA-seq was performed. 3 biological replicates were performed for each condition.