Transcriptomic profiling of human HAP1 cells before and after nutrient deprivation

Autophagy is a lysosomal degradation pathway critical for maintaining cellular homeostasis and viability, and is predominantly regarded as a rapid and dynamic cytoplasmic process. To improve our understanding of the transcriptional and epigenetic events associated with autophagy, we performed genome-wide transcriptomic and epigenomic profiling after nutrient deprivation in human wildtype and autophagy-deficient cells. We observed that nutrient deprivation leads to the transcriptional induction of numerous autophagy-associated genes. These transcriptional changes are reflected at the epigenetic level (H3K4me3, H3K27ac, and H3K56ac) and are independent of autophagic flux. Overall design: Transcriptome analysis of HAP1 WT, ATG7KO and RB1CC1KO cells with and without amino acid + serum starvation (6h EBSS). For each sample 3 replicates were included.