Transcriptomes analysis for the regulation of Z36 induced autophagy in HeLa cell death

Z36 is a small molecule that induces Beclin1-dependent autophagy and autophagic cell death in HeLa cells. This is different from the typical autophagy induced by Rapamycin, which plays a protective role for cells. To gain insights into the regulation of autophagy in cell death by Z36, high-throughput RNA-sequencing were performed on HeLa cells treated with DMSO (as control), Z36 and Rapamycin. Two biological replaces were collected for each of the three conditions. The sequencing generated more than 30 million reads for each sample. RNA-seq data showed that there were about 3000 DEGs with over 2 folds changes (|log2 (fold change)| > 1 & P value < 0.05) in Z36 treated cells versus those of DMSO. On the contrary, there were only 200 DEGs for cells treated with Rapamycin. Noteworthily, expression levels of autophagic genes were significantly changed in Z36 treated cells, and the change pattern was different from Rapamycin treated ones. 8 of the ATG genes were up-regulated for more than 2 folds (log2 > 1) after Z36 treatment, while Rapa only caused small changes for the ATG genes, with the highest log2 change of 0.7. These study indicate that Z36 leads to significant modulation of a large number of genes at transcriptional level. mRNA profiles of HeLa cells treated with DMSO (as control), Rapamycin (Rapa) and Z36 were generated by deep sequencing, in two biological replaces(1 and 3), using Illumina Hiseq 2000 Sequencing System