ZKSCAN3 in the transcriptional regulation of autophagy in human cells

Transcription factors can affect autophagy activity by promoting or inhibiting the expression of autophagy and lysosomal related genes. As a zinc finger family DNA-binding protein, ZKSCAN3 has been reported to function as a transcriptional repressor of autophagy, silencing of which can induced autophagy and promoted lysosome biogenesis in cancer cells. However, the studies in Zkscan 3 knockout mice showed that the deficiency of Zkscan3 did not induce autophagy and in-crease lysosome biogenesis. In order to further explore the role of ZKSCAN3 in the transcriptional regulation of autophagy in human cells, we generated ZKSCAN3 knockout HK-2 and Hela cells by CRISPR/Cas9 system and analyzed the differences in gene expression between ZKSCAN3 deleted cells and non-deleted cells through fluorescence quantitative PCR, Western blot and transcriptome sequencing, with special attention to the differences in gene expression of autophagy and lysosomal biogenesis. We found that ZKSCAN3 is not an essential regulator of autophagic or lysosomal gene expression, as the absence ZKSCAN3 had no significantly effect on the expression of autophagy or lysosomal genes. Overall design: To further and comprehensively characterize the transcriptome-wide transcriptional alterations caused by ZKSCAN3 deficiency, we performed whole transcriptome sequencing in WT and ZKSCAN3-KO cells. In HK-2 cells, we found that deletion of ZKSCAN3 resulted in 1408 genes significantly down regulation and 1270 genes significantly up regulation. Whereas in Hela cells, ZKSCAN3 deficiency led to 894 significantly genes down regulation and 617 genes significantly up regulation. Of these significantly differentially expressed genes, 161 were present in both HK-2 and Hela ZKSCAN3-KO cells.