Characterization of TFIIE-regulated genes by transcriptome analysis.

BACKGROUND/AIM: Previous studies on general transcription factor II E (GTF2E) showed that it is associated with certain groups of diseases, such as colon cancer and trichothiodystrophy, but the global effect of GTF2E on cellular processes is still not widely characterized. This study aimed to investigate and characterize the effect of GTF2E on the transcription level of genes and identify the cellular processes and diseases associated with GTF2E.

MATERIALS AND METHODS

The human colorectal carcinoma cell line HCT116 used in the study was transfected at a 30 nM concentration with siGTF2E1 or nontarget negative siRNA. After 72 h, cells were harvested and prepared for further analysis. A whole transcriptome analysis was performed on the HCT116 cell line obtained from the siGTF2E1 knockdown of the HCT116 cells (n = 3) and their nontarget negative siRNA controls (n = 3) using RNA sequencing. Cell viability was tested using an MTS assay.

RESULTS

Compared with the control group, 166 genes were identified at the time of the GTF2E1 knockdown and expressed differentially in the knockdown group, including 66 upregulated genes and 100 downregulated genes. One significantly enriched Gene Ontology term was identified, involving carbohydrate binding. One oncogene related to B cell chronic lymphocytic leukemia (B-CLL) was identified. Five genes associated with colon carcinoma were determined. Eleven genes involved in the development of atherosclerosis were identified. GTF2E1 knockdown caused a decrease in cell viability.

CONCLUSION

The GTF2E1 knockdown group exhibited an altered expression of multiple genes, some of which are related to the development of atherosclerosis, colon carcinoma, and B-CLL. This might shed light on the different regulatory effects of GTF2E and its association with certain diseases.