Figure 6

Abolishing Sirt6 expression impacts transcriptome responses to TNF-α stimulation in colonic epithelial cells. YAMC cells were transfected with Sirt6 siRNA as described in Materials and Methods. Forty-eight hours after transfection, cells were cultured with medium containing TNF-α (100 ng/mL) or medium alone for an additional 24 h. At the end of treatment, cells were harvested for RNA extraction, followed by RNA-seq transcriptome analysis. (A) Differential gene expression analysis (log2 ratio ≥ 0.415 fold change) was carried out to determine genes that were altered in YAMC cells transfected with siSirt6 compared with scramble siRNA (siControl) under either naïve condition (purple circle) or TNF-α stimulation (orange circle). Venn diagram demonstrates the number of shared or specific genes of each group of cells. (B) Analysis of Gene Ontology (GO) terms to identify enriched GO terms associated with Sirt6 silencing. The genes from each category in the Venn diagram were subjected to GO analysis to identify GO terms enrichment using GESA software. Results are illustrated as a scatterplot using the REViGO visualization tool. The circle size is proportional to the frequency of the GO term, while the color represents the normalized enrichment score generated from GESA (red: higher; blue: lower). (C) The genes from each category in the Venn diagram were further subjected to hierarchical cluster analysis of common differentially expressed genes associated with Sirt6 silencing in naïve and TNF-α stimulation conditions.