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. 2020 Mar 20;111(5):1818–1828. doi: 10.1111/cas.14370

Figure 5.

Figure 5

Identification of activating transcription factor 3 (ATF3) target genes. A, Knockdown of ATF3 in Epstein‐Barr virus (EBV)‐infected MKN7 (MKN7_EB) cells. ATF3 was knocked down by shRNA lentivirus targeting ATF3 (shATF3). Western blot analysis showed marked decrease of ATF3 expression in the nucleus. Right, comparison of ratios of the intensity of ATF3 to that of lamin A in nucleus (n = 3). Values are shown as the mean ± SD. B, RNA sequencing analysis of gene expression alterations by knockdown of ATF3. Among the 659 genes neighboring possible peaks bound by ATF3, 96 genes were downregulated in MKN7_EB when ATF3 was knocked down (red dots). C, Gene set enrichment analysis (GSEA) for the 96 ATF3 target genes. The 96 ATF3 target genes were significantly enriched in the genes highly expressed in MKN7_EB (normalized enrichment score [NES] = 1.88, P < .001). D, Relationship with cancer hallmarks. Among the 96 ATF3 target genes, the top 30 genes showing higher expression in MKN7_EB in GSEA were extracted. They were frequently related with cancer hallmarks, such as evading growth suppressors, sustaining proliferative signaling, and resisting cell death. FPKM, fragments per kilobase of exon per million mapped sequence reads; shNON, control nontarget shRNA