Fig. 6

Co-localization of ATF3 and p53 in genomic sites regulates gene expression in the DNA damage response. a Venn diagram showing the overlap between ATF3 peaks and p53 peaks under the DNA damage condition. b Genome browser views of p53 binding to several well-characterized p53 target genes. c Binding of p53 to indicated sites was validated by independent ChIP-qPCR assays. d Genome browser views of co-localization of ATF3 and p53 in representative genomic sites. e ATF3 and p53 were co-localized in genomic sites as demonstrated by re-ChIP assays. HCT116 cells treated with 1.5 μM of CPT for 4 h were first subjected to ChIP using the ATF3 antibody. The chromatin precipitated by the ATF3 antibody was then eluted from agarose beads, and subjected to the second round of ChIP using the p53 antibody. qPCR assays were used to quantitate re-ChIPed DNA. f Venn diagram showing the overlap of p53-binding sites containing the p53 motif or the ATF3 motif. g The ATF3 peak score correlated with the p53 peak score in the sites co-localized by ATF3 and p53. h ATF3 binding was often decreased in p53-knockout cells. p53-wildtype and knockout (p53-KO) HCT116 cells were subjected to ChIP-qPCR to measure binding of ATF3 to the indicated sites. i p53 binding was decreased in ATF3-knockout cells. ATF3-wildtype and knockout (ATF3-KO) HCT116 cells were subjected to ChIP-qPCR to measure binding of p53 to the indicated sites. j Expression of p53 target genes was repressed in ATF3-KO cells. Indicated cells were treated with 1.5 μM of CPT for qRT-PCR assays. ATF3 binding to these genes before and after CPT treatments in ATF3-WT cells were shown in Additional file 1: Figure S3