Kaiso (ZBTB33) engages with non-canonical binding motifs to regulate DNA damage responses in breast cancer cells

In breast cancer, nuclear localization of Kaiso (ZBTB33), a dual specificity transcription factor, is a hallmark of high grade ductal-type carcinomas, especially in estrogen receptor negative disease. Regulation of gene expression by Kaiso is orchestrated via its engagement to distinct Kaiso binding sequence (KBS) motifs defined as canonical (cKBS; TCCTGCNA ) or CG-containing palindromic KBS (CG-KBS; TCTCGCGAGA ), depending on context. While there exists a clinical connection between localization of Kaiso expression and breast cancer, it remains unclear how Kaiso controls bi-modal canonical versus noncanonical transcriptional modulation. Here, we have combined Kaiso-specific chromatin immunoprecipitation (ChIP) and Kaiso-Dam methyltransferase identification (Dam-ID) approaches to map genomic Kaiso binding sites in breast cancer cells. We find that Kaiso mostly occupies the non-canonical CG-KBS sites in transcriptionally active and hypo-methylated (H3K4me3 and H3K27Ac enriched) promoter regions. Noncanonical CG-KBS targets are actively transcribed and linked to fast biological processes such as metabolism, cell cycle regulation and DNA damage repair. Functionally, we show that Kaiso expression is essential to prevent DNA damage in breast cancer cells. Loss of Kaiso leads to reduced expression of DNA damage response gene expression and treatment with the chemotherapeutic agent cisplatin leads to overt accumulation of DNA damage in cells devoid of Kaiso. Our data thus favor a model in which Kaiso promotes fast transcriptional activation of key cellular processes in cancer cells through binding of its non-canonical consensus site.