ChIP-Seq analysis to identify direct binding of ZNF165

We found that the cancer testis antigen, ZNF165, is required for viability and modulates TGFß-induced gene expression in mesenchymal, Claudin-Low, TNBC. To begin to define ZNF165''s role in TNBC tumorigenesis, we performed ChIP-Seq analysis in the mesenchymal TNBC tumor derived cell line, WHIM12, stably expressing ZNF165-V5. This analysis uncovered 381 peaks associated with 410 genes and included TGFß target genes, SMURF2 and SMAD, that promote negative TGFß feedback regulation. Our results provide insight into how ZNF165 globally modulates TGFß signaling and nominates ZNF165 candidate gene targets. Overall design: WHIM12 cells were stably infected ZNF165-V5 were grown to 75% confluency. Chromatin was isolated, sonicated and immunoprecipitated using a V5 antibody. Purifed ChIP-ed DNA was then sequence, aligned to hg19 and HOMER was justed to identify significantly enriched peaks.