Cooptation of tandem DNA repeats for the control of epithelial-to-mesenchymal transition [ChIP-Seq]

During normal or pathological epithelial-to-mesenchymal transition, epithelium-specific gene expression is shut down, with the DNA-binding factor ZEB1 acting as a master suppressor of epithelial identity. Here, we show that ZEB1 occupies primate-specific tandem repeats (TRs) harboring dozens of copies of its DNA-binding motif and located within genomic loci relevant for epithelial identity. Deletion of one such repeat in a quasi-mesenchymal human cancer cell line induced the reacquisition of epithelial features and phenocopied the effects of ZEB1 gene deletion. Since ZEB1 binds clustered motifs in a non-cooperative manner, changes in its nuclear concentration enable graded adjustments of TR occupancy, thus fine-tuning repression level. In addition, high motif density in TRs allows ZEB1 binding (and shutdown of epithelial programs) despite differences in chromatin organization and accessibility among epithelial cell types. Chromatin from human pancreatic ductal adenocarcinoma cell line and human colon carcinoma cell line was immunoprecipitated with anti- ZEB1 or anti-CTCF antibodies and subjected to multiparallel sequencing. Experiments were carried out in unmodified cells (MiaPaCa2 and RKO) and genome edited clonal MiaPaCa2 cells (MiaPaCa2.delta-Repeats and the respective control MiaPaCa2.WT).