Spatial Organization of Chromatin of ZEB1 Gene Promoter Region in Pancreatic Ductal Adenocarcinoma Cells

Pancreatic Ductal AdenoCarcinoma (PDAC) is one of the most therapy-resistant tumors. Cultured cells originating from different stages of PDAC development are characterized by different levels of expression of a number of transcription factors. In particular, poorly differentiated high-grade PDAC cells are characterized by increased expression of ZEB1 gene encoding multifunctional transcription factor ZEB1, one of the main regulators of epithelial-mesenchymal transition. By the method of Circular Chromosome Conformation Capture (4C-seq) we studied the spatial organization of chromatin of regulatory region of ZEB1 gene in cultures of highly differentiated PDAC cells (Capan2) with low level of ZEB1 expression and poorly differentiated PDAC MIA PaCa2 cells with a high level of expression of this gene, and compared it with the chromatin organization of KLF5 gene. The number and distribution of contacts of the ZEB1 regulatory region with other chromatin regions are similar in these cell types and differ significantly from the pattern of distribution of contacts characteristic for KLF5 gene studied earlier. In Capan2 cells, the contacts of the regulatory region of the ZEB1 gene are tend to locate in regions with an increased level of H3K27ac modification, whereas in MIA PaCa2 cells these contacts are predominantly located in regions with a decreased level of H3K27ac. Consequently, the probability of contact of distant chromatin regions is primarily determined not by the degree of chromatin openness/activity of this region. To explain the data obtained, we assumed that the main regulator of the ZEB1 gene transcription level in the studied cells is a transcriptional repressor, whereas for the KLF5 gene main regulator is a transcriptional activator. According to a number of properties, one of the possible candidates for the role of this repressor may be the product of the ZNF438 gene. In addition, we have characterized a number of regions in contact with the ZEB1 promoter that are specific for MIA PaCa2 cells and contain potential regulators of this gene activity.