cis-Regulatory Circuits Regulating NEK6 Kinase Overexpression in Transformed B Cells Are Super-Enhancer Independent

Alterations in distal regulatory elements that control gene expression underlie many diseases, including cancer. Epigenomic analyses of normal and diseased cells have produced correlative predictions for connections between dysregulated enhancers and target genes involved in pathogenesis. However, with few exceptions, these predicted cis-regulatory circuits remain untested. Here, we dissect cis-regulatory circuits that lead to overexpression of NEK6, a mitosis-associated kinase, in human B cell lymphoma. We find that only a minor subset of predicted enhancers is required for NEK6 expression. Indeed, an annotated super-enhancer is dispensable for NEK6 overexpression and for maintaining the architecture of a B cell-specific regulatory hub. A CTCF cluster serves as a chromatin and architectural boundary to block communication of the NEK6 regulatory hub with neighboring genes. Our findings emphasize that validation of predicted cis-regulatory circuits and super-enhancers is needed to prioritize transcriptional control elements as therapeutic targets. [Display omitted] •NEK6, a mitotic kinase gene, is overexpressed in specific types of B cell lymphoma•Super-enhancer is dispensable for elevated NEK6 expression in transformed B cells•Genome engineering reveals regulatory elements for NEK6 cis-regulatory circuits•Need for rigorous testing of predicted cis-regulatory circuits and super-enhancers Huang et al. functionally dissect cis-regulatory circuits associated with NEK6, a mitotic kinase overexpressed in B cell lymphoma. Only a subset of predicted enhancers and CTCF sites cooperatively constructs the regulatory hub of NEK6. A super-enhancer is completely dispensable for maintaining NEK6 expression and architecture in transformed B cells.