EWS-FLI1-regulated Core Transcriptional Regulatory Circuit promotes Ewing sarcoma progression

We identify and validate an Ewing sarcoma-specific CRC, which is under control of EWS-FLI1. Formed by KLF15, TCF4 and NKX2-2, this CRC apparatus coordinates the gene expression programs in Ewing sarcoma cells. These data advance the understanding of the mechanistic basis of transactional dysregulation in Ewing sarcoma, and provide potential novel therapeutic strategies against this malignancy. Overall design: To elucidate the co-regulatory mechanism between CRC TFs and how they are controlled by EWS-FLI1 in Ewing sarcoma, ChIP-Seq was performed using specific antibodies against KLF15, TCF4 or NKX2-2 in A673 cells. Importantly, KLF15, TCF4 and NKX2-2 co-occupied both the super-enhancers and promoters of all TFs including themselves, forming an interconnected circuitry as predicted by our method. To further establish the regulatory effect of CRC TFs on the transcriptome, we performed RNA sequencing (RNA-seq).