Epigenome editing of microsatellite repeat enhancers reveals specific regulatory functions and tumor dependencies [ChIP-Seq]

Various types of repetitive sequences are dysregulated in cancer but their contributions to oncogenesis are yet to be determined. Here we combine nascent transcription profiling with epigenome editing to test the function of GGAA microsatellites in Ewing sarcoma, a pediatric bone cancer where the oncogenic fusion protein EWS-FLI1 induces chromatin features of active enhancers at this class of repeats. Silencing of chromatin through epigenome editing at specific GGAA repeats abolished local nascent transcription, decreased the expression of neighboring target genes and, in the case of a repeat associated with the SOX2 locus, reduced the growth of tumor xenografts. Our studies directly demonstrate that repeat elements can acquire enhancer functions in cancer and become critical components of oncogenic gene regulation programs. Raw data for MSC Samples GSM2857574-GSM2857587 are subject to privacy restrictions and were not submitted. ChIP-seq for the histone modifications H3K4me1, H3K4me3, H3K9ac, H3K27ac, H3K27me3 and the transcription factor EWS-FLI1 in mesenchymal stem cells (MSC). EWS-FLI1 was expressed in MSCs with lentiviral expression vectors. ChIP-seq for the histone modifications H3K27ac, H3K9me3 and the transcription factor EWS-FLI1 in Ewing sarcoma cells (A673). dCas9-KRAB and specific guide RNAs targeting a GGAA repeat enhancer either near NKX2-2 or SOX2 were expressed in Ewing sarcoma cells (A673) using a lentiviral expression vector. ChIP-seq for the histone modifications H3K4me3 and H3K27ac in the lung carcinoma cells NCI-H810.