Chromatin profiling of the relationship between EWS/FLI, LSD1, and K27ac in multiple Ewing sarcoma cell lines

The purpose of this study was to define the genome-wide functional relationship between LSD1 and EWS/FLI in Ewing sarcoma cells. We found EWS/FLI and LSD1 co-localize throughout the genome and that EWS/FLI induces a large change in the genomic distribution of LSD1, and that this also occurs for the LSD1 interacting partner, REST. Overall design: A673, EWS502, SKNMC, and TC71 cells were collected for CUT&RUN. Two independent replicates were performed for each sample including EWS/FLI, LSD1, and H3K27ac, with a non-specific IgG control. Samples were submitted for 150-bp paired end sequencing. Bigwigs for LSD1 and EWS/FLI were generated by MACS2 and represent the fold-enrichment over control; replicates are combined when present. Bigwigs for H3K27ac and relevant non-specific control are spike-in normalized representations of the aligned reads.