Chromatin profiling of the relationship between EWS/FLI, LSD1, and H3K27 acetylation

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. Overall design: A673 cells were assayed with either wildtype ("A673"), depleted ("EFKD"), or depleted and ectopically rescued (714 or "wtEF") levels of EWS/FLI. For knockdown of shRNAs were retrovirally delivered targeting either EWS/FLI ("EFKD") or luciferase as a negative control ("A673") and cells were selected in 2 µg/mL puromycin. For rescue cDNAs were retrovirally transduced and cells were selected in puro with 100 µg/mL hygromycin B. For CUT&Tag two independent replicates were performed for each sample including LSD1 and H3K27ac, with a non-specific Rb IgG control. Samples were submitted for 150-bp paired end sequencing. Bigwigs for H3K27ac and relevant non-specific control, and all CUT&Tag samples are spike-in normalized representations of the aligned reads.