Chromatin profiling of the relationship between EWS/FLI, LSD1, and the enhancer landscape - H3K4 methylation

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 chromatin occupancy of LSD1. Overall design: A673 cells were assayed with either wildtype ("A673") or depleted ("EFKD") levels of EWS/FLI. For knockdown, 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 (Sigma P8833). For histone H3K4 methylation marks, three replicates of 50-bp single end sequencing were performed with input controls for each replicate. Bigwigs for H3K4 methylation marks were generated by MACS2 and represent the fold-enrichment over control; replicates are combined when present.