Extended Data Fig. 8: Comparative CUT&RUN Analysis between parental and edited K562 cells.
From: Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1
(a) Metagene plot (mean) for H3K4me2 signal at the LSD1 peaks (± 5 kb) across the 498 downregulated genes (top) and 498 unaffected control genes (bottom). The parental K562 cells are represented in black, while the edited K562 cells are depicted in pink. Two replicates (left and right) display variations in the 498 unaffected control regions. (b) Metagene plot (mean) for H3K14ac signal at the LSD1 peaks (± 5 kb) across the 498 downregulated genes (top) and 498 unaffected control genes (bottom). Similar to (a), the parental K562 cells are shown in black, and the edited K562 cells are shown in pink. Subtle variations in the 498 unaffected control regions are seen across two biological replicates, alongside reduced read counts in the downregulated genes. (c) Metagene plot (mean ± SEM) of IgG control signal within the scaled gene bodies ± 20 kb of the 498 downregulated genes (top left) and 498 unaffected control genes (bottom left), for both parental (black) and edited K562 cells (pink). Metagene plot (mean) of IgG control signal at the LSD1-bound regions within the 498 downregulated genes (top right) and 498 unaffected control genes (bottom right), for both for both parental (black) and edited K562 cells (pink) are shown. (d) Genomic distribution of LSD1 in parental and edited K562 cells. The left Venn diagram illustrates that approximately 53% of LSD1 peaks from parental K562 cells directly overlap with LSD1 peaks from edited K562 cells. About 43% of these overlapping peaks were located in the promoter region of all LSD1-bound genes. In contrast, only around 20% of the non-overlapping peaks were found in the promoter regions of LSD1-bound genes, suggesting a redistribution of LSD1 in numerous non-promoter regions. SEACR relaxed mode was employed to identify these LSD1 peaks, which were subsequently compared with LSD1 peaks from the Encode database (K562 cells, ENCFF054XCG). Both parental and edited K562 cells’ LSD1 peaks exhibit approximately 40% direct overlap with the LSD1 peaks from the Encode database.
