Figure 5 ∣. Identification and validation of silencer-hijacking in AML.

a-b, Two examples of silencer-hijacking. a is for the KMT2C gene in AML 270 and b is for the JAK1 gene in AML 168. Below the Hi-C maps are the H3K27me3 CUT&Tag data. c-d, KMT2C and JAK1 expression across all AML and normal samples. e, Pie chart showing percentages of different types of neo-loops. When enhancers and silencers are present in the same 10Kb loop anchor, annotation of P-E vs. P-S loops is determined by the ratio of H3K27ac vs. H3K27me3 signals (Details in the method section). f, Expression of genes with hijacked silencers (n=33 genes). P value by one-sided Wilcoxon rank-sum test. Box plot: line denotes the median, top/bottom of boxes denotes first/third quartiles and whiskers extend to 1.5 times the interquartile range. g, Design of the CRISPR interference experiment for the hijacked silencers. This figure was created with BioRender.com. h-i, Hijacked silencers that were targeted by dCas9-UTX in Kasumi-1 and THP-1 cells. Upper panel, reconstructed Hi-C maps for the regions surrounding the translocation breakpoints. Neo-loops are marked by blue circles. Promoters are marked by orange vertical bars and the green vertical bars highlight the hijacked silencers. Lower panel: CUT&Tag for H3K27me3 and dCas9 after CRISPRi treatment. The grey vertical bars highlight the regions with the most reduced H3K27me3 signals. j, qPCR results of EXD1 in Kasumi-1 cells (left) and ALG10 mRNA expression in THP-1 cells (right) when the hijacked silencers were de-repressed (n=3 technical replicates in 2 biological replicates). The control group underwent the same procedures with non-human genome targeting sgRNA. P value calculated by two-sided Student’s t-test. Data show mean ± s.e.m. k, List of the recurrent cancer-related genes whose promoters were located in the anchors of neo-loops.