Fig. 2: Epigenome and super-enhancer analysis in HPRT3, HPRT2, and HPRT1 cells and sequence tag density plots of H3K27Ac and BRD4 occupancy and chromatin accessibility at the IRF4 and PAX5 genes in HPRT3-DLBCL cells.

A H3K27Ac ChIP-Seq analysis was performed on the chromatin from RT-DLBCL cells. Ranked ordering of SE (ROSE) analysis was performed utilizing the H3K27Ac sequence-tag density and H3K27Ac signal at enhancers. B ATAC-Seq analysis was performed on the nuclei from RT-DLBCL cells to determine chromatin accessibility. Publicly available ATAC-Seq data from normal CD34+ HPCs were downloaded from GEO. Log2 fold-changes in peaks from selected RT-relevant genes as determined by ATAC-Seq analysis are shown. Red arrows indicate significant differences in accessibility in the three RT-DLBCL subtypes compared to each other and normal CD34+ cells. C, D Integrated Genome Viewer (IGV) plots showing H3K27Ac and BRD4 ChIP-Seq signal density and ATAC-Seq determined chromatin accessibility at the IRF4 and PAX5 genes in clonally-related HPRT3-DLBCL cells. The blue bars beneath the signal tracks indicate the position of the super enhancer for IRF4 and PAX5 as determined by ROSE analysis.