CNVs at CREs at the TRA locus are associated with gene expression in DLBCL. (A) Gain and loss of a CRE interacting with the MMP14 and PRMT5 promoters. The top panel shows the position of CNVs at the CRE, with copy number gains and losses represented by solid and dashed lines, respectively. The second panel shows chromatin looping interactions between the MMP14 and PRMT5 promoters and CREs, with the interaction between the promoters and the considered CRE colored yellow. The third panel details chromatin immunoprecipitation–sequencing histone mark signals in naive B cells. The bottom panel shows positions of BRD4-bound enhancers in DLBCL.⁴  CNV status at CRE and expression of MMP14 (B) and PRMT5 (C) in DLBCL tumors. Although the CREs are lost in 20 tumors, only 19 tumors are considered in the differential expression analysis, as 1 tumor also has a CNV at the target genes. Association between copy number status and gene expression assessed through linear regression. Boxplot hinges extend to the most extreme data points that are no more than 1.5 times the interquartile range from the box.