Viral oncogene manipulates YY1 to alter host 3D genome organization and promote B cell proliferation

YY1 plays essential roles in regulating enhancer-promoter interactions. Here we report that Epstein-Barr virus (EBV) nuclear antigen leader protein (EBNALP), essential for EBV immortalization of naïve B lymphocytes(NBLs), manipulates YY1 to alter enhancer-promoter interactions during transformation. EBNALP colocalized with TOP2B and was tethered to DNA through DPF2 in lymphoblastoid cell lines(LCLs). EBNALP inactivation led to reduced looping at enhancers including CCND2 identified by H3K27ac HiChIP, with reduced TOP2B, DPF2, and YY1 DNA binding. EBNALP interacted with YY1 in LCLs by immune precipitation and colocalized by immunofluorescence. DPF2 CRISPR knock out reduced EBNALP and YY1 DNA binding. CRISPRi repression of CCND2 enhancers reduced CCND2 TSS H3K27ac and CCND2 expression. EBNALP also repressed enhancer looping at enhancers including CASP1. EBNALP inactivation led to increased enhancer looping with increased TOP2B, DPF2, and YY1 binding these enhancer sites.DNA accessibility increased at these sites following EBNALP inactivation by ATAC-seq. H3K9me3 was enriched at EBNALP repressed enhancer sites in LCLs.These data identified novel mechanisms through which EBVmanipulates YY1’s function to rewire host DNA elements and reorganize the host genome to facilitate EBV mediated growth transformation.