Epstein-Barr virus nuclear antigen 2 (EBNA2) regulation of transcription through the cell transcription factor RBPJ is essential for resting B-lymphocyte (RBL) conversion to immortal lymphoblast cell lines (LCLs). ChIP-seq of EBNA2 and RBPJ sites in LCL DNA found EBNA2 at 5,151 and RBPJ at 10,529 sites. EBNA2 sites were enriched for RBPJ (78%), early B-cell factor (EBF, 39%), RUNX (43%), ETS (39%), NFκB (22%), and PU.1 (22%) motifs. These motif associations were confirmed by LCL RBPJ ChIP-seq finding 72% RBPJ occupancy and Encyclopedia Of DNA Elements LCL ChIP-seq finding EBF, NFκB RELA, and PU.1 at 54%, 31%, and 17% of EBNA2 sites. EBNA2 and RBPJ were predominantly at intergene and intron sites and only 14% at promoter sites. K-means clustering of EBNA2 site transcription factors identified RELA-ETS, EBF-RUNX, EBF, ETS, RBPJ, and repressive RUNX clusters, which ranked from highest to lowest in H3K4me1 signals and nucleosome depletion, indicative of active chromatin. Surprisingly, although quantitatively less, the same genome sites in RBLs exhibited similar high-level H3K4me1 signals and nucleosome depletion. The EBV genome also had an LMP1 promoter EBF site, which proved critical for EBNA2 activation. LCL HiC data mapped intergenic EBNA2 sites to EBNA2 upregulated genes. FISH and chromatin conformation capture linked EBNA2/RBPJ enhancers 428 kb 5′ of MYC to MYC. These data indicate that EBNA2 evolved to target RBL H3K4me1 modified, nucleosome-depleted, nonpromoter sites to drive B-lymphocyte proliferation in primary human infection. The primed RBL program likely supports antigen-induced proliferation.pstein Barr virus (EBV) infection is highly prevalent in all human populations. EBV is also an important cause of endemic Burkitt Lymphoma (1), Hodgkin Lymphoma (2), and lymphoproliferative disorders in immune-suppressed (3) and HIV-infected people (4). In early primary human infection, EBV infects peripheral resting B lymphocytes (RBLs) and expresses six nuclear (Epstein-Barr virus nuclear antigen, EBNA) and two integral membrane (LMP) proteins. EBNAs and LMPs convert RBLs into proliferating lymphoblastoid cells (LCLs), which are malignant in the absence of effective T-cell responses. Because EBNAs and LMPs include >4,000 amino acids, T-cell immune responses normally eliminate most EBV-infected cells. Lymphocytes with down-regulated EBV protein expression persist in tonsils and lymph nodes and are reservoirs for reactivated EBV infection (4). EBV conversion of RBLs into LCLs in vitro (5) is a relevant and experimentally useful model for EBV proliferative effects in B-lymphocytes.In converting RBLs to LCLs, EBNA2 and EBNALP are expressed first. EBNA2 up-regulates EBV and cell gene expression, including EBV LMP1 and cell MYC, CD23, and CD21 (6-9). EBNA2 associates with DNA through RBPJ, which also mediates Notch binding to DNA (10, 11). The B-lymphocyte and macrophage lineage ETS protein, PU.1, is also important in EBNA2 activation of the EBV LMP1 promoter (12, 13). The EBNA2 C-terminal acidic domain recruits basal ...