FIG 1.

EBNA1 binds cellular DNA near the ULBP1 transcription start site. (A) Levels of ULBP1 increase soon after EBV infection of primary B cells and quickly decline to initial levels. Levels of MICA and MICB do not change significantly. ULBP2 to -6 mRNAs were below the detection threshold (below 25 normalized reads on average). Data are derived from http://ebv-b.helmholtz-muenchen.de/. (B) EBNA1 PWM-predicted binding sites (red and blue sequences) associated with the NKG2D ligand ULBP1 gene. The location of each binding site is given relative to the ULBP1 transcriptional start site. (C) An EMSA showing EBNA1 binding to a positive-control oligonucleotide (EBV Rep* site 1; lanes 1 to 3), oligonucleotides that include ULBP1 site 1 (lanes 4 to 6) or ULBP1 site 2 (lanes 7 to 9), and a negative-control oligonucleotide (a portion of the EBV Raji origin; lanes 10 to 12). For each oligonucleotide, EBNA1 amounts added were none in the left lanes, 1.5 μg EBNA1 in the middle lanes, and 6 μg in the right lanes (n = 3; a representative image is shown). (D) Chromatin immunoprecipitation (ChIP)-qPCR measurement of EBNA1 binding to the sites identified in panel A relative to EBNA1 binding to a negative-control region in the genome (proximal to the rhodopsin gene, where there are no expected EBNA1-binding sites) in 721 lymphoblastoid cells. Data shown are relative to IgG binding at each of the sites (n = 5; error bars show standard error). *, P < 0.05.