Simple repeat sequence in Epstein-Barr virus DNA is transcribed in latent and productive infections.

The BamHI K region of Epstein-Barr virus DNA is transcribed in latently infected cells from Burkitt tumors and in growth-transformed B-lymphocytes latently infected with Epstein-Barr virus. We determined the nucleotide sequence of a 1,153-base pair HinfI fragment in BamHI fragment K from the B95-8 Epstein-Barr virus isolate. The fragment contains a remarkable 708-base pair simple sequence repeat array, designated IR3, which is composed of only three nucleotide triplet elements: GGG, GCA, and GGA. The triplets are organized into three repeat units: GCAGGA, GCAGGAGGA, and GGGGCAGGA. Immediately 3' of IR3 are tandem nearly perfect direct repeats of two different 24-base pair sequences. IR3 is conserved at a colinear position in the DNAs of other Epstein-Barr virus isolates, and a homologous sequence maps at the same location in the genome of a genetically related baboon herpesvirus, herpesvirus papio. IR3 is transcribed from left to right in latently infected, growth-transformed IB4 cells. It encodes part of a 2.0-kilobase exon of the 3.7-kilobase cytoplasmic polyadenylated RNA previously detected in IB4 cells (van Santen et al., Proc. Natl. Acad. Sci. U.S.A. 78:1930-1934, 1981). IR3 also encodes parts of 2.4- and 1.0-kilobase RNAs in productively infected B95-8 cells.