Long internal direct repeat in Epstein-Barr virus DNA

Abstract

The nucleotide sequence of the long internal reiteration, IR1, of Epstein-Barr Virus DNA has been determined. The repeat unit is 3,071 base pairs which are 66.8% guanine plus cytosine. There is a CCAAT sequence 39 nucleotides 5' to a TATAA, which could indicate a promotor for transcription. The longest open reading frame is 1,124 base pairs. Also within IR1 is a sequence homologous to the papovavirus origin of DNA replication. The ori-like sequence is within a long palindromic region which is 500 base pairs overall. The palidromic region shares common features with the Alu family members and with eucaryotic transposable elements. The juncture between the short unique region (Ul) and IR1 is also sequenced. The transition occurs in BamHI-C at 1,214 base pairs before the BamHI site in the first repeat of IRL. The transition from IR1 to the rightward unique region (U2) has been reported to be at 636 base pairs after the BamHI site in the last repeat of IRL. Thus, relative to the start of IR1 at the juncture with Ul, the last copy of IR1 is a partial repeat which contains only the beginning 1,850 base pairs. MATERIALS AND METHODS Viral DNAs. Plasmids pDK10 (BamHI-C), pDK51 (BamHI-V), and pDK14 (BamHI-V), which contain 286

Spliced RNA from the IR1-U2 region of Epstein-Barr virus: presence of an open reading frame for a repetitive polypeptide.

“…Alternatively, transcription might be initiated within IRI. The IRI repeat of B95-8 contains a CCAAT-34 nucleotide-TATAAA sequence (Cheung and Kieff, 1982;Jones and Griffin, 1983) which promotes transcription in a HeLa cell extract (Van Santen et al, 1983). In this hypothesis, however, translation could be initiated only if some IRI repeats located within the 5' end of the precursor were processed in a different way than described here.…”

“…Nucleotide sequence of the Ti cDNA The sequencing strategy used for the TI cDNA is shown in Figure 3 and the nucleotide sequence is given in Figure 4. Comparison with the nucleotide sequence of BamHI-V (Cheung and Kieff, 1982;Jones and Griffin, 1983), and BamHI-X and H (B.G.Barrell, personal conmmunication) restriction fragments showed that the precursor RNA is transcribed rightward and spliced following the GT-AG rule (Breathnach and Chambon, 1981;Mount, 1982). Two exons of 66 and 132 nucleotides are located respectively between nucleotides 1340 and 1405, and between nucleotides 1487 and 1618 of the BamHI-V restriction fragment (Jones and Griffin, 1983).…”

“…The viral genome is -170 x I03 bp. Several clusters of repeated sequences, designated TR, IRI, IR2, IR3 and IR4 (Given et al, 1979;Kinter and Sugden, 1979;Cheung and Kieff, 1982;Dambaugh and Kieff, 1982;Heller et al, 1982aHeller et al, , 1982bJones and Griffin, 1983) divide the genome into the five Ul, U2, U3, U4 and U5 regions (Figure lA). In latently infected cells, the IR1-U2 region is transcribed into polyadenylated RNAs (Rymo, 1979;Thomas-Powell et al, 1979;King et al, 1980King et al, , 1981Van Santen et al, 1981Arrand and Rymrro, 1982;Heller et al, 1982b;Weigel and Miller, 1983) which probably encode polypeptides of importance for the process of growth transformation .…”

The EB virus genome in Daudi Burkitt's lymphoma cells has a deletion similar to that observed in a non-transforming strain (P3HR-1) of the virus.

“…The complete DNA sequences of B95-8 BamHI fragments W (Cheung and Kieff, 1982;Jones and Griffin, 1983) and H (see Figure 2), and the partial sequence of BamHI-Y (our unpublished data, and B.G.Barrell, personal communication), and the sequence of Daudi EBV BamHI WH fragment (see Figure 3), coupled with transcriptions and marker rescue experiments (cited below) allow us to address these questions. The data of van Santen et al (1981) and Hummel and Kieff (1982) suggest that at least two mRNAs may be encoded in the region considered here.…”

“…To compare the sequence from clone lOG with corresponding sequences from B95-8, most of BamHI-Y and all of BamHI-H from the latter virus strain were also sequenced. The primary structure of BamHI-W had been determined previously (Cheung and Kieff, 1982;Jones and Griffin, 1983). The sequence of BamHI-H is given in Figure 2.…”