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Journal of Virology, December 2004, p. 14062-14065, Vol. 78, No. 24
0022-538X/04/$08.00+0 DOI: 10.1128/JVI.78.24.14062-14065.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Division of Microbiology & Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia
Received 21 May 2003/ Accepted 2 September 2004
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Background. Epstein-Barr virus (EBV), a DNA tumor virus and member of the herpesvirus family, efficiently transforms primary B cells and is an etiologic agent of infectious mononucleosis. In addition, numerous studies have implicated EBV in the development of various human lymphoid and epithelial malignancies, including Burkitt's lymphoma, nasopharyngeal carcinoma, Hodgkin's lymphoma, immunoblastic lymphoma, peripheral T-cell lymphoma, and gastric carcinoma (4, 13, 19).
EBV primarily establishes a latent infection in which the viral genome persists as an episome (2). Several different programs of latency-associated EBV gene expression have been described. During infectious mononucleosis, during ex vivo infection of B cells, and in EBV-associated posttransplant lymphoproliferative disease, EBV enters a program of gene expression known as latency III, which results in B-cell growth transformation (13). The latency III program is characterized by the expression of a wide array of viral proteins, including six different Epstein-Barr nuclear antigens (EBNAs 1, 2, 3a, 3b, 3c, and 4) and three latency-associated membrane proteins (LMPs 1, 2a, and 2b). Transcription of the EBNAs initiates at one of two promoters, Cp or Wp (Fig. 1) (18). Notably, Wp is encoded within the major internal repeat (IR-1) of EBV and as such is present in multiple copies (Fig. 1). Alternative 3' processing and splicing of long primary transcripts results in the production of the mature transcripts encoding the various EBNAs (Fig. 1). Upon ex vivo infection of B cells, EBNA gene transcription initially arises from the proximal EBNA gene promoter Wp, followed by induction of EBNA gene transcription from the distal EBNA gene promoter Cp (23). EBNA 1 upregulates transcription from Cp and Wp by binding to oriP, the latency-associated origin of replication located upstream of Cp (12) (Fig. 1), which also functions to maintain the viral episome in proliferating B cells (1). EBNA 2, which acts through a direct interaction with the cellular transcription factor CBF1/RBP-J
, also upregulates EBNA gene transcription from Cp via an enhancer located just upstream of Cp (3, 6, 20) (Fig. 1). The EBNA 3 family also interacts with CBF1/RBP-J
and serves to negatively regulate EBNA gene transcription initiation from Cp (27) (Fig. 1). Thus, EBNA gene transcription during type III latency is autoregulated by the EBNA gene products (Fig. 1).
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FIG. 1. Schematic illustration of EBNA gene transcription during different EBV latency programs. EBV encodes six EBNAs and two LMPs. In the latency I and II programs, the only EBNA gene expressed is EBNA 1, which is transcribed from the Qp promoter (16). The LMP genes are expressed during the latency II program but are absent from the latency I program. The latency III program, or growth program, involves transcription of all six EBNA genes, driven from either Cp or Wp. A combination of alternative 3' processing and alternative splicing leads to the production of the mature transcripts encoding each EBNA gene product. In addition to the six EBNA genes, the LMP genes are also expressed during the latency III program. Transcription of the EBNA and LMP genes is autoregulated, as shown here and discussed in the text.
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In contrast with the data supporting the transcriptional-interference model, it has been shown that during the initial stages of EBV infection of peripheral B cells, the region around Wp becomes densely methylated by day 21 postinfection (21). The kinetics of the appearance of Wp methylation correlated well with the extinguishing of Wp-initiated transcription as detected by a reverse transcription (RT)-PCR assay (21). Consistent with this model, ex vivo methylation of Wp regulatory sequences has been shown to strongly suppress Wp-initiated transcription (5, 14, 21). Thus, those authors argue that methylation of Wp is the primary mechanism by which Wp activity is downregulated during the establishment of LCLs. This model is difficult to reconcile with the previous analyses of Cp and Wp activity from transiently transfected reporter constructs, which demonstrate a direct impact of Cp-initiated transcription on Wp-initiated transcription in the absence of any methylation of either Cp or Wp sequences (11, 12). In addition, the rapid induction of Wp-initiated transcription upon withdrawal of EBNA 2 in the er/eb 2.5 LCL (24) seems unlikely to involve alterations in the methylation status of Wp and thereby indicates that there must be unmethylated copies of Wp. Finally, previous mutagenesis (26) and methylation cassette (10) analyses have demonstrated a critical role for the enhancer region upstream of the first copy of Wp (Wp1) in Cp-initiated transcription. Based on those data, it is surprising if methylation of this enhancer region upstream of Wp1 would be tolerated in LCLs. To further address this issue, we have examined the methylation status of Wp in several low-passage-number LCLs.
Analysis of Wp methylation in low-passage-number LCLs. We randomly selected a panel of eight LCLs that we had previously established, all of which had been passaged only a limited number of times postestablishment. Among these were LCLs immortalized with two different strains of EBV (B95.8 and Akata), as well as several LCLs infected with recombinant EBVs generated by rescuing the immortalizing capacity of the P3HR-1 clone 16 virus (25, 26). Notably, our previous analyses of recombinant EBVs generated by the latter approach have demonstrated that they harbor a smaller IR-1 region, comprised of only two or three copies of the BamHI W repeat, than that of wild-type strains of EBV (25). Notably, real-time RT-PCR analysis of the abundance of EBNA gene transcription initiating from Wp or Cp in these LCLs revealed that (i) as previously shown (22), in the established and extensively passaged LCLs X50-7 and JY, EBNA gene promoter usage is strongly polarized (X50-7 cells exclusively utilize Wp and JY cells exclusively utilize Cp to drive EBNA gene transcription) and (ii) as previously shown (25), both Cp and Wp are active in low-passage-number LCLs (significant levels of Wp-initiated EBNA gene transcripts were apparent in all low-passage-number LCLs analyzed) (Table 1). The presence of Wp-initiated EBNA transcripts in these LCLs argues strongly for the presence of some hypomethylated copies of Wp in the EBV genomes harbored in these LCLs.
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TABLE 1. Both Cp and Wp are active in low-passage-number LCLsa
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FIG. 2. Analysis of Wp methylation in low-passage-number LCLs. Genomic DNA was isolated from the indicated LCLs and from the EBV-positive Burkitt's lymphoma cell line Rael. As a negative control, DNA was also isolated from the EBV-negative Burkitt's lymphoma cell line DG75. DNA was bisulfite treated, amplified with primers designed to amplify bisulfite-modified DNA, cloned, and sequenced as previously described (9, 10). The primers used were those previously described (9, 10). The genome coordinates of the CpGs in the amplified region are shown on the left side of the panel. Also shown are the positions of known regulatory regions. , unmethylated CpGs; , methylated CpGs. Each numbered column shows the data obtained from an independent bisulfite PCR amplification. The vertical arrows denote those bisulfite PCR clones for which no CpG methylation was observed. The B95-A and B95-C LCLs were established by infection of peripheral blood B cells with B95.8 virus. The Ak-C1 and Ak-C2 LCLs were established by infection of peripheral blood B cells with Akata virus. The 25-3, 22-19, 17-20, and 28-8 LCLs were established by infection of peripheral blood B cells with immortalizing virus recovered from P2HR-1 clone 16 cells transfected with a plasmid containing the EBV BamHI W, Y, and H fragments, the 3' EBNA-leader protein-encoding exons, the entire EBNA 2 coding exon, and flanking sequences, as previously described (26, 27).
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Analysis of the methylation status of the EBV genome during restricted viral latency in the memory B-cell compartment has provided a strong correlation between methylation of Wp and Cp and the absence of detectable Cp- or Wp-initiated transcripts (10, 15). Based on those data, we have argued that targeted methylation of the IR-1 region of the viral genome is important for long-term maintenance of virus infection in vivo (10). Perhaps the hypermethylation of Wp observed at day 21 postinfection (21) reflects (i) viral genome methylation in B cells that then fail to progress to LCLs and (ii) the establishment of a restricted form of EBV latency in tissue culture. Thus, only those EBV-infected B cells in which there was low-to-modest methylation of the IR-1 repeat region would become immortalized and grow out in culture. Because the previously reported RT-PCR analyses of Cp- and Wp-initiated EBNA gene transcription (21) were not carried out with a limiting dilution analysis, this group could not assess whether the EBNA gene transcripts detected arise from B cells harboring viral genomes in which Wp is hypermethylated. The analyses of EBV genome methylation and viral gene transcription in peripheral B cells during the acute phase of infectious mononucleosis (21) also suffer from the same experimental limitation. Comparison of the levels of Wp methylation observed at day 21 postinfection (21) to the levels found in our analysis of eight low-passage-number LCLs argues that there is selection against EBV genomes in which Wp is hypermethylated. Further careful analysis of the relationship between IR-1 methylation and the transition to Cp utilization will be required before it can be resolved whether methylation plays a role in EBNA gene promoter utilization.
We thank members of the Speck lab for helpful advice on this research.
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. J. Virol. 70:4228-4236.[Abstract]
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