RNA polymerase Ill-transcribed EBER 1 and 2 ... - CiteSeerX

Journal of General Virology (1992), 73, 1687-1692.

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Printed in Great Britain

RNA polymerase Ill-transcribed EBER 1 and 2 transcription units are expressed and hypomethylated in the major Epstein-Barr virus-carrying cell types J. Minarovits, 1. L.-F. Hu, 1 Z. Marcsek, 2 S. Minarovits-Kormuta, 1 G. Klein ~ and I. Ernberg 3 1Department of Tumor Biology, Karolinska Institute, Box 60400, S-104 O1 Stockholm, Sweden, 2joint Research Organization of the Hungarian Academy of Sciences and the Semmelweis Medical University, Department of Cell Biology, Budapest, Hungary and 3Department of Virology, Karolinska Institute, Stockholm, Sweden

The genome of Epstein-Barr virus (EBV) codes for two non-translated small RNA molecules, EBER 1 and 2. We found that both EBERs are expressed in the major EBV-carrying cell types, group I and III Burkitt's lymphoma (BL) cell lines, lymphoblastoid cell lines (LCLs) and in two nude mouse-passaged nasopharyngeal carcinoma (NPC) tumours. The relative amount of EBER 1 and EBER 2 varied in different host cells but did not correlate with the cellular phenotype. The EBER coding and flanking sequences were predomin-

antly hypomethylated at HpalI sites not only in LCLs which usually carry hypomethylated EBV genomes but also in BL and NPC cell lines harbouring EBV episomes that are highly methylated in other regions. Thus, the EBER trancription units, actively transcribed by RNA polymerase III in the major EBV-carrying cell types, represent a methylation-free region in the EBV genome similarly to regulatory sequences of the latent membrane protein gene when the latter is transcribed by RNA polymerase II.

Introduction

Steitz, 1986). Their transcription has been studied mainly in BL cell lines; both of them are transcribed by RNA polymerase III (Arrand & Rymo, 1982; Jat & Arrand, 1982; Howe & Shu, 1989). In addition to intragenic RNA polymerase III control regions, however, upstream elements associated with typical class II promoters also influence the transcription of EBER genes (Howe & Shu, 1989). As far as we know there has been no comparative analysis of EBER 1 and EBER 2 expression in BL cell lines of group I versus group III phenotype and in LCLs to date. DNA methylation has been implicated in the control of viral gene expression (Doerfler, 1983). We have found previously that the methylation pattern of EBV DNA depends on the phenotype of the host cell (Minarovits et al., 1991). It is predominantly unmethylated in LCLs but is highly methylated at CCGG sequences in BL biopsy samples and in Rael cells, a stable group I BL cell line. In Rael cells, however, we also found an unmethylated region in the BamHI C fragment, within oriP, the latent origin of EBV replication (Ernberg et al., 1989). Another methylation-free region was detected in EBV genomes carried by NPC cells. Although the BamHI N fragment encoding LMP have been found to be highly methylated, the LMP regulatory sequences have been found to be unmethylated in LMP-expressing, but not in LMPnegative, NPC biopsies (Hu et al., 1991).

The expression of latent (i.e. non-lytic) viral genes is differentially regulated in the three main Epstein-Barr virus (EBV)-carrying cell types, Burkitt's lymphoma (BL) cells, nasopharyngeal carcinoma (NPC) cells and lymphoblastoid cell lines (LCLs). BL cells in vivo as well as group I BL cell lines growing in vitro that maintain the BL biopsy phenotype express only EBNA 1 (a nuclear antigen involved in the maintenance of EBV episomes). In 65% of NPC biopsies the latent membrane protein (LMP) is coexpressed with EBNA 1. The control of latent EBV gene expression is even less stringent in LCLs and in group III BL cell lines of immunoblast phenotype: they synthesize EBNAs 1 to 6 and LMP (Rowe et al., 1987; F~hreus et al., 1988). In addition to the growth transformation-associated proteins, BLs and LCLs also express two non-polyadenylated small RNA molecules, EBER 1 and EBER 2 (166 and 172 nucleotides, respectively), encoded by the BamHI C fragment of the EBV genome (Rymo, 1979; Lerner et al., 1981 ; Arrand & Rymo, 1982; Jat & Arrand, 1982; Howe & Steitz, 1986). Following infection of primary B lymphocytes with B958 virus, EBER expression follows the synthesis of EBNAs (Rooney et al., 1989). In BLs and in lymphoblastoid cells the EBERs are localized in the nuclei (Howe & 0001-0572 © 1992 SGM

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J. Minarovits and others

The present study had two main purposes. We wished to estimate the expression of EBER 1 and EBER 2 in group I and III BL cell lines, LCLs and NPCs using separately cloned EBER 1 and 2 sequences as probes (in earlier studies on BLs, LCLs and NPCs the BamHI C and EcoRI J fragments of the EBV genome used did not distinguish between EBER 1 and 2 RNAs or only EBER 1 expression was analysed (Weigel et al., 1985; Rowe et al., 1987; Gilligan et al., 1990). As sequence-specific methylation of promoter and adjacent regions of RNA polymerase III-transcribed genes has not been extensively investigated, we also wished to analyse the DNA methylation patterns of the EBER-encoding region in the major EBV-carrying cell types and determine whether its methylation status correlated with EBER 1 and 2 expression. We found that both EBER genes were expressed in all of the BLs, LCLs and NPC cells analysed. No methylated HpalI sites could be detected within the EBER 1 and 2 coding sequences and their 5' and 3' flanking sequences with the exception of an HpalI site localized upstream of EBER 1 class II promoter elements. This site was completely or partially methylated in four different BL cell lines but its methylation did not inhibit expression of EBER 1.

Methods Cell lines and tissue culture. LCLs and BL cell lines were grown in RPMI 1640 tissue culture medium (Gibco) supplemented with 5 ~ foetal calf serum. The cells were fed every 3 to 4 days and cultured at 37 °C in incubators with a 5% CO2 atmosphere and high humidity. The following cell lines were analysed: Rael, Akata and Mutu BL I C1 216 which are group I BL cell lines maintaining the BL biopsy phenotype; Jijoye p79, Mutu BL III CI 99 and Namalwa which are group III BL cell lines with an LCL-like pbenotype; CB-M I-RaI-STO, IARC 176B, Cherry, NAD-20-E95-STO, IARC 171 and CBC-Seb-CHI-20 which are LCLs and B95-8 which is an EBV-producing marmoset cell line. The NPC tumours C15 (Busson et al., 1988) and CAO (Cao, 1987) were maintained in vivo in nude mice. DNA isolation and analysis o f DNA methylation. High M, D N A was isolated from cell lines and biopsy samples and digested with HpalI (CpG methylation-sensitive) or MspI (CpG methylation-insensitive), both recognizing CCGG (Waalwijk & Flavell, 1978), as described in a previous study (Ernberg et al., 1989). Separation of the digested DNA fragments by agarose gel electrophoresis, transfer to Hybond N membranes (Amersham) and hybridization with [32p]dCTP-labelled EBV fragments was done according to standard procedures (Maniatis et aL, 1982). The probes were removed from the filters by repeated washings (10 min each) in boiling 0-1 x SSC 0-1~ SDS. Complete removal of the label was monitored by autoradiography before hybridization with a new probe. Probes. A cloned 0.5 kb SstI-Sau3AI subfragment of the EcoRI J fragment of EBV DNA containing EBER 1 coding sequences (pJJJ 1) and a cloned 0-5 kb Sau3AI-EcoRI subfragment of the EcoRI J fragment, containing EBER 2 coding sequences (pJJJ 2, Jat & Arrand, 1982~ Fig: 1) was a gift from Dr Nigel Sharp, St George's Hospital

(a) 6006

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EBER 1

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7467 l

EBER 2

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(b) 4107226 I

371 )

IIII

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428 II

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255 I

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436 7467

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EBER 1 EBER

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EcoRI J Fig. I. Regions of the EBV genome analysed in this study. Thick lines indicate coding sequences for EBER 1 and EBER 2. The cleavage sites for MspI, based on the DNA sequence of the B95-8 genome, are represented by small vertical bars above the lines. An MspI site absent from the B95-8 sequence but present in the EBV genomes carried by Rael, CB-M 1-RaI-STO, Akata, Mutu BLI C1216 and Mutu BLIII C199 cells is indicated by a small vertical bar below the line in (a). Numbers above the lines indicate major fragments (in bp) resulting from complete cleavage with MspI. Numbers above the small vertical bars flanking the probed regions indicate nucleotides in the B95-8 sequence. The probes pJJJ l, pJJJ 2 and EcoRI J are represented by thick lines below the maps.

Medical School, London, U.K. These DNA fragments show little or no cross-reaction when hybridized to EBER l or EBER 2 RNAs, respectively Oat & Arrand, 1982). The cloned EcoRI J fragment of the EBV genome was a gift from Dr Lars Rymo, Gothenburg, Sweden. RNA isolation and Northern blot analysis. Total cellular RNA was isolated from cell cultures and homogenates of nude mouse-passaged NPC tumours by centrifugation of a guanidinium isothiocyanate lysate through a CsCl cushion (Maniatis et al., 1982). RNA (10 txg per lane) was subjected to electrophoresis through a 1~ agarose gel containing formaldehyde and transferred to a Hybond N membrane (Amersham). Filters were then hybridized to probes pJJJ l, pJJJ 2 and a plasmid containing cDNA corresponding to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (Tso et al., 1985). The conditions for hybridization and washing were the same as those for the Southern blots.

Results Expression of EBERs in BL cell lines and LCLs Fig. 2 shows the expression of EBER 1 and EBER 2 in group I and III BL cell lines, LCLs and B95-8, a virusproducing marmoset cell line. All of these cell lines expressed both EBERs. The amount of EBER 1 relative to EBER 2 RNA in various host cells was calculated from densitometric readings of the autoradiographs and the results are summarized in Table 1.

Methylation patterns of the EBER coding and flanking D N A s e q u e n c e s in L C L s

The methylation analysis of EBER 1 and EBER 2 coding region in LCLs is shown in Fig. 3. In all of the LCLs analysed the HpalI sites localized within the EBER

Expression and methylation of EBER genes (a) 1 2

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Table 1. Relative amounts of EBER 1 and EBER 2 RNAs in BLs, LCLs and B95-8 cells

10 11 12 13

Cell line Group 1 BLs Rael Akata Mutu BL I C1 216 Group II1 BLs Jijoye p79 Mutu BL III CI 99 Namalwa LCLs CB-M I-RaI-STO IARC 176B Cherry N AD-20-E95-STO IARC 171 CBC-Seb-CHI-20 Marmoset cell line B95-8

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10 11 12 13

28S

EBER 1/ EBER 2*

EBER 1/ GAPDH

Eber 2/ GAPDH

1.18 1.41 2.25

0.547 0-217 2.956

0.465 0.154 1-302

2.26 0.66 0.51

0-043 0-083 0.041

0.019 0.126 0.080

0.72 1-33 2.89 1-89 3.6 3.32

0.087 0.281 0.509 0.051 0.072 1.944

0.121 0.2l 1 0.176 0-027 0.020 0-585

t -97

0.900

0-458

* Relative amounts of R N A were calculated on the basis of densitometric measurements using an LKB Ultroscan XL Laser Densitometer.

18S

Fig. 2. Northern blot analysis of EBER 1 and 2 expression in BLs, LCLs and B95-8 cells. Total cellular R N A s were hybridized to an (a) EBER 1- or (b) EBER 2-specific probe. Lane 1, Rael; lane 2, Akata; lane 3, Jijoye p79; lane 4, Mutu BL I C1216; lane 5, Mutu BL III C199; lane 6, Namalwa; lane 7, CB-M 1-RaI-STO; lane 8, IARC 176B; lane 9, Cherry; lane 10, NAD-20-E95-STO; lane 11, IARC 171 ;lane 12, CBCSeb-CHI-20; lane 13, B95-8. Positions of 28S and 18S ribosomal R N A s are indicated.

genes and in their flanking sequences were unmethylated, resulting in HpalI and MspI fragments of identical size. It cannot be excluded, however, that one of the two HpalI sites, only 13 bp apart from each other in the EBER 1 gene, is methylated, since the resulting HpalI fragment cannot be distinguished from the unmethylated cleavage product by electrophoresis through 1.5~ agarose gels. Owing to restriction fragment length polymorphismism, the MspI cleavage pattern of Cherry and CBM 1-Ral-STO differs from that of the B95-8 transformed IARC 171 and NAD20-E95-STO.

Methylation patterns of the EBER coding and flanking DNA sequences in BL cell lines In the BL cell lines (Fig. 4), similarly to the LCLs, at least four HpalI sites were unmethylated in the EBER 1 and 2 coding region. In the BL cell lines Rael and Akata, and in

the group I and III Mutu clones there was an additional MspI site upstream from the EBER 1 gene and this site is absent from the B95-8 genome. This extra CCGG sequence (indicated in Fig. I a) is completely methylated in Rael and Mutu BLI CI 216 cells and partially methylated in Akata and Mutu BLIII C1 99 cells. All of the HpalI sites assayed were unmethylated in B95-8 cells.

Expression and methylation of the EBER coding region in nude mouse-passaged NPCs Both EBERs were expressed in the nude mouse-passaged NPC lines C15 and CAO (Fig. 5a). Hybridization of MspI-digested DNAs with the EBV EcoRI J fragment resulted in an altered cleavage pattern in both NPCs compared to B95-8 (Fig. 5b). Comparison of the HpalI and MspI fragments, however, indicated that the 326 and approximately 436 bp fragments are flanked by unmethylated CCGG sequences in the EBER coding region, whereas a 371 bp fragment lying outside this region is flanked by methylated HpalI sites.

Discussion The transcription units of small R N A (EBER) genes of EBV combine R N A polymerase II and III promoter elements (Howe & Shu, 1989). The R N A polymerase II promoter elements include an Spl protein-binding site, an activating transcription factor-binding site and a TATA box-like sequence. All of these elements are


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-436 -326

Fig. 4. Methylation patterns of the EBER 1 and 2 coding and flanking sequences in BL lines and B95-8. HpaII- (odd lanes) or MspI- (even lanes) digested DNAs were hybridized with an (a) EBER 1- or (b) EBER 2-specific probe. Sizes of MspI fragments of B95-8 DNA are indicated. The following DNAs were analysed: Rael (lanes 1 and 2); Akata (lanes 3 and 4); Mutu BL I C1216 (lanes 5 and 6); Mutu BL III CI 99 (lanes 7 and 8); B95-8 (lanes 9 and 10).

Fig. 3. Methylation analysis of the EBER 1 and 2 coding and flanking sequences in LCLs. Total cellular DNA was digested with HpalI (odd lanes) or MspI (even lanes); the resulting fragments were separated on a 1.5~ agarose gel, blotted to a Hybond N membrane and hybridized with an (u) EBER 1- or (b) EBER 2-specific probe. Sizes of MspI fragments of B95-8 DNA, carried by two of the LCLs, are indicated. The following DNAs were analysed: IARC 171 (lanes 1 and 2); NAD20-E95-STO (lanes 3 and 4); Cherry (lanes 5 and 6); CB-M1-RaI-STO (lanes 7 and 8).

l o c a l i z e d w i t h i n 77 n u c l e o t i d e s u p s t r e a m o f the t r a n s c r i p t i o n a l i n i t i a t i o n site o f E B E R 1 or E B E R 2. T h e i n t r a g e n i c R N A p o l y m e r a s e I I I c o n t r o l regions consist o f boxes A a n d B w h i c h d e t e r m i n e the i n i t i a t i o n site a n d the level o f t r a n s c r i p t i o n , respectively. A l t h o u g h b o t h E B E R genes r e q u i r e u p s t r e a m s e q u e n c e s for m a x i m u m

e x p r e s s i o n in t r a n s i e n t t r a n s f e c t i o n assays, t h e i r t r a n s c r i p t i o n by R N A p o l y m e r a s e I I I in vitro is i n d e p e n d e n t o f the u p s t r e a m sequences ( H o w e & Shu, 1989; J a t & A r r a n d , 1982). T h e c o m b i n a t i o n o f R N A p o l y m e r a s e I I a n d I I I p r o m o t e r e l e m e n t s m a y c o n t r i b u t e to the u b i q u i t o u s e x p r e s s i o n o f E B E R s in all o f the m a j o r E B V c a r r y i n g cell types, BLs, L C L s a n d N P C s . It has been c o n s i s t e n t l y o b s e r v e d t h a t the E B E R 2 gene is t r a n s c r i b e d m o r e efficiently in vitro t h a n is the E B E R 1 gene. I n contrast, in the BL line Raji, t h e a b u n d a n c e o f E B E R 1 R N A g r e a t l y exceeds t h a t o f E B E R 2 R N A (Jar & A r r a n d , 1982; H o w e & Shu, 1989). W e f o u n d t h a t the r e l a t i v e a m o u n t o f E B E R 1 c o m p a r e d to E B E R 2 R N A was v a r i a b l e in g r o u p I a n d I I I BLs a n d in L C L s ( T a b l e 1). T h e E B E R 1 / E B E R 2 R N A r a t i o d i d n o t correlate w i t h the p h e n o t y p e o f the cells.

Expression and methylation of EBER genes (b) (a) 1 2

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34

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3 4 bp

-686 -436 -371 - 326

Fig. 5. Expression and methylation analysis of EBER 1 and 2 transcription units in N PC lines C 15 and CAO. (a) Total cellular RNA hybridized to an EBER 1- (lanes 1 and 2) or EBER 2- (lanes 3 and 4) specific probe. Lanes 1 and 3, NPC C15 RNA; lanes 2 and 4, CAO RNA. Sizes of 32p-labelled fragments of bacteriophage lambda DNA are indicated. (b) HpalI- (odd lanes) or MspI- (even lanes) digested DNAs were hybridized to the EcoRI J fragment of EBV DNA. Lanes I and 2, N PC C 15; lanes 3 and 4, CAO; lanes 5 and 6, B95-8. The sizes of B95-8 MspI fragments are indicated. The 436 bp fragment comigrated with a 428 bp fragment.

We observed earlier that the overall methylation of the EBV genome follows cell type-specific patterns. In LCLs the EBV D N A is hypomethylated whereas Rael, a stable group I BL cell line, carries highly methylated EBV genomes like the BL and NPC biopsies. Certain regions of functional importance, however, are exempt from methylation even if the overall level of EBV D N A methylation is high, for instance the two HpalI sites within the oriP region in Rael cells and the regulatory sequences of the LMP gene in NPCs expressing LMP (Ernberg et al., 1989; Hu et al., 1991 ; Minarovits et al., 1991). The HpalI sites in the EBER l and 2 transcription units are unmethylated in all of the cell lines analysed, with the exception of a single HpalI site upstream of the EBER 1 transcription unit. This site (indicated in Fig. 1a) is completely methylated in the group I BL cell lines Rael and Mutu BL I C1216 and is partially methylated in Akata (a group I BL cell line) and Mutu BL III CI 99 (a group III BL cell line) (Fig. 4). As this site is far upstream of the RNA polymerase II-like promoter elements of the EBER 1 gene, its methylation may not influence EBER 1 transcription; however, it may reflect the higher overall level of EBV D N A methylation in BLs compared to LCLs. Methylation at this site did not result in a decrease of the relative amount of EBER 1 transcripts compared

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to that of EBER 2 since the EBER 1/EBER 2 ratio is higher in the group I Mutu clone (where this site is completely methylated) than in the group III clone (harbouring the same virus), where its methylation is partial. In addition, the relative amount of EBER 1 R N A is higher in Rael cells (where this site is completely methylated) than in CB-M I-Ral-STO, an LCL harbouring the virus rescued from Rael cells, where it is unmethylated. Methylation of CCGG sequences in the internal regulatory region of the R N A polymerase Ill-transcribed VAI gene of adenovirus type 2 inhibits its expression in an in vitro cell-free transcription system (Jutterman et al., 1991). Box B in the intragenic R N A polymerase III control region of the EBER 1 gene is flanked by two HpalI sites on its 5' and 3' ends (Jat & Arrand, 1982). At least one of these sites remains unmethylated in BL cells, LCLs and in the NPCs C15 and CAO. The 3' end of box B in the EBER 2 internal control region is also flanked by a HpalI recognition sequence that is also consistently unmethylated in the EBER 2-expressing cells included in our study. We concluded that both EBERs are expressed in the major EBV-carrying cell types. CCGG sequences in the region of the R N A polymerase Ill-transcribed EBER 1 and 2 transcription units are hypomethylated even if other regions of the EBV genome are highly methylated in the host cell (e.g. in Rael cells). This phenomenon is similar to the hypomethylation of regulatory (but not coding) sequences of the LMP gene, transcribed by R N A polymerase II, in LMP-expressing NPC biopsies (Hu et al., 1991). We are grateful to Dr Nigel Sharp and Dr Lars Rymo for providing EBV DNA clones and to Dr Alan Rickinson and Dr Kenzo Takada for providing BL cell lines. This study was supported by the Swedish Cancer Society and PHS grant 5 RO1 CA28380-03 from the National Cancer Institute. J.M. is on leave from the Microbiological Research Group of the National Institute of Hygiene, Budapest, Hungary, as a recipient of a fellowship from CRI/Concern. L.-F. H. is supported by CRl/Concern and by the National Science Foundation and National Oncogene Research Centre, China.

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(Received 22 August 1991; Accepted 24 February 1992)