Viral gene expression in BCBL-1 single-cell clones with or without KSHV ORF57 expression

To perform a comprehensive genome-wide analysis of KSHV RNA splicing and its regulation by ORF57, we carried out RNA-seq of total RNA isolated from BCBL-1 single-cell clones carrying a wild-type (WT, clone B4) or ORF57 knock-out (57KO, clone #6) KSHV genome 24 h after induction of viral lytic replication with valproic acid (VA24) [21] (Fig 1A). Interestingly, for an unknown reason, all selected single-cell WT clones transfected with the empty Cas9 vector express a much lower amount of ORF57 protein when compared to the parental BCBL-1 cells but still support KSHV lytic replication (Fig 1B). We selected the WT B4 clone, instead of the WT B8 cells or even the parental BCBL-1 cells, for parallel RNA-seq comparison with the 57KO clone #6 cells because the WT B4 clone cells expressed the lowest amount of ORF57 essential for KSHV lytic replication [21,22] and thus could give us a similar amount of viral RNA reads for unambiguous RNA splicing analysis of viral RNA transcripts most sensitive to ORF57 regulation. Principal component analysis of differentially expressed genes from three group samples in RNA-seq showed well-separated expression profiles for each group, indicating the high quality of the cDNA library preparation and RNA-sequencing. Each group of four samples exhibited 239 (WT B4 latent), 233 (WT B4 lytic), and 236 (57KO #6 lytic) million combined high-quality RNA-seq reads (Fig 1A). By mapping the sequence libraries to a host GRCh38 (hg38)/BCBL-1 KSHV (GenBank Acc. No. HQ404500) chimeric genome using STAR aligner [23], we found the reduced expression of ORF58 and ORF59 in the 57KO cells when compared with WT B4 cells, as expected [24,25] (Fig 1C and S1 Table). Surprisingly, there was only a slight expression decrease (1.3-fold, p <0.01) for PAN RNA from the 57KO #6 cells to WT B4 cells (Fig 1C and S1 Table), despite that PAN RNA has been identified as a sensitive downstream target of ORF57 [24,26]. We subsequently verified the RNA-seq results by quantitative RT-qPCR (Fig 1D). We showed a ~73 (68–78)-fold reduction of ORF59 and only ~7 (4–10)-fold reduction of abundant PAN RNA in the 57KO #6 cells when compared with the WT B4 cells. Data suggest an unknown compensatory mechanism for PAN RNA expression in the absence of ORF57 in the course of long-term selection of single-cell clones.

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Fig 1. Viral gene expression in BCBL-1 single-cell clones.

(A) Samples used for RNA-seq including WT single-cell clone B4 of BCBL-1 cells carrying Cas9 vector lacking gRNAs expression and 57KO single-cell clone #6 carrying a plasmid expressing gRNA2+4 (pABC8) described in previous studies [21]. Total RNA from uninduced clone B4 cells representing WT cells with latent infection (4 samples, A1-4), clone B4 cells treated with 1 mM valproic acid for 24 h (VA24) representing the WT cells with the lytic infection (4 samples, B1-4), and clone #6 cells treated with 1 mM valproic acid for 24 h (VA24) representing the 57KO cells with the lytic infection (4 samples, C1-4) were subjected to RNA-seq. Total RNA-seq reads uniquely mapped to the human (hg38)/KSHV (GenBank Acc. No. HQ404500) chimeric genome were counted in each group of four samples. (B) Relative protein expression of ORF57, ORF50, and Cas9 in parental BCBL-1 (P) and BCBL-1 single-cell clones containing a wild-type genome (WT clones B4 and D8) or an ORF57-null genome (57KO clone #6) under 24 h of KSHV lytic infection induced by 1 mM valproic acid (VA 24h). Immunoblot was performed with each protein corresponding specific antibody, with β-tubulin serving as a protein loading control. (C) RNA-seq reads-coverage of KSHV ORF58-59 and PAN RNA loci in one representative sample each from WT B4 and 57KO #6 cells with KSHV lytic infection induced by 24 h VA treatment. The numbers in the upper right corner represent the reads-coverage depth. (D) Validation of PAN and ORF59 RNA expression from WT B4 and 57KO #6 cells by RT-qPCR. Total RNA from WT B4 and 57KO #6 cells with KSHV lytic infection described in panel C was used for the assays.

https://doi.org/10.1371/journal.ppat.1010311.g001

Mapping of KSHV RNA splice junctions from the WT KSHV to ORF57-null KSHV genome in BCBL-1 cells

As our previous study showed high reliability in qualitative and quantitative analysis of genome-wide RNA splicing of mouse papillomavirus (MmuPV-1) [27] by using STAR aligner [23], the splice reads uniquely mapped to the KSHV genome were extracted, pooled together, and used for viral RNA splicing analysis. Because both groups exhibited an almost equal sequence library size, we did not perform any further read counts normalization. In total, we identified 22,978 viral RNA splice junction reads derived from 269 viral splice junctions in the cells with the WT genome and 25,087 viral RNA splice junction reads derived from 255 viral splice junctions in the cells with the 57KO genome (Fig 2A). Among those viral RNA splice junctions, 145 were commonly detected in both WT and 57KO cells. However, many identified viral RNA splice junctions were supported with only a few reads and were not consistently detected in all samples within individual groups, indicating they represent rare, low-frequency RNA splicing events (see details in S2 Table). Therefore, we next focused only on more prevalent viral RNA splice junctions supported by at least 10 or more (≥10) splice reads. Even though applying this threshold led to ~5-fold reduction of the number of viral RNA splice junctions to 57 in the cells with the WT genome and 70 in the cell with the 57KO genome, the splice reads assigned to these junctions counted for 98% of all identified viral splice reads, indicating that these RNA splice junctions represent most of the viral RNA splicing events (Fig 2A) with 54 in the WT and 64 in the 57KO consistently being detected in all four samples in each group (S2 Table). As expected, the highly prevalent splice junctions were found in viral RNAs from the WT to 57KO genome, with 50 viral RNA splice junctions commonly detected in the viral RNAs expressed from both genomes. The remaining 7 viral RNA splice junctions passed the minimal 10 reads threshold only in the WT and the other 20 only in the 57KO genome (Fig 2B).

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Fig 2. Identification of KSHV RNA splice junctions by RNA-seq.

(A) The number (count) of all detected KSHV RNA splice junction and those with the splice reads (≥10 reads) identified by STAR aligner [23] in WT B4 and 57KO #6 cells (combined 4 samples in each group) with lytic KSHV infection induced by 24 h treatment with 1 mM valproic acid. “Reads” are the number and percentage (%) of all supporting splice reads from all splice junctions. (B) The Venn diagram shows the overlapped RNA splice junctions with ≥10 supporting splice reads between the WT and 57KO genome. (C) The Sashimi graphs generated by IGV showing the viral genomic locations and frequency of RNA splicing events in individual groups. The black triangles indicate the notable RNA splicing differences between the 57KO and WT genome in the cells.

https://doi.org/10.1371/journal.ppat.1010311.g002

Mapping the obtained splice junctions to the reference KSHV genome revealed a landscape of viral RNA splicing with clusters of split genes being separated by the genomic regions lacking splice sites (Fig 2C). We also observed several noticeable differences between RNA splicing from the WT to the 57KO genome (Fig 2C). To determine the biological relevance of the detected viral splicing events, all highly prevalent splice junctions were mapped to each annotated KSHV transcripts with previously mapped or predicted transcriptional start sites (TSS) and polyadenylation cleavage sites [8–10]. The RNA-seq reads-coverage was used to estimate RNA splicing efficiency. Finally, the coding potential of individual spliced RNA isoforms was analyzed to predict the effect of RNA splicing on the viral proteome.

KSHV RNA splicing profile from the WT genome in BCBL-1 cells

All 57 highly prevalent splice junctions with ≥10 splice reads detected in viral RNAs from the WT genome were named SJ-1 to SJ-57 in the order from the KSHV genome 5′ to 3′ direction and are summarized in Table 1. They mapped to transcripts from 33 annotated KSHV genes (Figs 3 and 4), confirming the previous estimates that ~30% of KSHV genes are undergoing RNA splicing when expressed [14]. These include almost all previously reported splice junctions identified either in the single gene locus or in the gene cluster regions [9], but we were unable to detect any RNA splice junction within the ORF29 gene as reported [5]. In addition, several minor alternative RNA splice junctions previously reported in ORF4 and K8.1 RNAs were detected in this study but did not pass the threshold of ≥10 splice reads [28,29]. In contrast, we identified numerous novel splice junctions, some of which were previously detected in other RNA-seq studies but not properly annotated [30]. These include additional new splice junctions in viral transcripts of ALT RNA, ORF70/K3, K5, ORF45/48, K10, and a major latent locus, indicating a higher complexity of RNA splicing of these transcripts (Figs 3 and 4). We also identified several novel RNA splicing events in the genes that were not found to be spliced in previous studies. These include splice junctions in the ORF2 and K4.1/4.2 loci (Fig 4). Despite their relatively low prevalence, the RT-PCR results support the newly detected introns in the KSHV WT genome in BCBL-1 cells (S1 Fig). Other examples of novel splice junctions detected, validated, and functionally annotated in our study are the junctions between K5 encoding membrane-based E3-ubiquitin ligase and K6 encoding viral cytokine vMIP-I [31]. Interestingly, we identified that splice junctions could be not only mapped to individual K5 (SJ-23, -24, -25) and K6 (SJ-31, -32, -33) transcripts, but also five new splice junctions spanning over K6 gene to K5 (SJ-26, -27, -28, -29, -30) (Fig 5A). The existence of these splice junctions suggests the expression of not only monocistronic K6 and K5 transcripts but also K6/K5 bicistronic transcripts, which are further processed by RNA splicing. The alternative splicing in both K5 and K6 monocistronic RNAs occurs in their 5′ UTRs and is mediated by several alternative 5′ ss and single 3′ ss right upstream of their corresponding coding regions (Fig 5A). Interestingly, expression of several upstream ORFs (uORF) was detected in both 5′ UTRs [9]. Thus, the observed RNA splicing may regulate K5 and K6 expression by removing these uORFs to efficiently translate K5 and K6 proteins, which requires further experimental validations. The splicing of bicistronic RNA occurs between a 5′ ss upstream of the K6 ORF and a 3′ ss upstream of the K5 ORF. This RNA splicing removes the entire K6 code region without affecting the K5 coding capacity. Therefore, the spliced K6/K5 mRNA under control by the K6 promoter encodes only K5 protein (Fig 5A). The existence of these RNA splicing events was confirmed by RT-PCR (Fig 5B). Together these data reveal a comprehensive profile of KSHV genome-wide RNA splicing events during KSHV lytic infection.

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Fig 3. Mapping of KSHV RNA splice junctions from the plus strand of viral genome.

The diagrams depicting all splice junctions (colored arches) with ≥10 supporting splice reads mapped to viral transcripts expressed from the plus strand of the KSHV genome, with the splicing events being numbered in the order from the genome 5′ to 3′ direction. The numbered blue arches represent splice junctions detected from the WT genome and green from the 57KO genome in the cells (see Tables 1 and 3). The arch thickness represents a relative abundance of detected splice junction reads. The RNA-seq reads-coverage from one representative sample from the WT and 57KO genome in the cells with lytic infection is shown below the arches, with the reads-coverage depth shown in the upper right corner. The annotated KSHV ORFs are marked by full arrows, blue for ORFs encoded from the plus or orange for ORFs from the minus DNA strand. The dashed boxes are predicted non-coding exons. The black triangles represent mapped (full) or predicted (empty) transcriptional start sites [9, 10]. The black hexagons mark the mapped polyadenylation cleavage sites [8]. The 5′ splice donor (D) and 3′ splice acceptor (A) sites are marked with vertical arrows. Horizontal arrows mark the positions of primer sets used in RT-PCR.

https://doi.org/10.1371/journal.ppat.1010311.g003

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Fig 4. Mapping of KSHV RNA splice junctions from the minus strand of viral genome.

The diagrams depicting all splice junctions (colored arches) with ≥10 supporting splice reads mapped to viral transcripts expressed from the minus strand of the KSHV genome, with the splicing events being numbered in the order from the genome 5′ to 3′ direction. The numbered orange arches represent splice junctions detected from the WT genome and pink arches from the 57KO genome in the cells (see Tables 1 and 3). The arch thickness represents a relative abundance of detected splice junction reads. The RNA-seq reads-coverage from one representative sample from the WT and 57KO genome in the cells with lytic infection is shown above the arches, with the reads-coverage depth shown in the upper right corner. See other details in Fig 3. LTc—constitutive latent promoter, LTi—inducible latent promoter, LTd—distal latent promoter, oriL—lytic origin of replication.

https://doi.org/10.1371/journal.ppat.1010311.g004

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Fig 5. Alternative RNA splicing detected and verified from the K5/K6 locus.

(A) The RNA splice junctions mapped to K5 and K6 locus in the WT genome. Below is the predicted structure of K5, K6, and K6/K5 transcripts with thick black lines representing the exons and dotted lines the introns. The arrows represent the primers used in RT-PCR shown in (B). See other details in Fig 3. (B) Verification of the mapped RNA splice junctions in K5/K6 expression in BCBL-1 cells with lytic KSHV infection. Total RNA extracted from the parental BCBL-1 cells with VA 24 h treatment was examined by RT-PCR. The reaction without reverse transcriptase (RT-) was used as a negative control. The predicted sizes of amplificons from unspliced and spliced transcripts are displayed under each gel electrograph. All spliced products amplified were gel purified and confirmed by sequencing. The number of supporting splice reads from the WT genome in the cells with lytic KSHV induction are in the parentheses.

https://doi.org/10.1371/journal.ppat.1010311.g005

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Table 1. Identified RNA splice junctions (SJ) with ≥10 splice reads from the KSHV WT or 57KO genome in BCBL-1 cells.

The positions of 5′ and 3′ splice sites (SS) are based on the KSHV reference genome GenBank Acc. No. HQ404500. The reads-number represents a total number of splice reads in the WT or 57KO group during lytic replication (see S2 Table for the details). The SJ fold change (FC) represents splice junction-reads change in BCBL-1 cells with the KSHV 57KO versus WT genome during viral lytic replication. The asterisk marks significant (p ≤ 0.05) change by Student t-test. The transcript FC for the annotated genes was determined by Limma Voom differential gene expression analysis (see S1 Table for the details), with the color gradient red for decrease and green for increase. The genes with significant expression changes (p ≤0.01) are marked with an asterisk. N/D—not determined.

https://doi.org/10.1371/journal.ppat.1010311.t001

KSHV RNA splice sites and their usage in viral RNA splicing

During RNA splicing, the intron recognition is mediated by binding of U1 snRNP to 5′ ss and U2 snRNP to 3′ ss. The binding affinity of these factors depends on the sequences surrounding the individual splice sites. Thus, analysis of splice site surrounding sequences can be used to determine the strength of each splice site and ultimately the efficiency of intron removal. We found that viral RNA splicing in the WT KSHV genome is mediated by a total of 187 distinct 5′ ss and 138 3′ ss. The identified 57 RNA splice junctions supported by ≥10 splice junction reads in the WT genome were found being mediated by splicing from 47 distinct 5′ ss to 35 3′ ss (Tables 1 and 2). The introns within the splice junctions are all canonical “GU-AG” introns. We found that most viral 5′ ss participate in splicing of a single intron. Only 9 (19%) of all 47 WT 5′ ss use an alternative 3′ ss, with the 5′ ss at nt 69,684 located in the ORF47/48 intergenic region being spliced mostly to three alternative 3′ ss (Fig 4 and Table 2). Similarly, only 8 (23%) of all 35 WT 3′ ss are associated with an alternative 5′ ss usage. A striking exception is that the 3′ ss at nt 26,091 upstream of K5 could accept 8 different 5′ ss for various RNA splicing events (Fig 4 and Table 2).

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Table 2. The sequence and strength of identified KSHV splice sites.

The position and sequences of KSHV 5′ (A) and 3′ (B) splice sites (SS) of splice junction (JS) with ≥10 splice reads. The numbered splice junctions (SJ) are shown in Figs 3, 4 and 6 (see Tables 1 and 3 for more details). In green color are the numbered splice junctions with ≥10 reads identified only in the 57KO genome. The strength (colored gradient) of individual SS was determined by MAX:ENT model [32].

https://doi.org/10.1371/journal.ppat.1010311.t002

To understand the contribution of splice sites to KSHV RNA splicing regulation, we analyze their strength by a maximum entropy (MAX:ENT) model based on sequence composition surrounding 5′ ss and 3′ ss [32]. As shown in Table 2, most WT 5′ ss represent the optimal 5′ ss with a median MAX:ENT 8.24, and only six 5′ ss have a suboptimal MAX:ENT below 4.0 (Table 2A). While most suboptimal intron 5′ ss contribute to relatively low-frequency splicing, two of these splice sites mediate RNA splicing to express functional K8.1 (SJ-8) and K15 (SJ-54) proteins. Their relative weakness could be overcome by their optimal exon size of the upstream exons (K8.1, K15) and presumably the stimulatory effect by splicing of adjacent introns (K15) [33]. Like 5′ ss, most WT KSHV 3′ ss are relatively strong, with a median MAX:ENT 8.32 (Table 2B). Interestingly, the only weak 3′ ss with MAX:ENT under 4.0 was mapped at nt 20,263 within the ORF70 coding region and the splicing of this intron in the ORF70 coding region subjects to ORF57 regulation (see our data in the latter text). Another relatively weak 3′ ss (MAX:ENT 4.42) was found in the LANA 5′ UTR at nt 126,373 and could accept a 5′ ss at nt 126,873 (SJ-50) for LANA RNA splicing. Interestingly, the same 5′ ss is also spliced to a much stronger (MAX:ENT 11.34), but distal 3′ ss at nt 122,971 upstream of ORF72 encoding vCyclin (SJ-49) [16]. Both RNA splicing events in the polycistronic LANA RNA occur in comparable frequency, indicating that the relative weakness of the proximal 3′ ss in LANA RNA may allow splicing of this 5′ ss to a more distal strong 3′ ss in order to facilitate the expression of all latent proteins from this polycistronic RNA transcribed from the single latent constitutive promoter [15].

KSHV RNA splicing profile from the 57KO genome in BCBL-1 cells

Similarly, we analyzed the biological significance of viral splice junctions detected in viral RNAs from the 57KO genome in BCBL-1 cells. As mentioned above, we identified 70 viral splice junctions with ≥ 10 splice junction reads from the 57KO genome, of which 50 were also observed from the WT KSHV genome (Fig 2B). The additional 20 splice junctions (SJ-58 to SJ-77) with ≥ 10 splice junction reads were found in the 57KO genome, but less than 10 splice junction reads in the WT KSHV genome (Table 3). These RNA splice junctions could be split into two groups based on their mapping. The first group represents splice junctions mapped to viral transcripts with notable splice sites in the WT genome (Figs 3 and 4), but these splice sites could be alternatively spliced to another splice site in the 57KO genome, thus creating a new splice junction enriched in the 57KO genome. This group of viral RNA transcripts includes the alternatively spliced RNAs from ORF50/K8/K8.1 (SJ-61 to -63), ALT RNA (SJ-66 and -67), K14/ORF74 (SJ-68 and -69), ORF70/K3 (SJ-70), K5/K6 (SJ-71), and ORF45/46/47/48 (SJ-72 and -73) (Figs 3, 4 and S2A). The second group represents nine novel splicing events not reported or documented in the KSHV intronless RNA transcripts. They were detected from viral lncRNA PAN (SJ-58 and -59) and antisense RNA to ORF43 (SJ-60), antisense RNA to K11 (SJ-64 and -65), ORF49 (SJ-74), and antisense RNA to ORF50 (SJ-75 to -77) (Fig 6A). These splice junction reads could be readily detected and verified by RT-PCR and sequencing (Fig 6B). It is worth noting that most of these RNA splice junctions could also be detected from the WT genome with less than 10 splice junction reads (S2B Fig and Table 3), but the SJ-68 was found only from the 57KO genome. Although detected in the expression of both 57KO and WT genomes, the spliced PAN RNA was just a tiny fraction among the abundant PAN transcripts. We identified total 54 RNA splice junction reads in the WT cells out of total 3,307,738 reads mapped to the PAN locus (S1 and S2 Tables). Similarly, we identified total 86 splice junction reads out of total 2,057,347 reads mapped to PAN in the 57KO cells. Thus, the splice junction reads from the PAN region represent only 0.0016% of the WT and 0.0042% of the 57KO total PAN reads. Nevertheless, these data indicate that loss of ORF57 expression led to alternative splicing of KSHV RNAs by activation of cryptic splice site usage in the intron-containing and/or intronless viral transcripts.

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Fig 6. Mapping of 57KO-specific splice junctions in intronless and antisense viral transcripts.

(A) The RNA splice junctions supported with ≥10 splice reads from the 57KO genome were mapped to intronless viral transcripts. See Figs 3 and 4 for a detailed description. (B) RT-PCR validation of selected 57KO-specific RNA splicing events using total RNA from BCBL-1 57KO cells treated with VA for 24 h. The sizes of expected amplicons with indicated primer pairs in the presence of reverse transcriptase (+RT) are shown below, together with the chromatographs from Sanger sequencing confirming the mapped splice junctions. The asterisks (*) mark the non-specific RT-PCR amplicons. SJ-61+6 means a RT-PCR product from the double RNA splicing first from the splice junction SJ-61 and then SJ-6 (see Fig 3).

https://doi.org/10.1371/journal.ppat.1010311.g006

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Table 3. The additional splice junctions (SJ) with ≥10 splice reads detected predominantly from the 57KO genome in BCBL-1 cells.

For details, see Table 1.

https://doi.org/10.1371/journal.ppat.1010311.t003

We previously identified ORF57 protein as a viral splicing factor promoting splicing of K8 intron 2 to express functional K8α [17] by interaction with host splicing factor SRSF3 to attenuate its suppressive activity on K8 intron 2 splicing [18]. Surprisingly, we did not observe an obvious retention of K8 intron 2 from the 57KO genome over the WT genome (Fig 3 and Table 1). Although the cause of this discrepancy remains to be understood, we were assuming that the remaining expression of PAN RNA from the 57KO genome might compensate ORF57 loss by sponging SRSF3 in the 57KO cells. As expected, we found that overexpression of PAN RNA could promote K8 intron 2 splicing in HEK293T cells (S3A Fig). Additional reduction of SRSF3 RNA and protein levels due to virus-host shut off during lytic replication (S3B Fig) may further reduce the dependence of K8 splicing on ORF57, especially in the later stage of KSHV infection.

Presence of the long-range RNA splicing events crossing over the KSHV genome

Most previously described RNA splice junctions represent the highly prevalent splice junctions supported by ≥10 splice junction reads, which were mapped within well-defined transcriptional units (Figs 3, 4 and 6). However, we also detected numerous long-range splicing events crossing over the large parts of the virus genome both from the WT and 57KO genomes (Fig 2C). To better define these splicing events, we first extracted all splice junction reads covering an intron size ≥10 kb and had at least two splice reads either from one genome or both WT and 57KO genomes (Fig 7A). We found a total of 14 such splice junctions, 7 of them from the WT genome and 10 from the 57KO genome, with 3 found consistently from both genomes in BCBL-1 cells (S2 Table). A small overlap between the WT genome and the 57KO genome suggests a possible role of ORF57 in regulation of generating these RNAs. Most long-range splicing events occur in low frequency with a few (less than 10) splice reads and only two long-range splice junctions derived from ORF48 splicing to ORF25 (SJ-34) and from ORF48 splicing to the second exon of ORF29 (SJ-35) passed ≥10 supporting splice reads threshold (Fig 4 and Table 1). All long-range splice junctions were generated using canonical splice sites (S1 Table). To verify selected long-range splicing events, we performed RT-PCR using various sets of flanking primers on total RNA isolated from both WT and 57KO BCBL-1 cells. Sanger sequencing of the obtained RT-PCR products confirmed the mapped splice junctions (Fig 7B). Some of these long-range RNA splicing events were also detectable in iSLK/Bac16 and JSC-1 cells with lytic KSHV infection (Figs 7C and S4A). Together, these data indicate the existence of numerous conserved long-range splicing events in KSHV RNA processing. Although their biological relevance remains to be determined, these long-range spliced RNA isoforms may encode several new proteins (S4B Fig) lacking any homology to the known viral proteins worth further investigating in future studies.

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Fig 7. Long-range KSHV RNA splice identified in BCBL-1 cells with lytic KSHV infection.

(A) The Sashimi plot showing all splice junctions with an intron size ≥10 kb supported with at least 2 splice junction reads. See S2 Table for details. (B) Validations of selected long-range RNA splicing events by RT-PCR on total RNA from the WT genome or 57KO genome in the cells with lytic KSHV replication induced by VA for 24 h. Above the gel is a schematic showing a selected splicing event in orange arches for minus DNA strand-derived RNA transcripts and blue arches for plus DNA strand-derived RNA transcripts, relative genomic locations, predicted intron sizes, and primers used for RT-PCR. The arches lacking number-based nomenclature did not pass ≥10 of supporting splice reads (see S2 Table). Below is the gel electrograph of obtained RT-PCR products. The obtained RT-PCR products were reamplified and confirmed by Sanger sequencing. See sequencing primers in S6 Table. The chromatographs on the right show the identified splice junctions with the exonic sequences marked in black and the intronic sequences spliced out shown in red. The numbers represent exon-exon junction positions in the KSHV genome (GenBank Acc. No. HQ404500) after RNA splicing. (C) The conservation of long-range splicing events in JSC-1 and iSLK/Bac16 cells. Total RNA from the cells with induced KSHV lytic infection was used in RT-PCR using primers showed in (B). See S4A Fig for more details.

https://doi.org/10.1371/journal.ppat.1010311.g007

Genome-wide KSHV RNA splicing and circular RNA production

RNA splicing usually occurs from the 5′ to 3′ direction and produces a spliced RNA in linear form. However, RNA splicing may occasionally generate a circular RNA (circRNA) by back-splicing when a downstream 5′ ss splices back to the upstream 3′ ss crossing over the exon(s) [34]. Viral circRNAs were reported in KSHV-infected cells; many of them were generated from the RNA transcripts lacking any RNA splicing [35–37]. We subsequently performed viral circRNA prediction from the same RNA-seq library reads using CircRNA Identifier CIRI2 pipeline (https://sourceforge.net/projects/ciri/) [38,39] (S3 Table). As shown in Fig 8A, we predicted a total of eight KSHV viral circRNAs, of which 6 were from the WT and 2 from the 57KO genome. Among 6 circRNAs from the WT genome, one mapped to PAN, four to antisense PAN (also referred to as K7.3), and one to vIRF4 (K10). Only 2 viral circRNAs were predicted from the 57KO genome, with one mapped to the antisense PAN and the other to ORF57. The supporting back-splicing reads to individual circRNAs were relatively low, ranging from 2 to 9 back-splicing reads from all samples in each group. All viral circRNAs, except WT-circRNA-1, were predicted in low abundance in BCBL-1 cells by Toptan and colleagues [35]. Given the circRNA being generated by back-splicing from the splice sites used for linear RNA splicing, we next compared all predicted circRNAs in production coordination with those splice sites supported by at least two splice junction reads identified in our study (S4 Table). We found that most viral circRNAs (Fig 8A and 8B) are not supported by the splice sites used for linear RNA splicing, besides WT-circRNA-6 and KO-circRNA-2. As the ORF57 gene is reversely orientated in the 57KO genome [21], the KO-circRNA-2 was genuinely back-spliced by crossing over the exon 2 [40]. We subsequently performed the RT-PCR using several inverse primer pairs on total RNA from the WT and 57KO genome in BCBL-1 cells with lytic induction to verify the predicted viral circRNAs. Unfortunately, we failed to detect any circRNAs from the PAN region even using 40 amplification cycles and 500 ng of cDNA derived from total RNA extracted either from BCBL-1 cells with a WT or 57KO genome. Even we could not verify any; it is worth noting that the reported PAN circRNAs [35–37] appear mainly next to the ORF57-MRE-I motif we previously identified for PAN RNA stability [26] (Fig 8B). We noticed that the predicted PAN circRNAs from Toptan’s report were at different positions from the reported PAN circRNAs in Tagawa’s report (S5 Fig) [35, 36]. Ungerleider’s report had no description of PAN circRNAs at all [37]. Subsequently, we analyzed all reported PAN circRNAs with more than 1000 back-splicing junction reads along with our predicted PAN circRNAs for their splice site strength (S5 Fig and S5 Table). We found none of them give a reasonable splice site score strong enough to carry out a true RNA splicing reaction (S5 Fig). Data suggest that all predicted PAN circRNAs with the current prediction program were unreal.

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Fig 8. Linear RNA splicing and production of KSHV circRNAs.

(A) Identification of KSHV circRNAs from RNA-seq in BCBL-1 cells with a WT or 57KO genome during lytic replication induced by 24 h valproic acid treatment using a circular RNA prediction software CIRI2 [38, 39]. (B) Distribution and coverage of RNA-seq reads on PAN, detected linear PAN RNA splice junctions (red and blue arches) with minimum 2 splice junction reads and predicted viral PAN circRNAs (thick blue lines, see panel A for details) in WT and 57KO BCBL-1 cells with lytic replication. MRE-I represents the Mta or ORF57-responsive element I in PAN RNA identified by anti-ORF57 CLIP [26]. (C) The RNA-seq reads mapped to KSHV vIRF4 (K10) locus in WT (orange) and 57KO (pink) cells with reads-coverage depth shown in the upper right corner. The arches show a direction and number of splice reads detected for linear canonical splicing (orange and pink arches) and back-splicing (grey arches). Below is a diagram of KSHV vIRF4 locus with detected exons (orange boxes), introns (numbered orange arches) with the corresponding splice sites (D = splice donor and A = splice acceptor). The open triangle represents a predicted transcriptional start site (TSS). Predicted unspliced and spliced forms of WT-circRNA-6 are shown in grey. The primers used to amplify linear and circular vIRF4 RNAs are shown as arrows. (D) The effect of 57KO on the production of vIRF4 linear and circRNAs. The total RNA from WT or 57KO cells isolated 24 h after induction of viral lytic cycle with or without RNase R digestion was used as a template to amplify circular vIRF4 RNA using a primer pair of oVM490 and oVM516 and linear spliced vIRF4 RNA using a primer pair of oVM489 and oVM491 as shown in the panel C. Host GAPDH RNA was amplified as an RNA loading control with the primer pair shown in the S6 Table. The percentage of individual RNA was calculated based on band signal density using ethidium bromide-stained agarose gels using ImageLab software (BioRad) with the amount of PCR products obtained from WT RNA without RNase R treatment set as 100%. The asterisk (*) indicates a heteroduplex band derived from two RT-PCR products as described [75].

https://doi.org/10.1371/journal.ppat.1010311.g008

Interestingly, the predicted WT-circRNA-6 matches the previously identified circRNA from vIRF4 RNA [35,37]. We identified two linear RNA splicing events in vIRF4, SJ-42, and -43, with SJ-42 reads being about twice more abundant than SJ-43 (Fig 8C and Table 1). It is worth noting that retention of the SJ-43 intron is required to express full-length vIRF4 protein. The 3′ ss of the SJ-43 intron in vIRF4 also functions as an acceptor site for the generation of WT-circRNA-6, whereas the donor site used for WT-circRNA-6 production is in vIRF4 exon 3 and not even used for RNA splicing of linear vIRF4 RNA. As a result, the second intron could be spliced or retained in vIRF4 circRNAs, leading to the generation of two isoforms of circRNA (Fig 8C). We observed about two-fold reduction of splice junction reads in BCBL-1 cells with the 57KO genome when compared with the WT. Using different primer sets in RT-PCR and RNase R digestion, we were able to detect and distinguish the linear from circular vIRF4 RNAs and the reduced expression of vIRF4 RNA from the 57KO genome in BCBL-1 cells when compared with the WT genome (Fig 8D), where the linear vIRF4 RNA in the 57 KO cells appeared ~80% reduction and accompanied by ~20% reduction of the vIRF4 circRNA. Compared to GAPDH, we also found the linear vIRF4 RNA appeared unexpectedly a little more resistant to RNase R digestion (Fig 8D).

Effect of ORF57 on global KSHV RNA splicing

To fully comprehend the contribution of ORF57 to KSHV RNA splicing regulation, we also compared the number of splice reads assigned to each splice junction detected from both WT and 57KO genomes (see Table 1). Using a minimal 2-fold change cut-off, we identified 21 dysregulated RNA splicing events from the 57KO genome, with 11 being downregulated and 10 being upregulated. As expected, the most downregulated was the splicing of ORF57 first intron (SJ-9) due to the inversed ORF57 orientation in the 57KO genome [21]. Other downregulated splicing events due to lack of ORF57 expression were mapped to RNA transcripts from ORF2 (SJ-14), ORF70/K3 (SJ-18), K4.2/K4 (SJ-22), K5/K6 (SJ-25, -31, -32, and -33), ORF45/46 (SJ-37), K10 (SJ-42), and K15 (SJ-52). The RNA splicing events upregulated in the 57KO cells, ranging from 2.00- to 4.44-fold, were mapped to the transcripts of ALT RNA (SJ-12), ORF70/K3 (SJ-15 and -21), ORF48/ORF25 (SJ-34), ORF47/ORF45 (SJ-36, -39, -40), ORF48/ORF45 (SJ-41), and K15 (SJ-56 and -57). Even though the expression of most KSHV genes is not significantly altered from the 57KO genome, some of the observed splicing changes resulted in altered gene expression. A downregulation of ORF2, K6, and K4.2/K4 expression in the 57KO cells may at least partially explain a reduction of splice junction reads in these transcripts. On the contrary, the splicing of some transcripts, like ORF47/45, was increased from the 57KO genome despite their overall transcription level was reduced (Table 1). Together, this study discovered that ORF57 has both stimulatory and suppressive effects on KSHV RNA splicing, which could also be confirmed by RT-PCR (S2C Fig). Subsequently, we focused on the altered RNA splicing of KSHV K15 and ORF70/K3, two viral transcripts containing multiple introns and expressed from two different genomic loci without overlapping transcription. Thus, we could examine how ORF57 directly affects alternative RNA splicing of these two different transcripts.

KSHV ORF57 regulates alternative RNA splicing of K15

K15, located at the right end of the long unique region of the KSHV genome, encodes a viral membrane protein with a variable number of transmembrane domains [41,42]. Through its cytoplasmic C-terminus containing one proline-rich Src homology 3 (SH3) and two SH2-binding sites, K15 interacts with several host factors, such as phospholipase Cγ1 (PLC γ1) to activate numerous cellular signaling pathways [43]. K15 is expressed in both latent and lytic infected cells. During latency, K15 promotes the invasiveness of KSHV tumors, KSHV-induced angiogenesis, and the survival advantage of infected cells [44,45]. By activating PLC γ1, ERK1/2 and AKT1 signaling pathways, K15 promotes reactivation of KSHV from latency and is required for KSHV lytic replication [46,47]. K15 pre-mRNA harbors eight exons and seven short introns (Fig 9A). All internal introns are required to express K15 isoforms with a variable number of transmembrane domains via alternative splicing [41,42]. We found that the 57KO genome exhibited at least a 2-fold increase of its intron 1 (SJ-57) and intron 2 (SJ-56) splicing, but a substantial decrease (below 10 splice junction reads) of intron 6 (SJ-52) splicing (Table 1). Using the primer sets shown in Fig 9B, RT-PCR confirmed the increased intron 1 and intron 2 splicing in K15 RNA expressed from the 57KO versus the WT genome (Fig 9C). Calculated PSI (percentage spliced-in index) for both introns also showed a 2-fold increase of the splicing from the 57KO genome over the WT genome, as shown by RNA-seq analysis (Table 1). Consistently, we observed an increased amount of fully spliced K15 RNA expressed from the 57KO genome in BCBL-1 cells (Fig 9D). In contrast, expression of ORF57 from the WT genome led to an increased level of unspliced K15 RNA, accompanied by decreased level of fully spliced K15 RNA (Fig 9D). Retention of the intron 1 or intron 2 from K15 RNA splicing in the presence of ORF57 creates a premature termination codon in these isoforms of K15 RNA, presumably triggering the non-sense mediated RNA decay. We also observed a few other K15 introns with alternative RNA splicing in the WT or the 57KO genome, but none passed ≥10 reads threshold (S2 Table). More specifically, in the WT cells, we observed exon 5 skipping and use of an alternative 3′ ss in exon 8, whereas the cells containing the 57KO genome showed the usage of an alternative 5′ ss in exon 1 and an alternative 3′ ss in intron 1. Together, our data indicate that, by regulating K15 RNA splicing, ORF57 might alter the levels of full-length K15 protein and its isoforms during lytic infection.

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Fig 9. ORF57 regulates K15 RNA alternative splicing.

(A) The splice junctions and RNA-seq coverage of K15 transcripts detected in BCBL-1 cells bearing a WT (orange) or 57KO genome (pink) during KSHV lytic infection. Black arrows mark splice donor (D) and acceptor (A) sites. (B) Structure of the K15 pre-mRNA with the position of mapped pA cleavage site (CS) and predicted transcriptional start site (TSS). The thick black lines represent the exons and the dotted lines the introns. The arrows below show the positions and orientations of the primers used in RT-PCR listed in the S6 Table. (C and D) Gel electrographs of RT-PCR products obtained from total RNA from the WT and 57KO genomes in BCBL-1 cells undergoing lytic replication harvested 24 h after VA treatment, with the primer pairs shown in (B). The samples without reverse transcription (- RT) were used as a negative control. The host GAPDH was used as a loading RNA control. Unspl., unspliced pre-mRNA; Spl., spliced mRNA; PSI, percent spliced-in of the alternative exon (s) or splice site (% inclusion = inclusion/sum of inclusion + exclusion) [76].

https://doi.org/10.1371/journal.ppat.1010311.g009

KSHV ORF57 promotes the RNA splicing-dependent expression from K3 to ORF70

ORF70/K3, a bicistronic RNA with complex alternative splicing, is the second viral RNA of which splicing was notably affected from the 57KO genome (Table 1). It encodes viral thymidylate synthase ORF70 and viral E3-ubiquitin ligase K3 [48, 49]. We mapped two major introns in ORF70/K3 RNA as reported [6,50]. The 540 nt-long intron 1 (SJ-21) lies within the ORF70 coding region, while the 474 nt-long intron 2 (SJ-17) sits entirely into the intergenic region between ORF70 and K3 (Fig 10A). Similar to previous reports, we also observed low-frequent RNA splicing from the intron 1 donor site to the intron 2 acceptor site (SJ-19), resulting in removing a 1228 nt-long intron [6]. Several RNA isoforms generated from this region by alternative RNA splicing were reported in PEL cells with lytic KSHV infection [6,50]. These include an unspliced RNA transcript (isoform A), a single spliced RNA isoform retaining the intron 1 (isoform B), a single spliced isoform retaining the intron 2 (isoform C), a double-spliced isoform (isoform D), and a shortest isoform derived from RNA splicing of the intron 1 donor site to the intron 2 acceptor site (isoform E) (Fig 10B).

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Fig 10. Regulation of ORF70/K3 RNA alternative splicing by ORF57.

(A) The most prevalent splice junctions and RNA-seq reads-coverage of ORF70/K3 transcripts from the WT genome (orange) and the 57KO genome (pink) in BCBL-1 cells during KSHV lytic infection. (B) Diagrams of major ORF70/K3 splicing isoforms. Black boxes represent the exons and dashed lines the introns. The arrows below represent oligos used in Northern blot and RT-PCR (see S6 Table for the details). On the right are predicted sizes of all spliced isoforms and their relative abundance in the cells with the WT or 57KO genome. (C and D) Northern blot analysis of ORF70/K3 splicing isoforms expressed from the WT and 57KO genomes in BCBL-1 (C) and iSLK/Bac16 (D) cells with KSHV lytic replication. Total cell RNA was extracted and examined by Northern blot using two separate ³²P-labeled oligo probes (oVM441 and oVM476) (C and D) or by RT-PCR using a primer set of oVM440 and oVM442 shown in (B) in the absence (-) or presence (+) of reverse transcriptase (RT) (D, right panel and S2C Fig). The 18S rRNA in Northern blot and GAPDH RNA in RT-PCR analyses indicate the amount of total RNA in individual sample loading. (E-F) ORF57 binding to ORF70/K3 RNA. (E) Distribution of ORF57 CLIP-seq reads (blue) mapped to the ORF70/K3 locus. The red box marks the zoomed-in area shown below. The ORF57 CLIP-seq was described in our previous report [53], and the obtained reads are publicly available in NCBI GEO (Acc. No. GSE179726). The intron 1 3′ ss (acceptor site) at nt 20263 is indicated as an arrow A. (F) The RNA-immunoprecipitation (RIP) assay was performed using whole-cell extracts from valproic acid (VA) treated BCBL-1 cells after UV crosslinking with an anti-ORF57 antibody or a control non-specific IgG. The pulled-down RNA was used as a template in RT-PCR to detect ORF70/K3 RNA with oVM441 and oVM481 primers (B). (G) Splicing rescuing of ORF70/K3 B isoform production from the 57KO genome by ectopic ORF57 expression. The iSLK/Bac16 cells with the 57KO genome were transfected with the increased amount of ORF57-expression vector (pORF57) or an empty vector (pcDNA3.0), followed by 24 h induction of lytic replication with DOX/Bu treatment. Total RNA from the transfected cells was isolated and analyzed by Northern blot together with the RNA from non-transfected cells with a WT and 57KO KSHV genome as controls. The oVM441 probe was used to detect the ORF70/K3 splicing isoform and oVM11 for detection of ectopic (ecto.) or endogenous (endo.) ORF57 expression. The 18S rRNA indicates the amount of total RNA in individual sample loading. (H) Correlation of ORF57 expression with ORF70/K3 isoform production during KSHV lytic replication. Total RNA isolated from BCBL-1 cells at various time points after induction of lytic replication by valproic acid (VA) was analyzed by Northern blot using ORF70/K3-specific probe oVM441 (B) and ORF57-specific probe (oVM11) (S6 Table). The 18S rRNA level detected by ethidium bromide staining was used as a loading control.

https://doi.org/10.1371/journal.ppat.1010311.g010

Our RNA-seq analysis revealed a significant shift in ORF70/K3 RNA splicing between the WT and 57KO genomes during KSHV lytic infection. In BCBL-1 cells with the WT genome, ORF70/K3 RNA predominantly uses the intron 2 splicing to avoid disruption of the ORF70 ORF, with splicing efficiency of the intron 1 being ~5-fold less than that of the intron 2 (691 intron 1-spliced reads vs 3393 intron 2-spliced reads). On the contrary, in the cells with the 57KO genome, we observed almost equal splicing efficiency for both intron 1 and 2 (1839 intron 1-spliced reads vs 2048 intron 2-spliced reads), indicating a 2.66-fold increase of the intron 1 splicing efficiency but a 1.67-fold decrease of the intron 2 splicing efficiency in the 57KO cells. However, the splicing from the intron 1 5′ ss to the intron 2 3′ ss (SJ-19) appeared only a minimal change between the WT genome (26 reads) and 57KO genome (38 reads) (Table 1). Subsequently, we compared the abundance of individual isoforms by Northern Blot on total RNA extracted from the WT and 57KO genome in BCBL-1 cells with lytic replication to confirm these data. First, we use an antisense oligo probe derived from exon 2 (oVM441) to detect all predicted isoforms except isoform E. As shown in Fig 10C, three major RNA isoforms were detected from the WT genome, corresponding to the predicted RNA isoforms A (2.5 kb), B (2 kb), C (2 kb), and D (1.5 kb), with the 2 kb transcripts being the most prevalent. Two minor RNA species, between ~3–4 kb, are presumably expressed from the upstream promoters as reported [6,50]. However, in the cells with the 57KO genome, we detected only a single 1.5 kb RNA band corresponding to the double-spliced isoform D (Fig 10C). Since this probe could not differentiate the RNA isoform B from the isoform C due to their similar sizes, we reprobed the same membrane with the oligo probe from the intron 1 (oVM476). We observed two major RNA bands in the size of ~2.0 and 2.5 kb from the WT cells, but not from the 57KO cells, thus confirming their identity as the unspliced isoform A and the single spliced isoform B with retention of the intron 1 in the WT cells (Fig 10C). As expected, this probe cannot detect the double spliced isoform D missing both intron 1 and intron 2 (Fig 10C).

To investigate if ORF57-mediated regulation of ORF70/K3 RNA splicing is unique to BCBL-1 cells, we took advantage of inducible iSLK/Bac16 cells carrying a KSHV WT or 57KO genome generated using the same set of gRNAs for the 57KO in BCBL-1 cells [21]. Similar to BCBL-1 cells, we were able to detect the corresponding RNA isoforms A, B/C, D, and E in the cells carrying the WT genome, but only the isoform D in the cells carrying the 57KO genome (Fig 10D). These data reconfirmed that ORF57 regulates ORF70/K3 RNA splicing in the context of KSHV genome in iSLK/Bac16 cells.

KSHV ORF57 binds ORF70/K3 bicistronic RNA to regulate its RNA splicing

KSHV ORF57 is a viral RNA-binding protein that binds to its target RNAs via its disordered N-terminal domain [51,52]. To determine if ORF57 binds to ORF70/K3 bicistronic RNA to regulate its splicing, we first analyzed our recently published ORF57 CLIP-seq data representing the ORF57-associated RNAs in BCBL-1 cells during the viral lytic infection [53]. We identified the ORF57-bound ORF70/K3 RNA in the ORF57 CLIP-seq. Interestingly, among ORF57 CLIP-seq reads mapped to ORF70/K3 locus, the highest number of reads-peak covers a 75-nt region in the intron 1 of ORF70/K3 RNA (Fig 10E), 53 nts upstream of the nt 20263 3′ ss.

To further confirm ORF57 direct binding to ORF70/K3 RNA, we performed RNA-immunoprecipitation (RIP) using an anti-ORF57 antibody to immunoprecipitate the UV cross-linked RNA-protein complexes in the cell lysate prepared from BCBL-1 cells with KSHV lytic infection reactivated by valproic acid (VA) treatment for 24 h. The ORF70/K3 RNA in the RIP complex was RT-PCR amplified using ORF70-specific primers oVM441 and oVM481 spanning over the peak region identified by CLIP-seq. As shown in Fig 10F, we demonstrated that the anti-ORF57 antibody, but not a non-specific IgG control, efficiently pulled down the ORF70/K3 RNA.

Given a profound role of ORF57 in ORF70/K3 splicing, we next tested if restoration of ORF57 expression will rescue the isoform B expression in the 57KO cells. We transfected the iSLK/Bac16 57KO cells with an increased amount of the ORF57-expression vector, followed by the induction of the viral lytic infection by combined butyrate and doxycycline treatment. We used the corresponding amount of empty vector (pcDNA 3.0) as a negative control. The total RNA collected 24 h after induction was analyzed in Northern blot analysis. As expected in Fig 10G, the WT cells expressed mainly the B/C isoforms, while the D isoform was the most abundant in the 57KO cells. Most importantly, we found that ectopic ORF57 expression led to partially rescue the isoforms B/C expression from the 57KO genome in a dose-dependent manner. These data provide the strong evidence of ORF57’s role in regulation of ORF70/K3 RNA splicing.

K3 was proposed to be a viral immediate early gene [6, 50] and ORF57 is a viral early gene whose expression gradually increases during KSHV lytic cycle [54]. To see how ORF70/K3 RNA splicing correlates with ORF57 expression, we performed a time-course study in the WT BCBL-1 cells after induction of lytic KSHV infection by valproic acid and collected total cell RNA at 12, 24, and 36 h after VA induction to monitor the dynamic production of ORF70/K3 RNA isoforms by Northern blot analysis using an oVM441 probe described in Fig 10B. As shown in Fig 10H, all three RNA bands representing isoforms A, B/C, and D were detectable at 12, 24, and 36 h; however, their ratio displaced a substantial change between 12 and 24 h, from an approximate proportion 1.2 to 1 of isoforms D to B/C at 12 h to only 0.4 to 1 at 24 h, in favor of isoform B/C production in BCBL-1 cells with lytic KSHV infection. Consistently, this ORF57-induced isoform switch of ORF70/K3 RNAs was reproducible in iSLK/Bac16 cells with KSHV lytic infection in the other time course studies.

KSHV ORF57-mediated ORF70/K3 RNA splicing regulates the production of thymidylate synthase ORF70 and viral E3-ubiquitin ligase K3

Given the bicistronic nature of ORF70/K3 RNA, we next investigated how its RNA splicing regulated by ORF57 affects the expression of individual proteins. As mentioned above, ORF57-sensitive intron 1 lies entirely within the ORF70 coding region. Thus, only the RNA isoforms A and B retaining intron 1 could express a 337-aa full-length ORF70 protein (ORF70FL, Fig 11A). The RNA isoforms C and D lacking intron 1 would express a truncated or spliced ORF70 (ORF70SP) in size of 157 aa residues. ORF70SP lacks the central domain between aa 88 to 269, which bears a catalytic site of thymidylate synthase [55]. The isoform E potentially encodes a further 126 aa-long truncated ORF70 (ORF70TR), consisting of only the N-terminal 88 aa residues encoded by the first exon fused with additional 38 aa residues expressed from different frame (Fig 11A). Interestingly, the K3 coding region for viral E3-ubiquitin ligase remains intact in all spliced RNA isoforms.

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Fig 11. Ectopic ORF57 inhibits alternative splicing of bicistronic ORF70/K3 RNAs to regulate the expression of viral thymidylate synthase ORF70 and viral E3-ubiquitin ligase K3 in HEK293T cells.

(A) A number of the amino acid residues of full length (FL), spliced (SP), truncated (TR) ORF70 and K3 proteins expressed from the corresponding RNA splicing isoforms are shown on the right (see details in Fig 10B). (B) Diagram of an ORF70/K3 minigene with a FLAG-tag on the ORF70 N-terminus and a c-myc-tag on the K3 C-terminus. The minigene under control by a CMV IE promoter contains the viral genomic DNA fragment covering the K3 and ORF70 coding regions and their intergenic region to ensure RNA splicing of this bicistronic RNA transcript. (C and D) Western (C, WB) and Northern blot (D, NB) analyses of HEK293T cells transfected with various ratios of the ORF70/K3 minigene over the ORF57 expression (+) or empty (-) vectors. (C) Expression of ORF70 protein was detected by WB using an anti-FLAG and K3 protein using an anti-c-myc antibody. ?, unknown protein band. (D) The changes in ORF70/K3 RNA splicing from the minigene vector in HEK293T cells in the absence (-) or presence (+) of ectopic ORF57 expression were monitored by Northern blot analysis on total cell RNA with two separate oligoprobes shown in Fig 10B. The 18S rRNA level detected by ethidium bromide (EtBr) staining was used as a loading control. (E) A diagram depicting the role of ORF57 in the regulation of ORF70/K3 RNA alternative splicing to mediate a switch from K3 to ORF70 protein expression during KSHV lytic replication.

https://doi.org/10.1371/journal.ppat.1010311.g011

Due to the lack of available antibodies against ORF70 and K3, we cannot directly measure the effect of observed regulation of ORF70/K3 alternative RNA splicing by ORF57 on the expression of ORF70 and K3 proteins. Therefore, we constructed a minigene reporter by cloning the ORF70/K3 locus into a mammalian expression vector to monitor their expression by introducing two different epitope tags: FLAG-tag on the ORF70 N-terminus and c-myc on the K3 C-terminus (Fig 11B). The ORF70/K3 minigene was then transfected into HEK293T cells in various ratios with a control empty or an ORF57-expressing vector. Twenty-four after transfection, the cells were harvested and blotted with an anti-FLAG antibody to detect ORF70 and an anti-myc antibody for K3 protein detection. As shown in Fig 11C, the minigene in the absence of ORF57 mainly expressed K3 protein and also a small amount of ORF70 protein (lanes 3 and 5). On the contrary, ORF57 co-expression switched from K3 expression to all three isoforms of ORF70 protein, with ORF70FL being the most abundant (Fig 11C). The efficiency of the switch was dependent on the ORF57 level and was most prominent at the 2:1 ratio of the minigene plasmid versus the ORF57-expression vector (compare lanes 2, 4, and 6).

We next performed the Northern blot analysis of the corresponding total RNA samples using the same antisense oligoprobes described in Fig 10B. As shown in Fig 11D, in the absence of ORF57, we found a double-spliced isoform D as a major RNA isoform expressed from the minigene (lanes 1, 3, and 5), which could be confirmed by both exon 2 (oVM441) and intron 1 (oVM476) probes. In contrast, co-expression of ORF57 was found not only to stabilize all isoform RNAs expressed from the minigenes as reported [22, 26], but also to substantially increase the single spliced isoform RNA B and to slightly increase the unspliced pre-mRNA (isoform A) (lanes 2, 4 and 6). Together, we demonstrated that ORF57-mediated splicing of the minigene-derived ORF70/K3 RNA is responsible for controlling the expression levels of viral thymidylate synthase ORF70 and viral E3-ubiquitin ligase K3, which is independent of other viral factors.

Cell cultures

KSHV-positive BCBL-1 [20] and JSC-1 [73] cells were cultivated in RPMI 1640 medium (Thermo Fisher Scientific). The iSLK cells carrying KSHV Bac16 genomes [69] and HEK293T (ATCC) cells were cultivated in a DMEM medium (Thermo Fisher Scientific). All media were supplemented with 10% fetal bovine serum (FBS, Hyclone, Cytiva) and 1 × Penicillin-Streptomycin-Glutamine (Thermo Fisher Scientific). Hygromycin B (150 μg/ml), G418 (250 μg/ml) and 1 μg/ml puromycin were added to the culture media of iSLK/Bac16 cells to maintain the KSHV genome. The ORF57 knock-out (57KO) in BCBL-1 and iSLK/Bac16 cells was generated by a modified CRISPR/Cas9 technology as described [21]. The single clones of parental cells transfected with a plasmid expressing Cas9 lacking gRNA expression were also selected in parallel and used as control wild-type (WT) cells. To reactivate KSHV lytic replication, BCBL-1 and JSC-1 cells were treated with 1 mM final concentration of sodium salt of valproic acid (VA, Sigma-Aldrich) or 3 mM sodium butyrate (Bu, Sigma-Aldrich), respectively, for 24 h. KSHV replication in iSLK/Bac16 cells was reactivated by a combination of 1 μg/ml doxycycline (DOX, Clontech) and 1 mM sodium butyrate (Bu, Sigma-Aldrich). RNA samples were collected 24 h after the reactivation.

RNA-seq and ORF57 CLIP-seq data analysis

Total RNA from 4 replicates of BCBL-1 WT clone B4 and 57KO clone #6 cells were isolated by TriPure Reagent (Roche) 24 h after induction with VA. The genomic DNA was removed using RNeasy Mini Kit (Qiagen) on-column DNase-treatment. Total RNA-seq libraries were prepared with TruSeq Stranded Total RNA Library Kit and subjected to pair-end sequencing using HiSeq3000/4000 chemistry and 2 × 150 nts modality. Reads were trimmed with CutAdapt v.1.18 and mapped to human GRCh38 (hg38)/KSHV (GenBank Acc. No. HQ404500) chimeric genome using STAR aligner v.2.7.0f. [23]. The changes of viral gene expression between individual groups were determined by the Limma Voom package using reads mapped to annotated KSHV ORFs. The splice reads mapped to the KSHV genome were extracted to identify unique viral splice junctions. The distribution of splicing junction along the KSHV genome was visualized using Integrative Genomics Viewer (IGV, Broad Institute). The strength of viral splicing sites was calculated using the MaxEntScan::score algorithm [32]. The original sequence libraries were deposited in NCBI’s GEO repository (Acc. No. GSE194239). ORF57 CLIP-seq was detailed in our previous publication [53] and the obtained sequence libraries are publicly available in NCBI’s GEO depository (Acc. No. GSE179726). The obtained reads were mapped to chimeric human GRCh37 (hg19)/KSHV (GenBank Acc. No. U75698) reference genome using STAR aligner (version 2.7.6a) [23] and visualizes by IGV.

RNA-immunoprecipitation (RIP)

To isolate ORF57 bound RNAs, we performed a RIP assay as previously described [53]. Briefly, BCBL-1 cells treated with 1 mM valproic acid (VA) for 24 h were exposed to 480 mJ/cm² UV light of wavelength 254 nm. The cross-linked cells were lysed in the radioimmunoprecipitation assay buffer (RIPA, Boston Bioproducts) and the obtained cell extract was used for immunoprecipitation with protein A-agarose beads (Millipore-Sigma) coated with the rabbit anti-ORF57 antibody [51] or a control non-specific rabbit IgG (Thermo Fisher Scientific). The pulled-down RNA was released by proteinase K, extracted by phenol:chloroform, and precipitated. The extracted RNA was used for RT-PCR detections.

RT-PCR and RT-qPCR

Before RT, the total RNA isolated by TriPure Reagent (Roche) was treated with Turbo DNase (Thermo Fisher Scientific). The specific products were amplified using two-step RT-PCR using random hexamers and primers listed in the S6 Table. The reactions without reverse transcriptase were used as the negative controls. The RT-PCR products were separated in agarose gel, purified, and the splicing junctions were verified by Sanger sequencing. For RT-qPCR, the DNase-treated RNAs were converted to cDNAs by SuperScript First-Strand Synthesis System (Thermo Fisher Scientific) using random hexamers as recommended. The resulting cDNAs were used as templates in qPCR reactions containing TaqMan Universal PCR Master Mix (Thermo Fisher Scientific) and custom PrimeTime qPCR assay (IDT) for KSHV PAN and ORF59 RNAs [25,26]. The cellular GAPDH level detected by the TaqMan assay (Hs02758991_g1, Thermo Fisher Scientific) was used for the normalization. All amplifications were carried out on StepOne Real-Time PCR System (Thermo Fisher Scientific). The changes in expression level between individual samples were determined by the ΔΔC_t method.

Northern blot

Total RNAs isolated by TriPure reagent were separated along with Millennium RNA marker (Thermo Fisher Scientific) in formaldehyde-containing 1% agarose gel in 1 × MOPS buffer. After transfer, the membranes were hybridized overnight with antisense oligo probes (S6 Table) end-labeled with T4-PNK (New England Biolabs) using ³²P-γ-ATP (Perkin Elmer). Washed membranes were exposed to a phosphor imaging screen and scanned by GE Typhoon TRIO Imager (GE Healthcare). Obtained images were processed by Image Lab software (BioRad).

Plasmids and reporter plasmid construction

The construction of K8 splicing reporter pST3, containing KSHV K8β cDNA, was described in [29]. The plasmid pJM1 was generated by cloning KSHV PAN RNA into pcDNA3.0 (Invitrogen) [26]. KSHV ORF57 expression vector pORF57 [40] was used to rescue ORF57 expression in the iSLK/Bac16 57KO cells. The empty vector pcDNA3.0 (Invitrogen) used a negative control. To generate a minigene system for monitoring ORF70/K3 RNA splicing and protein expression (pVM140), the ORF70/K3 locus was amplified with oVM454 and oVM455 primers (see S6 Table for details) on BCBL-1 total DNA allowing its in-frame cloning into pCMV-FLAG-myc-22 (Sigma-Aldrich) using KpnI and NotI restriction sites. All plasmid transfections were performed by LipoD293 In Vitro DNA transfection reagent (SignaGen Laboratories) as recommended.

Western blot

Total proteins, prepared by cells direct lysis in SDS protein sample buffer, were separated in 4–12% Bis-TRIS NuPAGE gels (Thermo Fisher Scientific) in 1 × MES buffer and transferred onto a nitrocellulose membrane. The in-house produced anti-ORF57 polyclonal antibody was used to ORF57 expression [51]. The anti-ORF50 antibody was generously provided by Dr. Yoshihiro Izumiya (University of California, Davis). The anti-Cas9 mouse monoclonal antibody was purchased from Cell Signaling (cat. no. 14697). The anti-FLAG polyclonal antibody (cat. no. F7425, Sigma-Aldrich) was used for FLAG-ORF70 and anti-c-myc clone 9E10 antibody (a generous gift from Dr. Xuefeng Liu, Georgetown University) for K3-myc fusion detection in the reporter assay. Mouse monoclonal anti-K8 antibody were obtain from ProMab Biotechnologies (cat. no. 20015). In-house generated culture media from the mouse hybridoma clone (7B4) culture expressing anti-SRSF3 antibody was used for SRSF3 detection. The cellular β-tubulin detected by mouse monoclonal antibody (cat. no. T5201, Sigma-Aldrich) was used as a loading control. The secondary horseradish peroxidase-labeled secondary antibodies (Sigma-Aldrich) were used for signal development using ProSignal Pico ECL Reagent (GeneSee Scientific) captured by Chemidoc Touch Imager (BioRad).

Prediction and detection of circRNAs

KSHV circRNAs were predicted by CIRI2 pipeline (https://sourceforge.net/projects/ciri/) [38,39] with default setting using RNA-seq reads from BCBL-1 WT B4 and 57KO #6 cells. To experimentally confirm viral circRNAs expression, two μg of total RNA were treated with 5 U of RNase R (Lucigen) for 40 min at 37°C. The reactions containing the corresponding amount of RNA without RNase R treatment served as a negative control. The obtained RNAs were reverse transcribed with SuperScript IV (Thermo Fisher Scientific) at 50°C for 1 h in the presence of random hexamers, followed by detection of circular RNA as described [74]. For circRNA detection, 500 ng of cDNA were amplified by 40 PCR cycles using an inverse primer pair and SuperFi II DNA polymerase (Thermo Fisher Scientific). The linear RNAs were amplified using 100 ng of cDNA for 25 cycles of PCR amplification using a corresponding primer pair. All primers are listed in the S6 Table.