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. 2012 Jan;8(1):e1002484.
doi: 10.1371/journal.ppat.1002484. Epub 2012 Jan 26.

The viral and cellular microRNA targetome in lymphoblastoid cell lines

Rebecca L Skalsky  1 , David L Corcoran, Eva Gottwein, Christopher L Frank, Dong Kang, Markus Hafner, Jeffrey D Nusbaum, Regina Feederle, Henri-Jacques Delecluse, Micah A Luftig, Thomas Tuschl, Uwe Ohler, Bryan R Cullen
Affiliations

The viral and cellular microRNA targetome in lymphoblastoid cell lines

Rebecca L Skalsky et al. PLoS Pathog. 2012 Jan.

Abstract

Epstein-Barr virus (EBV) is a ubiquitous human herpesvirus linked to a number of B cell cancers and lymphoproliferative disorders. During latent infection, EBV expresses 25 viral pre-microRNAs (miRNAs) and induces the expression of specific host miRNAs, such as miR-155 and miR-21, which potentially play a role in viral oncogenesis. To date, only a limited number of EBV miRNA targets have been identified; thus, the role of EBV miRNAs in viral pathogenesis and/or lymphomagenesis is not well defined. Here, we used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) combined with deep sequencing and computational analysis to comprehensively examine the viral and cellular miRNA targetome in EBV strain B95-8-infected lymphoblastoid cell lines (LCLs). We identified 7,827 miRNA-interaction sites in 3,492 cellular 3'UTRs. 531 of these sites contained seed matches to viral miRNAs. 24 PAR-CLIP-identified miRNA:3'UTR interactions were confirmed by reporter assays. Our results reveal that EBV miRNAs predominantly target cellular transcripts during latent infection, thereby manipulating the host environment. Furthermore, targets of EBV miRNAs are involved in multiple cellular processes that are directly relevant to viral infection, including innate immunity, cell survival, and cell proliferation. Finally, we present evidence that myc-regulated host miRNAs from the miR-17/92 cluster can regulate latent viral gene expression. This comprehensive survey of the miRNA targetome in EBV-infected B cells represents a key step towards defining the functions of EBV-encoded miRNAs, and potentially, identifying novel therapeutic targets for EBV-associated malignancies.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Cellular and viral miRNAs detected in LCLs by deep sequencing.
A–D. miRNAs present in four LCLs (EF3D-AGO2, LCL35, LCL-BAC, SDLCL) were detected by deep sequencing. Shown is the distribution of reads mapping to cellular (orange, grey) and viral (dark blue) pre-miRNAs; the most abundant cellular miRNAs are highlighted. miR-17/92 includes reads mapping to miR-17, 18a, 19, 20a, and 92a. E. EBV miRNA expression as determined by deep sequencing. Read counts were normalized to the total number of reads mapping to pre-miRNAs in each library. F. Primer extension analysis detects six EBV miRNAs expressed in EF3D-AGO2.
Figure 2
Figure 2. Distribution of PAR-CLIP Clusters reveals 3′UTR bias.
A. Overlap of clusters in the five PAR-CLIP libraries. Shown is the breakdown of clusters mapping to 3′UTRs, 5′UTRs, coding regions (CDS), intergenic regions, introns, and mature miRNAs. Clusters from separate libraries were considered overlapping if, based on genome coordinates, they shared >50% of their nucleotides. B. miRNA-interaction 3′UTR sites specific to EBV-infected LCLs. miRNA-interaction sites present in at least two of the five LCL PAR-CLIP libraries were compared to miRNA-interaction sites present in two EBV-negative PEL PAR-CLIP libraries. 109 sites in 3′UTRs contain seed matches to only EBV miRNAs and are highly specific to EBV-infected LCLs. C and D. Breakdown of 3′UTR (C) and CDS (D) sites assigned to individual EBV miRNAs.
Figure 3
Figure 3. Luciferase reporter assays confirm miRNA-targeted 3′UTRs identified by PAR-CLIP.
A. 3′UTRs for 13 genes were inserted into the 3′UTR of firefly luciferase and tested against 11 different miRNA expression vectors for a total of 106 miRNA:3′UTR pairs. 3′UTR reporter plasmids were co-transfected into 293T cells with either EBV or cellular miRNA expression plasmids; lysates were assayed for luciferase activity. All values are relative to an internal renilla luciferase control and then, normalized to luciferase GL3 vector control (no 3′UTR) shown in Figure S3. Reported are the averages of two to five independent experiments performed in triplicates. PAR-CLIP-identified miRNA:mRNA interactions are highlighted in red. 3′UTRs containing a minimal 6mer seed match (nt 2-7) to the assayed miRNA but not identified by PAR-CLIP are shown in black. 32 miRNA:mRNA pairs resulted in >20% luciferase knockdown and are highlighted on the right. B and C. PAR-CLIP identified seed match sites in select 3′UTRs for BART miRNAs were mutated to NheI restriction enzyme sites in the luciferase reporter vectors to disrupt miRNA binding. Both the LY75 and DAZAP2 3′UTRs contain two PAR-CLIP-identified sites for miR-BART1-5p and miR-BART3-3p, respectively, and only the site with the highest read count was mutated. Luciferase assays were performed as in (A) and values are shown relative to an internal renilla luciferase control. D. Alignment of miR-BART3-3p, miR-BART1-3p, and cellular miR-29a, which share sequence homology.
Figure 4
Figure 4. High confidence targets of EBV miR-BHRF1-1 and miR-BHRF1-3.
A. 3′UTR clusters assigned to miR-BHRF1-1 (minimum seed match: 7mer1A) that were present in at least three of the five PAR-CLIP libraries and are specific to EBV-infected LCLs are shown in red with annotated gene symbols. Clusters that were absent from the LCL-BAC-D1 PAR-CLIP library are shown in white, and therefore, represent high confidence targets for miR-BHRF1-1. The four miR-BHRF1-1-assigned clusters present in LCL-BAC-D1 can also be assigned to miR-BART4-5p. B. Similar to A, 3′UTR clusters assigned to miR-BHRF1-3 that were present in at least two PAR-CLIP libraries are shown in red; clusters absent from the LCL-BAC-D3 library are shown in white. C. Alignment of miR-BHRF1-1 and miR-BART4-5p, which share an off-set seed sequence. D. EBV pre-miRNAs detected in LCL-BAC, LCL-BAC-D1, and LCL-BAC-D3 as determined by deep sequencing. Reported are the total number of reads mapping to each EBV pre-miRNA. E. PAR-CLIP identified seed match sites to miR-BHRF1-1 in three 3′UTRs (***highlighted in A) were deleted (GUF1 and NAT12) or mutated to an NheI restriction enzyme site (SCRN1) in luciferase reporter vectors to disrupt miRNA binding. Luciferase assays were performed as in Figure 3 and values are shown relative to an internal renilla luciferase control.
Figure 5
Figure 5. BHRF1 miRNAs target cellular mRNAs through seed match pairing.
Consecutive 6mer sequences were examined for pairing with clusters mapping to 3′UTRs and coding regions. A. Schematic showing the interrogated 6mers. The sequences for miR-BHRF1-1 and miR-BHRF1-3 are shown below; highlighted in red are the regions of each miRNA that show enrichment over background in pairing with clusters (nt 1-8 for miR-BHRF1-1 and nt 2-9 for miR-BHRF1-3). B. and C. 6mers from miR-BHRF1-1 and miR-BHRF1-3, respectively, were analyzed for matches to clusters in 3′UTRs or CDSs. Enrichment for a match is indicated in red, while absence of a match is indicated in grey. Numbers below indicate the 6mer sequence described in (A).
Figure 6
Figure 6. LMP1 is targeted by the miR-17/92 cluster.
A. EBNA2, BHRF1, and LMP1 transcripts are targeted by miRNAs in LCLs. Shown are clusters mapping to the EBV B95-8 genome in three PAR-CLIP libraries. Clusters mapping to non-coding RNAs are not shown. B. Multiple Ago2-interaction sites are present in the LMP1 3′UTR. Shown are read groups (grey), clusters (orange), and T>C conversions (red) present in reads mapping to the LMP1 3′UTR in three PAR-CLIP libraries. C. The LMP1 3′UTR contains an extensive seed match to the miR-17/20/106/93 family. Shown are the mature miRNA sequences for miR-106a, miR-17, and miR-20a as identified by deep sequencing and the sequence of the LMP1 3′UTR cluster containing the seed match site. This site was also identified in LCL-BAC-D1 and LCL-BAC-D3 PAR-CLIP libraries (Tables S13 and S14). D. miR-17/92 and miR-106b/25 inhibit the LMP1 3′UTR reporter. The LMP1 3′UTR luciferase reporter and renilla luciferase internal control vector were co-transfected into 293T cells with indicated miRNA expression plasmids. *By Student′s t test, p<0.01 compared to vector control. E. Inhibition of endogenous miR-17/20/106 using a sponge. LCL35 was transduced with pLCE-CXCR4s (control sponge, CXCR4s) or pLCE-miR-17/20/106s (sponge for miR-17/20/106) and FAC-sorted for high GFP expression. To assay miR-17/20/106 activity, cells were transduced with a firefly luciferase indicator to miR-17-5p and renilla luciferase as an internal control. For luciferase assays in D and E, lysates were harvested 48-72 hrs post-transfection or post-transduction and assayed for luciferase activity using the dual luciferase assay kit (Promega). All values are reported as the average of at least two experiments performed in triplicate with standard deviations and are relative to renilla luciferase (RLU  =  relative light units). F. Inhibition of endogenous miR-17/20/106 in LCL35 increases the protein levels of LMP1 and p21 (CDKN1A), a known target of miR-17/20/106. LCL35 was transduced with pLCE-CXCR4s or pLCE-miR-17/20/106s, FAC-sorted for high GFP expression, and lysates harvested 10 days post-FACS for Western blot analysis. Lanes were loaded in duplicate. Beta-actin is shown as a loading control.
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