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. 2010 Jan 15;37(1):135-42.
doi: 10.1016/j.molcel.2009.12.016.

A mammalian herpesvirus uses noncanonical expression and processing mechanisms to generate viral MicroRNAs

Hal P Bogerd  1 , Heather W Karnowski, Xuezhong Cai, Jinwook Shin, Michael Pohlers, Bryan R Cullen
Affiliations

A mammalian herpesvirus uses noncanonical expression and processing mechanisms to generate viral MicroRNAs

Hal P Bogerd et al. Mol Cell. .

Abstract

Canonical primary microRNA (pri-miRNA) precursors are transcribed by RNA polymerase II and then processed by the Drosha endonuclease to generate approximately 60 nt pre-miRNA hairpins. Pre-miRNAs in turn are cleaved by Dicer to generate mature miRNAs. Previously, some short introns, called miRtrons, were reported to fold into pre-miRNA hairpins after splicing and debranching, and miRNAs can also be excised by Dicer cleavage of rare endogenous short hairpin RNAs. Here we report that the miRNAs encoded by murine gamma-herpesvirus 68 (MHV68) are also generated via atypical mechanisms. Specifically, MHV68 miRNAs are transcribed from RNA polymerase III promoters located within adjacent viral tRNA-like sequences. The resultant pri-miRNAs, which bear a 5' tRNA moiety, are not processed by Drosha but instead by cellular tRNase Z, which cleaves 3' to the tRNA to liberate pre-miRNA hairpins that are then processed by Dicer to yield the mature viral miRNAs.

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Figures

Figure 1
Figure 1. Transcription and function of wild-type MHV68 microRNAs
(A) Proposed structure of pri-miR-M1-7. Proposed cleavage sites defining the base of the pre-miR-M1-7 intermediate are indicated by open arrows and Dicer cleavage sites by closed triangles. The previously cloned (Pfeffer et al., 2005) miR-M1-7-5p and miR-M1-7-3p miRNAs are highlighted. This structured RNA can be sub-divided into a 5′ “tRNA” domain, a central stem-loop I or “SLI” domain and a 3′ “SLII” domain, as indicated. (B) Northern analysis of RNA samples derived from MHV68-infected S11 cells or 293T cells transfected with pmiR-M1-1, pmiR-M1-5/6 or pmiR-M1-7X. The end-labeled probes used are complementary to the mature miRNA and are indicated above each panel. The mobility of RNA size markers is indicated. (C) The biological activity of MHV68 miRNAs was confirmed by co-transfecting 293T cells with an Rluc-based reporter containing artificial 3′ UTR target sites for each indicated MHV68 miRNA, together with a vector encoding the MHV68 miRNAs indicated at the base of the figure. Observed Rluc activities are given relative to a culture co-transfected with a control expression vector. Average of three separate experiments with S.D. indicated. (D) 293T cells were mock-transfected or transfected with pmiR-M1-1, pmiR-M1-5/6, pmiR-M1-7X or pCMV-miR-30a and, where necessary, treated with the Pol II inhibitor α-amanitin. Total RNA was harvested at 48 h post-transfection and mature miRNA expression detected by Northern analysis.
Figure 2
Figure 2. Functional organization of MHV68 pri-miR-M1-7
(A) This functional analysis of the indicated pri-miR-M1-7 mutants was performed in 293T cells, as described in Fig. 1C, except that a similar miR-30a-3p indicator construct was included as a control. Average of three experiments with S.D. indicated. (B) Northern analysis of mature miRNA and miRNA precursor expression in 293T cells using the same plasmids analyzed in panel A. The 32P-labeled oligonucleotide probes used were complementary to miR-M1-7-3p (lanes 1-6) or miR-30a (lanes 7-9). RNA size markers are indicated. U6 was used as a loading control. (C) Primer extension analysis to map the 5′ end of miR-M1-7-5p expressed in 293T cells transfected with the indicated expression vectors. The end-labeled primer is 16 nt in length, while mature miR-M1-7-5p is 22 nt (Fig. 1A). Mock-transfected 293T cells were used as a control.
Figure 3
Figure 3. RNAi analysis of the co-factor requirements for miR-M1-7 processing
(A) Northern analysis of the expression of mature miR-30a-3p in HeLa cells treated with a control siRNA or two distinct siRNAs specific for tRNase Z (Z1 and Z2) or Drosha (D1 and D2) and then transfected with pCMV-miR-30a. U6 RNA was used as a loading control. (B) Similar to panel A, except that these blots analyze HeLa cells co-transfected with the indicated siRNAs and either pmiR-M1-7X (lanes 1-4 and 14-16), pmiR-M1-7ΔSLII (lanes 5-7), pH1/M1-7 (lanes 8-10) or pH1/M1-7ΔSLII (lanes 11-13). Size markers are indicated and U6 was used as a loading control. (C) Quantitation of the level of expression of full-length wild-type pri-miR-M1-7 (tRNA-SLI+SLII), the miR-M1-7 tRNA-SLI intermediate, the SLI pre-miR-M1-7 intermediate and mature miR-M1-7-3p in HeLa cells transfected with pmiR-M1-7 and depleted for either RNase Z or Drosha by RNAi. Human miR-30a was used as a control. Average of four experiments with S.D. indicated. Data are presented relative to the level of expression of each RNA species in cells treated with a control siRNA, which was set at 1.
Figure 4
Figure 4. tRNase Z cleaves pri-miR-M1-7 to generate the predicted pre-miRNA
(A) Upper panel: In vitro processing of a 132 nt transcript, consisting of the tRNA and SLI domains of MHV68 pri-miR-M1-7, and of the 260 nt pri-miR-K5 transcript. 32P-labeled transcripts were incubated in the presence of recombinant FLAG-tRNase Z or FLAG-Drosha isolated from overexpressing 293T cells, and any resultant cleavage products separated by denaturing gel electrophoresis and visualized by autoradiography. Size markers are indicated at left. Lower panel: The protein preparations used in this experiment were analyzed by Western blot using a FLAG-specific antiserum. (B) Similar to panel A, except that a 200 nt 32P-labeled transcript, consisting of the predicted full-length pri-miR-M1-7 (Fig. 1A) was analyzed.
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