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Down-Regulation of a Host MicroRNA by a Herpesvirus saimiri Noncoding RNA

Demián Cazalla, Therese Yario, Joan Steitz

Science Vol. 328: 1563 – 1566, 18 June 2010.
DOI: 10.1126/science.1187197

This week’s attentive summary and analysis by David Koppstein, his first on the blog:

In this study, Cazalla and colleagues found complementarity of three endogenous microRNAs–miR-27, miR-16, and miR-142-3p–to two noncoding RNAs encoded by Herpesvirus saimiri, HSUR 1 and HSUR 2, which have conserved motifs reminiscent of cellular U snRNAs. They pursued this observation by pulling down Ago2 and looking for these HSURs, and conversely by pulling down Sm proteins and looking for the miRNAs. Interestingly, these CoIPs specifically pulled down the HSURs and miRNAs, respectively, that were bioinformatically predicted to interact. During these experiments, they noticed that a mutant strain of the virus that lacked HSURs 1 and 2 expressed miR-27 at significantly higher levels.

Cazalla and colleagues then performed experiments to determine what was causing the increased levels of miR-27 in the mutant strain. They designed a pulse-chase nucleofection protocol with a radiolabeled synthetic miRNA, and noted a significantly shorter half-life in the presence of HSURs 1 and 2. Since levels of the pre-miRNA and the passenger strand were unchanged, they concluded that the mature miRNA itself must be destabilized.

It was also noted that the destabilization of miR-27 had consequences on the transcriptional landscape of the cell. A validated target of miR-27, FOXO1, which is a transcription factor that is dysregulated in breast, prostate, and endometrial cancers, was observed to be significantly downregulated in the absence of HSUR 1. Cazalla et al. also recapitulated the downregulation of miR-27 in Jurkat T-cells by
combinations of stable lines expressing HSURs and knockdowns using chimeric oligoribonucleotides. Strikingly, they observed that the specificity of HSUR 1 could be artificially switched to target miR-20.

There are several questions raised by this paper. First, there is the tantalizing prospect that the mechanism of destabilization of miR-27 is the same as that described by Ameres et al. in the same edition of Science. Further work, especially deep sequencing analysis of small RNAs, will likely reveal whether this is the case. There is also the mystery of where the interactions between HSURs and miRNAs are taking place; HSURs are thought to be nuclear, but may shuttle to the cytoplasm during their maturation. It is also still unclear what genes are perturbed as a consequence of the decreased miR-27 levels, and how this may affect viral fitness. Finally, one wonders about the functional significance of the interaction of HSURs 1 and 2 with miR-142-3p and miR-16. In summary, this paper presents a novel mechanism by which a virus perturbs host gene expression using noncoding RNA.

Citation for researchblogging.org:

Cazalla D, Yario T, & Steitz J (2010). Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA. Science, 328 (5985), 1563-6 PMID: 20558719