Adenovirus Virus-Associated RNAII-Derived Small RNAs Are Efficiently Incorporated into the RNA-Induced Silencing Complex and Associate with Polyribosomes

Xu, Ning; Segerman, Bo; Zhou, Xiaofu; Akusjärvi, Göran

doi:10.1128/jvi.00885-07

Cited by 99 publications

(127 citation statements)

References 39 publications

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“…Moreover, these 2 RNAs were the most abundant VA RNAI-derived RNAs in the RISC fraction (36% and 32%, respectively; Fig. 2B, lower middle chart), confirming previous findings for lytically infected human cells (22). Whereas the 5=-arm-derived strand of VA RNAI starting at the "A" position, 5=mivaRNAI(A), was also highly incorporated into RISCs (27%), the incorporation of 5=mivaRNAI(G) was poor.…”

Section: Resultssupporting

confidence: 71%

Identification of RISC-Associated Adenoviral MicroRNAs, a Subset of Their Direct Targets, and Global Changes in the Targetome upon Lytic Adenovirus 5 Infection

Bellutti

Kauer

Kneidinger

et al. 2015

J Virol

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Adenoviruses encode a set of highly abundant microRNAs (mivaRNAs), which are generated by Dicer-mediated cleavage of the larger noncoding virus-associated RNAs (VA RNAs) I and II. We performed deep RNA sequencing to thoroughly investigate the relative abundance of individual single strands of mivaRNA isoforms in human A549 cells lytically infected with human adenovirus 5 (Ad5) at physiologically relevant multiplicities of infection (MOIs). In addition, we investigated their relative abundance in the endogenous RNA-induced silencing complexes (RISCs). The occupation of endogenous RISCs by mivaRNAs turned out to be pronounced but not as dominant as previously inferred from experiments with AGO2-overexpressing cells infected at high MOIs. In parallel, levels of RISC-incorporated mRNAs were investigated as well. Analysis of mRNAs enriched in RISCs in Ad5-infected cells revealed that only mRNAs with complementarity to the seed sequences of mivaRNAs derived from VA RNAI but not VA RNAII were overrepresented among them, indicating that only mivaRNAs derived from VA RNAI are likely to contribute substantially to the posttranscriptional downregulation of host gene expression. Furthermore, to generate a comprehensive picture of the entire transcriptome/targetome in lytically infected cells, we determined changes in cellular miRNA levels in both total RNA and RISC RNA as well, and bioinformatical analysis of mRNAs of total RNA/RISC fractions revealed a general, genome-wide trend toward detargeting of cellular mRNAs upon infection. Lastly, we identified the direct targets of both single strands of a VA RNAI-derived mivaRNA that constituted one of the two most abundant isoforms in RISCs of lytically infected A549 cells. IMPORTANCE Viral and cellular miRNAs have been recognized as important players in virus-host interactions.This work provides the currently most comprehensive picture of the entire mRNA/miRNA transcriptome and of the complete RISC targetome during lytic adenovirus infection and thus represents the basis for a deeper understanding of the interplay between the virus and the cellular RNA interference machinery. Our data suggest that, at least in the model system that was employed, lytic infection by Ad5 is accompanied by a measurable global net detargeting effect on cellular mRNAs, and analysis of RISC-associated viral small RNAs revealed that the VA RNAs are the only source of virus-encoded miRNAs. Moreover, this work allows to assess the power of individual viral miRNAs to regulate cellular gene expression and provides a list of proven and putative direct targets of these miRNAs, which is of importance, given the fact that information about validated targets of adenovirus-encoded miRNAs is scarce.

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Section: Resultssupporting

confidence: 71%

Identification of RISC-Associated Adenoviral MicroRNAs, a Subset of Their Direct Targets, and Global Changes in the Targetome upon Lytic Adenovirus 5 Infection

Bellutti

Kauer

Kneidinger

et al. 2015

J Virol

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“…[17][18][19] The apparent absence of RNAi restriction of some viruses could be explained by the counteraction of encoded viral RNA silencing suppressors (RSSs). Several mammalian viruses encode RSSs, 17,[20][21][22][23][24][25][26][27][28][29] although the efficiency of a few of them has been debated. 16,[30][31][32] Proposed RSSs encoded by HIV-1 are the transactivator Tat 20,27 and the Trans Activation Response (TAR) RNA.…”

mentioning

confidence: 99%

HIV-1 RRE RNA acts as an RNA silencing suppressor by competing with TRBP-bound siRNAs

et al. 2015

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Several proteins and RNAs expressed by mammalian viruses have been reported to interfere with RNA interference (RNAi) activity. We investigated the ability of the HIV-1-encoded RNA elements Trans-Activation Response (TAR) and RevResponse Element (RRE) to alter RNAi. MicroRNA let7-based assays showed that RRE is a potent suppressor of RNAi activity, while TAR displayed moderate RNAi suppression. We demonstrate that RRE binds to TAR-RNA Binding Protein (TRBP), an essential component of the RNA Induced Silencing Complex (RISC). The binding of TAR and RRE to TRBP displaces small interfering (si)RNAs from binding to TRBP. Several stem-deleted RRE mutants lost their ability to suppress RNAi activity, which correlated with a reduced ability to compete with siRNA-TRBP binding. A lentiviral vector expressing TAR and RRE restricted RNAi, but RNAi was restored when Rev or GagPol were coexpressed. Adenoviruses are restricted by RNAi and encode their own suppressors of RNAi, the Virus-Associated (VA) RNA elements. RRE enhanced the replication of wild-type and VA-deficient adenovirus. Our work describes RRE as a novel suppressor of RNAi that acts by competing with siRNAs rather than by disrupting the RISC. This function is masked in lentiviral vectors co-expressed with viral proteins and thus will not affect their use in gene therapy. The potent RNAi suppressive effects of RRE identified in this study could be used to enhance the expression of RNAi restricted viruses used in oncolysis such as adenoviruses.

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“…These observations are counterbalanced by the fact that, in contrast to two similar non-coding RNAs, i.e. EBER-1 from EBV (122,123) and hY1 from human cells (124), that are refractory to processing by Dicer (108), VAI and VAII RNAs may be processed by Dicer into miRNAs (107)(108)(109)(110), which may exert gene regulatory functions in adenovirus-infected cells. Nevertheless, the VAI/VAII RNA-mediated attenuation of the cellular miRNA pathway may confer an advantage to the virus through a decreased level in cellular antiviral miRNAs.…”

Section: Non-coding Rnas Expressed From Virusesmentioning

confidence: 73%

“…A) VAI and VAII RNAs from adenovirus 5 (Ad5). Adapted from Xu et al (109). B) EBER1 and EBER2 RNAs from Epstein-Barr virus.…”

Section: Discussionmentioning

confidence: 99%

“…Other groups have reported the identification of one to three different miRNAs generated from VAI and VAII RNAs of the adenovirus type 5, and originating from the 3′ stem region (107,109,110). VAII RNA represented a more potent substrate for Dicer and ~2-fold more VAII RNA-derived small RNAs were present in the total pool of small RNAs.…”

Section: Other Dna Viruses (Polyomavirus and Adenovirus)mentioning

confidence: 99%

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Current Knowledge of MicroRNAs and Noncoding RNAs in Virus-Infected Cells

Ouellet

Provost

2010

RNA Interference

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Within the past few years, microRNAs (miRNAs) and other non-coding RNAs (ncRNAs) have emerged as elements with critically high importance in post-transcriptional control of cellular and, more recently, viral processes. Endogenously produced by a component of the miRNA-guided RNA silencing machinery known as Dicer, miRNAs are known to control messenger RNA (mRNA) translation through recognition of specific binding sites usually located in their 3′ untranslated region. Recent evidences indicate that the host miRNA pathway may represent an adapted antiviral defense mechanism that can act either by direct miRNA-mediated modulation of viral gene expression or through recognition and inactivation of structured viral RNA species by the protein components of the RNA silencing machinery, such as Dicer. This latter process, however, is a double-edge sword, as it may yield viral miRNAs exerting gene regulatory properties on both host and viral mRNAs. Our knowledge of the interaction between viruses and host RNA silencing machineries, and how this influences the course of infection, is becoming increasingly complex. This review article aims to summarize our current knowledge about viral miRNAs/ ncRNAs and their targets, as well as cellular miRNAs that are modulated by viruses upon infection.

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Adenovirus Virus-Associated RNAII-Derived Small RNAs Are Efficiently Incorporated into the RNA-Induced Silencing Complex and Associate with Polyribosomes

Cited by 99 publications

References 39 publications

Identification of RISC-Associated Adenoviral MicroRNAs, a Subset of Their Direct Targets, and Global Changes in the Targetome upon Lytic Adenovirus 5 Infection

Identification of RISC-Associated Adenoviral MicroRNAs, a Subset of Their Direct Targets, and Global Changes in the Targetome upon Lytic Adenovirus 5 Infection

HIV-1 RRE RNA acts as an RNA silencing suppressor by competing with TRBP-bound siRNAs

Current Knowledge of MicroRNAs and Noncoding RNAs in Virus-Infected Cells

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