860 research outputs found

    Characterization the regulation of herpesvirus miRNAs from the view of human protein interaction network

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    <p>Abstract</p> <p>Background</p> <p>miRNAs are a class of non-coding RNA molecules that play crucial roles in the regulation of virus-host interactions. The ever-increasing data of known viral miRNAs and human protein interaction network (PIN) has made it possible to study the targeting characteristics of viral miRNAs in the context of these networks.</p> <p>Results</p> <p>We performed topological analysis to explore the targeting propensities of herpesvirus miRNAs from the view of human PIN and found that (1) herpesvirus miRNAs significantly target more hubs, moreover, compared with non-hubs (non-bottlenecks), hubs (bottlenecks) are targeted by much more virus miRNAs and virus types. (2) There are significant differences in the degree and betweenness centrality between common and specific targets, specifically we observed a significant positive correlation between virus types targeting these nodes and the proportion of hubs, and (3) K-core and ER analysis determined that common targets are closer to the global PIN center. Compared with random conditions, the giant connected component (GCC) and the density of the sub-network formed by common targets have significantly higher values, indicating the module characteristic of these targets.</p> <p>Conclusions</p> <p>Herpesvirus miRNAs preferentially target hubs and bottlenecks. There are significant differences between common and specific targets. Moreover, common targets are more intensely connected and occupy the central part of the network. These results will help unravel the complex mechanism of herpesvirus-host interactions and may provide insight into the development of novel anti-herpesvirus drugs.</p

    Target RNAs strike back on MicroRNAs

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    MicroRNAs are extensively studied regulatory non-coding small RNAs that silence animal genes throughout most biological processes, typically doing so by binding to partially complementary sequences within target RNAs. A plethora of studies has described detailed mechanisms for microRNA biogenesis and function, as well as their temporal and spatial regulation during development. By inducing translational repression and/or degradation of their target RNAs, microRNAs can contribute to achieve highly specific cell-or tissue-specific gene expression, while their aberrant expression can lead to disease. Yet an unresolved aspect of microRNA biology is how such small RNA molecules are themselves cleared from the cell, especially under circumstances where fast microRNA turnover or specific degradation of individual microRNAs is required. In recent years, it was unexpectedly found that binding of specific target RNAs to microRNAs with extensive complementarity can reverse the outcome, triggering degradation of the bound microRNAs. This emerging pathway, named TDMD for Target RNA-Directed MicroRNA Degradation, leads to microRNA 3â€Č-end tailing by the addition of A/U non-templated nucleotides, trimming or shortening from the 3â€Č end, and highly specific microRNA loss, providing a new layer of microRNA regulation. Originally described in flies and known to be triggered by viral RNAs, novel endogenous instances of TDMD have been uncovered and are now starting to be understood. Here, we review our current knowledge of this pathway and its potential role in the control and diversification of microRNA expression patterns.Fil: Fuchs Wightman, Federico. Consejo Nacional de Investigaciones CientĂ­ficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Ciudad Universitaria. Instituto de FisiologĂ­a, BiologĂ­a Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de FisiologĂ­a, BiologĂ­a Molecular y Neurociencias; ArgentinaFil: Giono, Luciana Eugenia. Consejo Nacional de Investigaciones CientĂ­ficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Ciudad Universitaria. Instituto de FisiologĂ­a, BiologĂ­a Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de FisiologĂ­a, BiologĂ­a Molecular y Neurociencias; ArgentinaFil: Fededa, Juan Pablo. Consejo Nacional de Investigaciones CientĂ­ficas y TĂ©cnicas. Centro CientĂ­fico TecnolĂłgico Conicet - La Plata. Instituto de Investigaciones BiotecnolĂłgicas. Instituto de Investigaciones BiotecnolĂłgicas "Dr. RaĂșl AlfonsĂ­n" (sede ChascomĂșs). Universidad Nacional de San MartĂ­n. Instituto de Investigaciones BiotecnolĂłgicas. Instituto de Investigaciones BiotecnolĂłgicas "Dr. RaĂșl AlfonsĂ­n" (sede ChascomĂșs); ArgentinaFil: de la Mata, Manuel. Consejo Nacional de Investigaciones CientĂ­ficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Ciudad Universitaria. Instituto de FisiologĂ­a, BiologĂ­a Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de FisiologĂ­a, BiologĂ­a Molecular y Neurociencias; Argentin

    Utilising proteomic approaches to understand oncogenic human herpesviruses

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    The γ‑herpesviruses Epstein-Barr virus and Kaposi's sarcoma‑associated herpesvirus are successful pathogens, each infecting a large proportion of the human population. These viruses persist for the life of the host and may each contribute to a number of malignancies, for which there are currently no cures. Large‑scale proteomic-based approaches provide an excellent means of increasing the collective understanding of the proteomes of these complex viruses and elucidating their numerous interactions within the infected host cell. These large‑scale studies are important for the identification of the intricacies of viral infection and the development of novel therapeutics against these two important pathogens

    GENOME-WIDE ANALYSIS OF CHICKEN MIRNAS AND DNA METHYLATION AND THEIR ROLES IN MAREK'S DISEASE RESISTANCE AND SUSCEPTIBILITY

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    Marek's disease (MD) is a T cell lymphoma in chickens and causes high mortality and morbidity in productive chickens. Two inbred chicken lines, resistant line 63 and susceptible line 72, with the same MHC haplotype, showed distinct disease outcomes after MDV infection. The current studies aimed to illustrate the role of microRNA (miRNAs) and DNA methylation in MD resistance and susceptibility in chickens. First, to ascertain the function of miRNAs, miRNA microarray experiments were used to identify miRNAs sensitive to MDV infection in the 2 lines. Most miRNAs were repressed in line 72 after MDV infection, while their transcription was steady in line 63. The miRNA target genes were identified in chickens. Cellular miRNA gga-miR-15b and gga-let-7iwere reduced in infected line 72 chickens and MD tumors. The downregulation of the two miRNAs increased the expression of ATF2 (activating transcription factor 2) and DNMT3a (DNA methyltransferase 3a) in infected line 72. These results indicated that miRNAs may play antiviral functions through modulating target gene expression. Next, to characterize the role of miRNAs in MDV infection, the selected chicken miRNAs were overexpressed in MDV infected DF-1 cells. The overexpressions of chicken miRNA gga-miR-15b and gga-let-7i, by using the retroviral based vector, significantly restricted MDV replications in vitro. MDV oncoprotein was repressed, suggesting that chicken miRNAs may limit MDV propagation. Finally, we found deregulation of transcription of DNA methyltransfereases (DNMTs) in lines 63 and 72 after MDV infection, which coordinated with the methylation alterations in the 2 lines. Infection induced differential methylation regions (iDMRs) that were identified through genome-wide DNA methylation quantification. Genes overlapping line-specific iDMRs were related with pathways of different functions in these two lines, implying the involvement of DNA methylation in MD- resistance and susceptibility. An in vitro study showed that DNA methylation inhibitor repressed viral spread and viral replication. In conclusion, the observed variations of miRNA expression and DNA methylation may be associated with disease predisposition in chickens

    Impact of ATP-dependent RNA Helicase DDX3X on Herpes Simplex Type 1 (HSV-1) Replication

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    Le criblage par siRNA de 49 protĂ©ines de l'hĂŽte qui sont incorporĂ©es dans les particules matures du virus herpĂšs simplex de type 1 (VHS-1) a rĂ©vĂ©lĂ© l'importance d'au moins 15 d’entre elle pour infectivitĂ© du virus (Stegen, C et al. 2013). Parmi celle-ci figure la protĂ©ine humaine DDX3X, qui est une ARN hĂ©licase ATP-dĂ©pendante. Cette protĂ©ine multifonctionnelle participe Ă  diffĂ©rents stages de l'expression gĂ©nique, tels que la transcription, la maturation et le transport d'ARNm ainsi que la traduction. DDX3X est impliquĂ©e dans la rĂ©plication de plusieurs virus tels que le Virus de l’immunodĂ©ficience humaine de type 1 (VIH-1), l'hĂ©patite B (VHB), le virus de la vaccine (VACV) et le virus de l'hĂ©patite C (VHC). Le rĂŽle exact de DDX3X dans le cycle de rĂ©plication du VHS-1 est toutefois inconnu. Ce mĂ©moire consiste en l’étude dĂ©taillĂ©e de l'interaction de DDX3X avec le virus. De maniĂšre surprenante, tant l’inhibition que la surexpression de DDX3X rĂ©duit de maniĂšre significative l'infectivitĂ© du VHS-1. Fait intĂ©ressant, lorsque nous avons restaurĂ© la dĂ©plĂ©tion de DDX3X par une construction rĂ©sistante aux ARNi utilisĂ©s, le virus pouvait de nouveau infecter les cellules efficacement, indiquant que le virus est sensible aux quantitĂ©s de cette protĂ©ine de son hĂŽte. Nos rĂ©sultats indiquent de plus que le virus modifie la localisation de DDX3X et cause son agrĂ©gation tĂŽt dĂšs les premiers temps de l'infection. Cependant, le virus ne modifie pas les niveaux cellulaires de DDX3X dans deux des trois lignĂ©es cellulaires examinĂ©es. Nous avons Ă©galement pu Ă©tablir que cette protĂ©ine n'a pas d'effet sur l'entrĂ©e du VHS-1, suggĂ©rant qu’elle agit Ă  un stade ultĂ©rieure de l’infection. En examinant cette relation plus en dĂ©tail, nos rĂ©sultats ont dĂ©montrĂ© que l’inhibition ou la surexpression de DDX3X inhibent toutes deux la production de nouvelles particules virales en rĂ©duisant l'expression des diverses classes cinĂ©tiques des protĂ©ines virales et ce au niveau de leur transcription. MalgrĂ© le rĂŽle connu DDX3X dans la stimulation de la rĂ©ponse immunitaire innĂ©e et la production d’interfĂ©rons de type I, l’impact de DDX3X sur la rĂ©plication du VHS-1 est ici indĂ©pendante de cette fonction. Ces travaux dĂ©montrent donc une nouvelle voie d’action de DDX3X sur les virus en agissant directement sur la transcription de gĂšnes viraux et la rĂ©plication du gĂ©nome d’un virus Ă  ADN. En comprenant mieux cette interactions hĂŽtepathogĂšne, il est maintenant envisageable de concevoir des nouvelles approches thĂ©rapeutiques contre ce virus.siRNA screening of 49 host proteins that are known to be incorporated in the mature virions of herpes simplex virus type 1 (HSV-1) revealed the importance of at least 15 cellular proteins for viral infectivity (Stegen, C et al. 2013). Among these, was the human protein DDX3X, a DEAD-box ATP-dependent RNA helicase. This multifunctional protein participates in different stages of gene expression such as mRNA transcription, maturation, mRNA export and translation. DDX3X has been shown to be involved in the replication of several viruses such as human immunodeficiency virus type 1 (HIV-1), hepatitis B virus (HBV) vaccinia virus (VACV) and hepatitis C virus (HCV). The exact role of DDX3X in HSV-1 replication cycle is not known. Here we sought to find the detailed interaction between DDX3X with HSV-1. Surprisingly, the down-regulation as well as overexpression of DDX3X, significantly reduced the infectivity of HSV-1, indicating that the virus is sensitive to the precise levels of DDX3X. Accordingly, when we rescued DDX3X back to its normal cellular levels by sequential transfection of DDX3X siRNA and siRNA resistant DDX3X plasmid, the virus was able to infect cells efficiently compare to wild-type conditions. Furthermore, the virus changes the localization of DDX3X and causes its aggregation at early times in the infection. However, the virus does not change the cellular levels of DDX3X in at least two of three different cell lines tested. Using a luciferase assay we were able to establish that this protein has no effect on the entry of HSV-1. In fact, depleting or overexpressing DDX3X impaired the production on newly assembled viral particles by blocking the expression of all classes of viral proteins at the transcription level. Despite the known role of DDX3X in the stimulation of innate immune response and interferon type I production, DDX3X appears to act on HSV-1 replication independently of this pathway. This highlights a novel route of action of DDX3X by acting at the transcription level and the consequent genome replication of a DNA virus. By better understanding such pathogen interactions, it might now be possible to design novel therapeutic approaches

    Systems-Biology Approaches to Discover Anti-Viral Effectors of the Human Innate Immune Response

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    Virus infections elicit an immediate innate response involving antiviral factors. The activities of some of these factors are, in turn, blocked by viral countermeasures. The ensuing battle between the host and the viruses is crucial for determining whether the virus establishes a foothold and/or induces adaptive immune responses. A comprehensive systems-level understanding of the repertoire of anti-viral effectors in the context of these immediate virus-host responses would provide significant advantages in devising novel strategies to interfere with the initial establishment of infections. Recent efforts to identify cellular factors in a comprehensive and unbiased manner, using genome-wide siRNA screens and other systems biology “omics” methodologies, have revealed several potential anti-viral effectors for viruses like Human immunodeficiency virus type 1 (HIV-1), Hepatitis C virus (HCV), West Nile virus (WNV), and influenza virus. This review describes the discovery of novel viral restriction factors and discusses how the integration of different methods in systems biology can be used to more comprehensively identify the intimate interactions of viruses and the cellular innate resistance

    Platelet Transcriptome Heterogeneity: A Role for RNA Uptake in Vascular Health and Disease

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    As our understanding of the platelet’s systemic role continues to expand beyond hemostasis and thrombosis, interrogation of the platelet’s ability to affect diverse biological processes is required. Studies of the platelet’s non-traditional roles have focused on developing our understanding of the platelet’s relation to specific disease phenotypes as well as elucidation of platelet characteristics, content, and function. The generic content, traditional function and heterogeneity of platelets have long been accepted; more ambiguous and controversial has been how these factors are interrelated. Investigation of platelet content revealed the presence of biologically functional RNA in anucleated platelets, the correlation of platelet RNA to distinct phenotypes, and the ability of platelets to transfer RNA to other vascular cells; however how these processes occur is unclear. To further interrogate platelet RNA processes, we utilized sorting and RNA sequencing to develop platelet subpopulation transcriptome profiles. We found that platelet heterogeneity extends to the platelet transcriptome: distinct RNA profiles exist dependent on platelet size. We hypothesized that this RNA heterogeneity is the result of RNA transfer between platelets and vascular cells. Using in vitro and in vivo modeling, we were able to show the novel ability of platelets to take up RNA from vascular cells, correlating to the unique functional profile associated with small platelet transcriptomes. These findings reveal a role for platelet RNA transfer in platelet RNA heterogeneity, with potential correlation to platelet functional diversity previously proposed. The ability of the platelet to bidirectionally transfer RNA within circulation has implications for vascular health and beyond
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