860 research outputs found
Characterization the regulation of herpesvirus miRNAs from the view of human protein interaction network
<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
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 3âČ-end tailing by the addition of A/U non-templated nucleotides, trimming or shortening from the 3âČ 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
The Îłâherpesviruses Epstein-Barr virus and Kaposi's sarcomaâassociated 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. Largeâscale 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 largeâscale 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
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
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MicroRNA regulation of CD8+ T cell responses.
MicroRNAs (miRNAs) are a class of short noncoding RNAs that play critical roles in the regulation of a broad range of biological processes. Like transcription factors, miRNAs exert their effects by modulating the expression of networks of genes that operate in common or convergent pathways. CD8+ T cells are critical agents of the adaptive immune system that provide protection from infection and cancer. Here, we review the important roles of miRNAs in the regulation of CD8+ T cell biology and provide perspectives on the broader emerging principles of miRNA function
Impact of ATP-dependent RNA Helicase DDX3X on Herpes Simplex Type 1 (HSV-1) Replication
Le criblage par siRNA de 49 protéines de l'hÎte qui sont incorporées dans les particules
matures du virus herpĂšs simplex de type 1 (VHS-1) a rĂ©vĂ©lĂ© l'importance d'au moins 15 dâentre
elle pour infectivité du virus (Stegen, C et al. 2013). Parmi celle-ci figure la protéine humaine
DDX3X, qui est une ARN hélicase ATP-dépendante. Cette protéine multifonctionnelle participe
à différents stages de l'expression génique, tels que la transcription, la maturation et le transport
d'ARNm ainsi que la traduction. DDX3X est impliquée dans la réplication de plusieurs virus
tels que le Virus de lâimmunodĂ©ficience humaine de type 1 (VIH-1), l'hĂ©patite B (VHB), le virus
de la vaccine (VACV) et le virus de l'hépatite C (VHC). Le rÎle exact de DDX3X dans le cycle
de rĂ©plication du VHS-1 est toutefois inconnu. Ce mĂ©moire consiste en lâĂ©tude dĂ©taillĂ©e de
l'interaction de DDX3X avec le virus. De maniĂšre surprenante, tant lâinhibition que la
surexpression de DDX3X réduit de maniÚre significative l'infectivité du VHS-1. Fait
intéressant, lorsque nous avons restauré la déplétion de DDX3X par une construction résistante
aux ARNi utilisés, le virus pouvait de nouveau infecter les cellules efficacement, indiquant que
le virus est sensible aux quantités de cette protéine de son hÎte. Nos résultats indiquent de plus
que le virus modifie la localisation de DDX3X et cause son agrégation tÎt dÚs les premiers temps
de l'infection. Cependant, le virus ne modifie pas les niveaux cellulaires de DDX3X dans deux
des trois lignées cellulaires examinées. Nous avons également pu établir que cette protéine n'a
pas d'effet sur l'entrĂ©e du VHS-1, suggĂ©rant quâelle agit Ă un stade ultĂ©rieure de lâinfection. En
examinant cette relation plus en dĂ©tail, nos rĂ©sultats ont dĂ©montrĂ© que lâinhibition ou la
surexpression de DDX3X inhibent toutes deux la production de nouvelles particules virales en
réduisant l'expression des diverses classes cinétiques des protéines virales et ce au niveau de
leur transcription. Malgré le rÎle connu DDX3X dans la stimulation de la réponse immunitaire
innĂ©e et la production dâinterfĂ©rons de type I, lâimpact de DDX3X sur la rĂ©plication du VHS-1
est ici indĂ©pendante de cette fonction. Ces travaux dĂ©montrent donc une nouvelle voie dâaction
de DDX3X sur les virus en agissant directement sur la transcription de gĂšnes viraux et la
rĂ©plication du gĂ©nome dâun virus Ă ADN. En comprenant mieux cette interactions hĂŽtepathogĂšne,
il est maintenant envisageable de concevoir des nouvelles approches thérapeutiques
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
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 âomicsâ 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
As our understanding of the plateletâs systemic role continues to expand beyond hemostasis and thrombosis, interrogation of the plateletâs ability to affect diverse biological processes is required. Studies of the plateletâs non-traditional roles have focused on developing our understanding of the plateletâs 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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