Analysis of the Interaction Between Viruses, Mirnas and the Rnai Pathway PDF Download
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Languages : en
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The microRNA (miRNA) and RNA interference (RNAi) pathways have recently emerged as an important aspect of virus-host cell interaction. This interaction can occur in several different ways and may favor either the virus or the host cell. Plants and invertebrates use RNAi as a first line of defense against virus infection by cleaving long, double-stranded viral transcripts into small interfering RNAs. However, it remains to be determined whether mammalian cells also initiate a similar response to infection. Here we present evidence that mammalian cells in fact do not induce an antiviral RNAi defense in response to infection by primate retroviruses. Viruses may also interact with host cells by encoding miRNAs to regulate either cellular or viral gene expression. Here we demonstrate that herpes simplex virus type 1 (HSV-1) encodes at least five miRNAs which are primarily expressed during latency. Two of these miRNAs modulate expression of viral genes required for productive replication. We hypothesize that down regulation of these viral genes by these latency associated miRNAs allows HSV-1 to establish and maintain the latent state.
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Languages : en
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Book Description
The microRNA (miRNA) and RNA interference (RNAi) pathways have recently emerged as an important aspect of virus-host cell interaction. This interaction can occur in several different ways and may favor either the virus or the host cell. Plants and invertebrates use RNAi as a first line of defense against virus infection by cleaving long, double-stranded viral transcripts into small interfering RNAs. However, it remains to be determined whether mammalian cells also initiate a similar response to infection. Here we present evidence that mammalian cells in fact do not induce an antiviral RNAi defense in response to infection by primate retroviruses. Viruses may also interact with host cells by encoding miRNAs to regulate either cellular or viral gene expression. Here we demonstrate that herpes simplex virus type 1 (HSV-1) encodes at least five miRNAs which are primarily expressed during latency. Two of these miRNAs modulate expression of viral genes required for productive replication. We hypothesize that down regulation of these viral genes by these latency associated miRNAs allows HSV-1 to establish and maintain the latent state.
Author: Jennifer Lin Umbach
Publisher:
ISBN:
Category : Electronic dissertations
Languages : en
Pages :
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Book Description
The microRNA (miRNA) and RNA interference (RNAi) pathways have recently emerged as an important aspect of virus-host cell interaction. This interaction can occur in several different ways and may favor either the virus or the host cell. Plants and invertebrates use RNAi as a first line of defense against virus infection by cleaving long, double-stranded viral transcripts into small interfering RNAs. However, it remains to be determined whether mammalian cells also initiate a similar response to infection. Here we present evidence that mammalian cells in fact do not induce an antiviral RNAi defense in response to infection by primate retroviruses. Viruses may also interact with host cells by encoding miRNAs to regulate either cellular or viral gene expression. Here we demonstrate that herpes simplex virus type 1 (HSV-1) encodes at least five miRNAs which are primarily expressed during latency. Two of these miRNAs modulate expression of viral genes required for productive replication. We hypothesize that down regulation of these viral genes by these latency associated miRNAs allows HSV-1 to establish and maintain the latent state.
Author: Alfonso J. Rodriguez-Morales
Publisher: BoD – Books on Demand
ISBN: 1789848245
Category : Medical
Languages : en
Pages : 179
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Book Description
Tropical emerging diseases pose a significant risk for the circulation of old and new pathogens in areas previously unknown, also implying the possibility of new morbidities and mortalities and new consequences for naïve populations. Globalization, migration and travel are key factors for tropical diseases, and represent the need for integration of tropical medicine, travel medicine and epidemiology in the understanding of such complex situations. Neglected tropical diseases such as leprosy or Chagas disease, arboviral diseases, HIV, Ebola, and arenaviral infections are just a few examples. This book tries to update significant epidemiological and clinical research in many aspects with a multinational perspective.
Author: Sergio Alpuche
Publisher:
ISBN:
Category :
Languages : en
Pages :
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"Eukaryotic cells possess different mechanisms of gene regulation at various stages from transcription to translation. RNA interference (RNAi) is a mechanism of post-transcriptional gene modulation based on short double-stranded RNA sequences called micro RNAs (miRNA). MiRNAs are partially complementary to a specific sequence in messenger RNAs (mRNA) and their binding to a targeted mRNA mediates its repression and/or degradation. In humans, RNAi controls over 50 % of protein-coding genes. The improper functioning of this process leads to the development of different pathologies. Internal or external factors influence the malfunctioning of RNAi. Among them, viral infections fine-tune RNAi, which can be beneficial or detrimental for viral replication. Human immunodeficiency virus type-1 (HIV-1) and Zika virus (ZIKV) are two different viruses that have distinct mechanisms of infection. Nonetheless, both viruses change the miRNA landscape through modifications in the RNAi pathway. This thesis explores the interplay between RNAi and either HIV-1 or ZIKV. In the first project, we re-evaluated the relationship between RNAi and HIV-1. Our experiments demonstrated that RNAi is functional in HIV-1 replicating cells. Besides, proteins of the RNA induced silencing complex (RISC) are not relocalized in HIV-1 producing cells. In contrast, we showed that HIV-1 Gag interacts specifically with Dicer, an essential protein of the RISC. We found that Gag does not change the cleavage of precursor. miRNAs by Dicer but modifies their availability. Gag modifies the loading of specific miRNAs on Dicer, which leads to sequestration or higher loading of particular miRNAs. Among these miRNAs, we found miR-642a 3p that has been predicted to target the AFF4 protein. AFF4 is an essential component of the virus transcription and its absence profoundly impairs HIV-1 replication.Our second goal was to examine mRNAs and miRNAs in an integrative analysis of infected cells with ZIKV. Because little information on the neurological consequences after ZIKV infection were available at the beginning of our study, we first compared two different viral strains. We determined that a Brazilian isolate was more cytopathic than an early Asian one in distinct cell types. Then, using the Brazilian virus, we studied the impact of ZIKV infection on the expression of host mRNAs and miRNAs in fetal mice neurons. Notably, we determined a downregulation of NPAS4 and NR4A transcripts, which have been linked to the neurogenesis process. Moreover, our integrative analysis showed a correlation between dysregulated mRNAs and miRNAs in the infected cells. Particularly, NR4A3 transcripts might be controlled by the dysregulated levels of miR-7116-5p and miR-7013-5p upon the infection.The results presented in this thesis contribute to the understanding of 1) HIV-1-induced modification of miRNAs loaded on Dicer and their consequences on mRNAs expression and 2) ZIKV cytopathicity and its impact on miRNAs and mRNAs expression profile in murine fetal neurons"--
Author: Owen Dunkley
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
"As an obligate intracellular pathogen, the human immunodeficiency virus type 1 (HIV-1) targets and co-opts a diverse set of host processes to overcome cellular barriers to infection, including pathways involved in the regulation of gene expression. It remains controversial whether HIV-1 affects the RNA interference (RNAi) pathway, a key post-transcriptional regulatory mechanism that is being used to develop a new class of gene therapies. To better understand the replication cycle of the virus and inform the development of future antiviral therapies, we investigated the hypothesis that HIV-1 changes the substrates and functionality of the RNAi system in specific contexts. To investigate our hypothesis, we first aimed to identify regulatory networks associated with blocks in virus replication during latency. We characterized a novel cellular model for HIV-1 infection that was designed to study events in HIV-1 latency reversion that follow transcription initiation. We then reactivated this model using differently acting latency reversing agents, to then sequence long and short RNA transcriptomes associated with latency maintenance and reversion. These data contributed new genes and regulatory RNA networks to our understanding of latency, and possibly new targets for RNA therapies. We next analyzed an interaction between the HIV-1 protein Gag and the RNAi enzyme Dicer, which leads to the specific enrichment of three microRNAs (miRNAs) on Dicer. A combination of bioinformatic analyses were used to identify the targets of these miRNAs and to define a target-specific hypothesis for the function of this interaction. Using gene reporter assays, Western blots and reverse transcription quantitative polymerase chain reactions, we explored one miRNA-target interaction in depth, showing that this miRNA inhibits HIV-1 expression and that Gag promotes viral expression by increasing expression of the target, possibly by inhibiting the antiviral miRNA. Finally, we sought to develop a testing platform to distinguish between RNAi substrates that could be used in combination therapies against HIV-1. We designed a novel protocol that can score RNAi substrates with four primary measures: cellular toxicity, inhibition of HIV expression, inhibition of HIV replication, and ability to lock proviruses in a latent state. Due to delays related to cloning, this protocol could not be fully employed in this manuscript. However, we individually tested the first three endpoints and used a surrogate fourth endpoint to make preliminary assessments of the therapeutic potential of several molecules. Here, we describe two workflows used to gain better insight into interactions between HIV-1 and the RNAi pathway, and further designed a protocol for testing small RNAs for their potential to lock the HIV-1 in a latent state"--
Author: Ronald P. van Rij
Publisher: Humana Press
ISBN: 9781493958252
Category : Medical
Languages : en
Pages : 425
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Book Description
Viruses and RNAi share an intricate relationship at many levels. RNAi is an important antiviral defense mechanism in plants and invertebrates, microRNAs – of viral or cellular origin – affect many aspects of virus biology, and replication of many, if not all, mammalian viruses can be suppressed by RNAi. Antiviral RNAi: Concepts, Methods, and Applications provides a collection of protocols for the analysis of viral small RNAs and natural antiviral RNAi responses as well as for the development and optimization of RNAi-based antiviral drugs. As RNAi is a central regulatory mechanism in the cell, the methods in this volume can also be applied out of the context of a virus infection. Divided into five convenient parts, this detailed volume reviews important basic concepts in the field of antiviral RNAi, provides experimental and bio-informatic tools for the analysis of small silencing RNAs, covers methods to biochemically dissect RNAi-based antiviral defense and viral counter-defense mechanisms, describes methods for the design, expression, and delivery of therapeutic antiviral siRNAs, and finally presents genome-wide RNAi approaches for the identification of factors involved in virus replication. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Antiviral RNAi: Concepts, Methods, and Applications serves as an ideal guide for both novice and experienced researchers alike striving to dissect the role of RNAi in the viral life cycle or to further boost the development of novel therapeutics and experimental tools based on RNAi technology.
Author: Ronald P. van Rij
Publisher: Humana Press
ISBN: 9781617790362
Category : Medical
Languages : en
Pages : 0
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Book Description
Viruses and RNAi share an intricate relationship at many levels. RNAi is an important antiviral defense mechanism in plants and invertebrates, microRNAs – of viral or cellular origin – affect many aspects of virus biology, and replication of many, if not all, mammalian viruses can be suppressed by RNAi. Antiviral RNAi: Concepts, Methods, and Applications provides a collection of protocols for the analysis of viral small RNAs and natural antiviral RNAi responses as well as for the development and optimization of RNAi-based antiviral drugs. As RNAi is a central regulatory mechanism in the cell, the methods in this volume can also be applied out of the context of a virus infection. Divided into five convenient parts, this detailed volume reviews important basic concepts in the field of antiviral RNAi, provides experimental and bio-informatic tools for the analysis of small silencing RNAs, covers methods to biochemically dissect RNAi-based antiviral defense and viral counter-defense mechanisms, describes methods for the design, expression, and delivery of therapeutic antiviral siRNAs, and finally presents genome-wide RNAi approaches for the identification of factors involved in virus replication. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Antiviral RNAi: Concepts, Methods, and Applications serves as an ideal guide for both novice and experienced researchers alike striving to dissect the role of RNAi in the viral life cycle or to further boost the development of novel therapeutics and experimental tools based on RNAi technology.
Author: Helena J. Maier
Publisher: Humana
ISBN: 9781071609026
Category : Medical
Languages : en
Pages : 278
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Book Description
This detailed new edition provides a comprehensive collection of protocols applicable to all members of the Coronavirinae sub-family currently and that are also transferrable to other fields of virology. Beginning with a section on detection, discovery, and evolution, the volume continues with coverage of propagation and titration of coronaviruses, genome manipulation, study of virus-host interactions, as well as imaging coronavirus infections. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Coronaviruses: Methods and Protocols, Second Edition serves as a valuable guide to researchers working to identify and control viruses with increased potential to cross the species barrier and to develop the diagnostics, vaccines, and antiviral therapeutics that are required to manage future outbreaks in both humans and animals.
Author: Aiming Wang
Publisher: Springer
ISBN: 3319329197
Category : Science
Languages : en
Pages : 341
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Book Description
Topics covered in this book include RNA silencing and its suppression in plant virus infection, virus replication mechanisms, the association of cellular membranes with virus replication and movement, plant genetic resistance to viruses, viral cell-to-cell spread, long distance movement in plants, virus induced ER stress, virus diversity and evolution, virus-vector interactions, cross protection, geminiviruses, negative strand RNA viruses, viroids, and the diagnosis of plant viral diseases using next generation sequencing. This book was anticipated to help plant pathologists, scholars, professors, teachers and advanced students in the field with a comprehensive state-of-the-art knowledge of the subject.
Author: Marion Declercq
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
RNA decay is a central cellular process as it regulates RNA stability and quality and thereby gene expression, which is essential to ensure proper cellular physiology and establishment of adapted responses to viral infection. Global takeover of gene expression machineries and rewiring of the cellular environment is key to the success of viral infection. Cellular proteome and viral replication are tightly connected and cellular RNA processing, stability, quality and decay accordingly influence the fate of the viral cycle. Growing evidence points towards the existence of a large interplay between eukaryotic RNA turnover machineries and viral proteins. Viruses not only evolved mechanisms to evade those RNA degradation pathways, but they also manipulate them to promote viral replication.Influenza A viruses (IAV) are major pathogens responsible for yearly epidemics and occasional pandemics. To complete their viral cycle, IAVs rely on many cellular proteins and establish a complex and highly coordinated interplay with the host proteome. Growing evidence supports the existence of a complex interplay between IAV viral proteins and RNA decay machineries. Unraveling such interplay is therefore essential to gain a better understanding of the IAV life cycle, required for the development of antiviral strategies. This led us to systematically screen interactions between viral proteins involved in IAV replication and a selected set of 75 cellular proteins carrying exoribonucleases activities or associated with RNA decay machineries. A total of 18 proteins were identified as interactors of at least one viral protein tested. Analysis of the interaction network highlighted a specific and preferential targeting of RNA degradation pathways by IAV proteins. Among validated interactors, a targeted RNAi screen identified nine factors as required for viral multiplication. We chose to focus on the 3'-5' exoribonuclease 1 (ERI1), found in our screen as an interactor of several components of the vRNPs (viral RiboNucleoProtein) (PB2, PB1 and NP). The ERI1 protein is a major player in the control of cellular gene expression as it is essential for the maturation and decay of histone mRNA, maturation of 5.8S rRNA and miRNA homeostasis in mammalian cells. Exploring the interplay between ERI1 and viral proteins during the course of IAV infection we found that i) ERI1 promotes viral transcription, and both of its activities - RNA binding and exonuclease - are required, ii) ERI1 interacts with viral proteins in an RNA dependent manner, iii) ERI1 interacts with the transcribing vRNPs, iv) viral proteins interact with a form of ERI1 that is associated to histone mRNA. Ultimately, our data point to a model where ERI1 associated to histone mRNA is co-opted by the transcribing viral polymerase, thereby promoting IAV multiplication, through a mechanism that remains to be precisely determined. Targeting of ERI1 by IAV is another example further supporting the intricate interplay between IAV and RNA decay machineries, used to rewire cellular gene expression in order to create a favorable environment for viral replication.
