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Role of RNA structure and protein factors in the control of HIV-1 splicing

Jean-Michel Saliou
2009 Frontiers in Bioscience  
Site A7 is regulated by downstream and upstream elements 7. Regulatory elements located in other HIV-1 RNA regions 8. HnRNP A1 a general host down-regulator of HIV-1 RNA splicing 9.  ...  TABLE OF CONTENTS 1. Abstract 2. Introduction 3. Overview of HIV-1 alternative splicing in the context of viral infection 4.  ...  (A) Model of site A3 inhibition by hnRNP A1 and H. (B) Model of site A3 activation by SC35. Figure 6 . 6 Effect of mutations in ESE2 and ESS2 on the splicing pattern of HIV-1 RNA.  ... 
doi:10.2741/3408 pmid:19273230 fatcat:lqp6atqqszcpxpouwxhjvi5mmm

Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection

Nam Nguyen Quang, Sophie Goudey, Emmanuel Ségéral, Ammara Mohammad, Sophie Lemoine, Corinne Blugeon, Margaux Versapuech, Jean-Christophe Paillart, Clarisse Berlioz-Torrent, Stéphane Emiliani, Sarah Gallois-Montbrun
2020 Retrovirology  
Alternative splicing is a key step in Human Immunodeficiency Virus type 1 (HIV-1) replication that is tightly regulated both temporally and spatially.  ...  To get further insights into alternative splicing regulation, we then compiled quantifications of splice site (SS) usage and transcript levels to build "splice trees", a quantitative representation of  ...  We thank Pierre de la Grange, Noémie Robil et Agathe Delaune from GenoSplice technology for their expertise in genomic analyses of transcriptomes, Gordon Langsley (Comparative cell biology of apicomplexan  ... 
doi:10.1186/s12977-020-00533-1 pmid:32807178 fatcat:x7eiuxrlm5crfiegp6ehcwydsq

New windows into retroviral RNA structures

Dhivya Jayaraman, Julia Claire Kenyon
2018 Retrovirology  
The multiple roles of both viral and cellular RNAs have become increasingly apparent in recent years, and techniques to model them have become significantly more powerful, enabling faster and more accurate  ...  Techniques to model the three-dimensional structures of these large RNAs have also recently developed.  ...  This is seen as an increase in backbone flexibility by enhanced SHAPE reagent binding, and was applied to HIV-2 [8] and alternative foldings in HIV-1 [22] , to identify different types of long-range  ... 
doi:10.1186/s12977-018-0393-6 pmid:29368653 pmcid:PMC5784592 fatcat:orqufdqbxnhqhfo73as3rzmk6i

Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing

Usama Ashraf, Clara Benoit-Pilven, Vincent Lacroix, Vincent Navratil, Nadia Naffakh
2019 Trends in Microbiology  
Alteration of host cell splicing is a common feature of many viral infections which is underappreciated because of the complexity and technical difficulty of studying alternative splicing (AS) regulation  ...  Recent advances in RNA sequencing technologies revealed that up to several hundreds of host genes can show altered mRNA splicing upon viral infection.  ...  HIV-1 entry triggers early changes in the phosphorylation of five SR proteins, including SRRM2 which regulates the splicing of HIV-1 transcripts [18] .  ... 
doi:10.1016/j.tim.2018.11.004 pmid:30577974 fatcat:zrinncfz6jeb7ih7wgrqrwd7fi

IIIDB: a database for isoform-isoform interactions and isoform network modules

Yu-Ting Tseng, Wenyuan Li, Ching-Hsien Chen, Shihua Zhang, Jeremy JW Chen, Xianghong Zhou, Chun-Chi Liu
2015 BMC Genomics  
In fact, alternative splicing can often change the internal structure of a pathway by rearranging specific PPIs.  ...  To fill the gap, we systematically predicted genome-wide isoform-isoform interactions (IIIs) using RNA-seq datasets, domain-domain interaction and PPIs.  ...  Acknowledgements The National Institutes of Health (NIH) [  ... 
doi:10.1186/1471-2164-16-s2-s10 pmid:25707505 pmcid:PMC4331710 fatcat:eyzha6vhebcw3hx24aied7dw4u

Integrated and Total HIV-1 DNA Predict Ex Vivo Viral Outgrowth

Maja Kiselinova, Ward De Spiegelaere, Maria Jose Buzon, Eva Malatinkova, Mathias Lichterfeld, Linos Vandekerckhove, Ronald Swanstrom
2016 PLoS Pathogens  
Total HIV-1 DNA, unspliced (us) and multiply spliced HIV-1 RNA, and 2LTR circles were quantified by digital PCR in peripheral blood, at 3 time points.  ...  Integrated HIV-1 DNA was associated with total HIV-1 DNA (p<0.001, R² = 0.85), us HIV-1 RNA (p = 0.029, R² = 0.40), and VOA (p = 0.041, R 2 = 0.44).  ...  Acknowledgments We would like to thank the patients and all the health care professionals who participated in this study.  ... 
doi:10.1371/journal.ppat.1005472 pmid:26938995 pmcid:PMC4777389 fatcat:vznn7xatzrg5lecofx5de644j4

Beyond the replication-competent HIV reservoir: transcription and translation-competent reservoirs

Amy E. Baxter, Una O'Doherty, Daniel E. Kaufmann
2018 Retrovirology  
Recent years have seen a substantial increase in the number of tools available to monitor and study HIV reservoirs.  ...  Lastly, we detail some of the key contributions that the study of these transcription and translation-competent reservoirs has made thus far to investigations into HIV persistence, and outline where these  ...  Availability of data and materials Not applicable.  ... 
doi:10.1186/s12977-018-0392-7 pmid:29394935 pmcid:PMC5797386 fatcat:6zwzusl6fjgmzix43gfzyl7rla

Retroviral RNA Dimerization: From Structure to Functions

Noé Dubois, Roland Marquet, Jean-Christophe Paillart, Serena Bernacchi
2018 Frontiers in Microbiology  
Recent studies reported RNA switches models regulating not only gRNA dimerization, but also translation and packaging, and a spatio-temporal characterization of viral gRNA dimerization within cells are  ...  This review summarizes our current understanding on the structural features of the dimerization signals for a variety of retroviruses (HIVs, MLV, RSV, BLV, MMTV, MPMV. . .), the mechanisms of RNA dimer  ...  Ferhadian for his help with drawing the HIV-1 SL1 duplex structures with PyMOL.  ... 
doi:10.3389/fmicb.2018.00527 pmid:29623074 pmcid:PMC5874298 fatcat:47uuos4jjrh6xj6mizqqqg7w5a

Epitranscriptomic Addition of m5C to HIV-1 Transcripts Regulates Viral Gene Expression

David G. Courtney, Kevin Tsai, Hal P. Bogerd, Edward M. Kennedy, Brittany A. Law, Ann Emery, Ronald Swanstrom, Christopher L. Holley, Bryan R. Cullen
2019 Cell Host and Microbe  
In addition, loss of m5C dysregulates the alternative splicing of viral RNAs.  ...  These data identify m5C as a post-transcriptional regulator of both splicing and function of HIV-1 mRNA, thereby affecting directly viral gene expression.  ...  Loss of NSUN2 Affects HIV-1 Alternative Splicing HIV-1 RNAs are extensively alternatively spliced, and we therefore wondered if m 5 C modifications affect this process.  ... 
doi:10.1016/j.chom.2019.07.005 pmid:31415754 pmcid:PMC6714563 fatcat:qcvbvubykndq5jh6mca4ghpt7e

Cat and Mouse: HIV Transcription in Latency, Immune Evasion and Cure/Remission Strategies

Aurélie Delannoy, Mikaël Poirier, Brendan Bell
2019 Viruses  
Here, we provide an overview of the rapidly evolving field of HIV cure/remission research, highlighting recent progress and ongoing challenges in the understanding of HIV reservoirs, the role of HIV transcription  ...  We emphasize that a better understanding of the game of "cat and mouse" between the host immune system and the HIV virus is a crucial knowledge gap to be filled in both cure and vaccine research.  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/v11030269 pmid:30889861 pmcid:PMC6466452 fatcat:n4jr2r2pdneuflx2hhmucxojse

The cell biology of HIV-1 and other retroviruses

Eric O Freed, Andrew J Mouland
2006 Retrovirology  
and integration; gene expression/regulation of retroviral Gag and genomic RNA; and assembly/release.  ...  HIV-1 and other Retroviruses (July 20-23, 2006, Emory University, Atlanta, Georgia).  ...  on their work prior to submission of this manuscript.  ... 
doi:10.1186/1742-4690-3-77 pmid:17083721 pmcid:PMC1635732 fatcat:gwpooey4qjfy5c6abacvc6beua

Prolonged persistence of a novel replication-defective HIV-1 variant in plasma of a patient on suppressive therapy

Samantha Rassler, Roberto Ramirez, Nadeen Khoury, Gail Skowron, Gautam K. Sahu
2016 Virology Journal  
Conclusions: This is the first identification of a natural point mutation (GU-to-GC) in the conserved 5′-MSD motif of HIV genomic RNA.  ...  Cell-free residual HIV-1 virions (RVs) persist in plasma below 20-50 vRNA copies/ml in most patients on suppressive antiretroviral therapy (ART).  ...  We thank Becky Matuszek for coordinating the patients' visits and sample donations for the study.  ... 
doi:10.1186/s12985-016-0617-0 pmid:27655142 pmcid:PMC5031319 fatcat:a4ojfjjlvnfzdbpckpicbx3jei

The changing paradigm of intron retention: regulation, ramifications and recipes

2019 Nucleic Acids Research  
Intron retention (IR) is a form of alternative splicing that has long been neglected in mammalian systems although it has been studied for decades in non-mammalian species such as plants, fungi, insects  ...  The fate of an intron to be, or not to be, retained in the mature transcript is the direct result of the influence exerted by numerous intrinsic and extrinsic factors at multiple levels of regulation.  ...  ACKNOWLEDGEMENTS We thank the funding agencies for research and fellowship support.  ... 
doi:10.1093/nar/gkz1068 pmid:31724706 pmcid:PMC7145568 fatcat:id5psu3qfrc5fctsoodzyiu4xy

Cell-Permeable Peptides Containing Cycloalanine Residues

Hao Wu, Guillaume Mousseau, Sonia Mediouni, Susana T. Valente, Thomas Kodadek
2016 Angewandte Chemie International Edition  
We present here an efficient alternative to the N-methylation for the purpose of morphing proteinbinding peptides into more serum stable and cell permeable compounds.  ...  Here we introduce an alternative strategy involving the efficient incorporation of "cycloalanine" residues into peptides.  ...  After this period of time, cytoplasmic and nuclear RNA were extracted and analyzed by quantitative RT-qPCR using primers recognizing total HIV mRNA, multiply spliced (Tat, Rev, Nef), singly spliced (Env  ... 
doi:10.1002/anie.201605745 pmid:27529332 pmcid:PMC5220248 fatcat:2dqmriay3fgtvh6hjnyhwqfxum

Proceedings of the Frontiers of Retrovirology Conference 2016

Irena Zurnic, Sylvia Hütter, Ute Lehmann, Nicole Stanke, Juliane Reh, Tobias Kern, Fabian Lindel, Gesche Gerresheim, Martin Hamann, Erik Müllers, Paul Lesbats, Peter Cherepanov (+639 others)
2016 Retrovirology  
Viral subtyping was done using online tools and drug resistannce mutations were screened using the Stanford University HIV Drug Resistance Database for Interpretation and the International AIDS Society-USA  ...  Our 205 cohort samples with a viral load above 2000 copies/ml were amplified by PCR and sequenced.  ...  Simulation of genomic RNA folding suggests that introduction of the tag sequence induced an alternative folding structure in a region enriched in splice sites and splicing regulatory sequences.  ... 
doi:10.1186/s12977-016-0294-5 fatcat:4oldvixbkjfkdfkl3ouqlrrxka
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