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Wiley Interdisciplinary Reviews. RNA

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https://www.readbyqxmd.com/read/29193740/viral-internal-ribosomal-entry-sites-four-classes-for-one-goal
#1
REVIEW
Justine Mailliot, Franck Martin
To ensure efficient propagation, viruses need to rapidly produce viral proteins after cell entrance. Since viral genomes do not encode any components of the protein biosynthesis machinery, viral proteins must be produced by the host cell. To hi-jack the host cellular translation, viruses use a great variety of distinct strategies. Many single-stranded positive-sensed RNA viruses contain so-called internal ribosome entry sites (IRESs). IRESs are structural RNA motifs that have evolved to specific folds that recruit the host ribosomes on the viral coding sequences in order to synthesize viral proteins...
November 29, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29152905/the-gait-translational-control-system
#2
REVIEW
Abul Arif, Peng Yao, Fulvia Terenzi, Jie Jia, Partho Sarothi Ray, Paul L Fox
The interferon (IFN)-γ-activated inhibitor of translation (GAIT) system directs transcript-selective translational control of functionally related genes. In myeloid cells, IFN-γ induces formation of a multiprotein GAIT complex that binds structural GAIT elements in the 3'-untranslated regions (UTRs) of multiple inflammation-related mRNAs, including ceruloplasmin and VEGF-A, and represses their translation. The human GAIT complex is a heterotetramer containing glutamyl-prolyl tRNA synthetase (EPRS), NS1-associated protein 1 (NSAP1), ribosomal protein L13a (L13a), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH)...
November 20, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29124890/new-perspectives-on-telomerase-rna-structure-and-function
#3
REVIEW
Cherie Musgrove, Linnea I Jansson, Michael D Stone
Telomerase is an ancient ribonucleoprotein (RNP) that protects the ends of linear chromosomes from the loss of critical coding sequences through repetitive addition of short DNA sequences. These repeats comprise the telomere, which together with many accessory proteins, protect chromosomal ends from degradation and unwanted DNA repair. Telomerase is a unique reverse transcriptase (RT) that carries its own RNA to use as a template for repeat addition. Over decades of research, it has become clear that there are many diverse, crucial functions played by telomerase RNA beyond simply acting as a template...
November 9, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29105333/rna-versatility-flexibility-and-thermostability-for-practice-in-rna-nanotechnology-and-biomedical-applications
#4
REVIEW
Farzin Haque, Fengmei Pi, Zhengyi Zhao, Shanqing Gu, Haibo Hu, Hang Yu, Peixuan Guo
In recent years, RNA has attracted widespread attention as a unique biomaterial with distinct biophysical properties for designing sophisticated architectures in the nanometer scale. RNA is much more versatile in structure and function with higher thermodynamic stability compared to its nucleic acid counterpart DNA. Larger RNA molecules can be viewed as a modular structure built from a combination of many 'Lego' building blocks connected via different linker sequences. By exploiting the diversity of RNA motifs and flexibility of structure, varieties of RNA architectures can be fabricated with precise control of shape, size, and stoichiometry...
November 3, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29071794/posttranscriptional-control-of-airway-inflammation
#5
REVIEW
Wendy Ezegbunam, Robert Foronjy
Acute inflammation in the lungs is a vital protective response, efficiently and swiftly eliminating inciters of tissue injury. However, in respiratory diseases characterized by chronic inflammation, such as chronic obstructive pulmonary disease and asthma, enhanced expression of inflammatory mediators leads to tissue damage and impaired lung function. Although transcription is an essential first step in the induction of proinflammatory genes, tight regulation of inflammation requires more rapid, flexible responses...
October 26, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28994236/mrna-transport-in-fungal-top-models
#6
REVIEW
Dierk Niessing, Ralf-Peter Jansen, Thomas Pohlmann, Michael Feldbrügge
Eukaryotic cells rely on the precise determination of when and where proteins are synthesized. Spatiotemporal expression is supported by localization of mRNAs to specific subcellular sites and their subsequent local translation. This holds true for somatic cells as well as for oocytes and embryos. Most commonly, mRNA localization is achieved by active transport of the molecules along the actin or microtubule cytoskeleton. Key factors are molecular motors, adaptors, and RNA-binding proteins that recognize defined sequences or structures in cargo mRNAs...
October 10, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28990312/cyclic-di-gmp-regulation-of-virulence-in-bacterial-pathogens
#7
REVIEW
Cherisse L Hall, Vincent T Lee
Signaling pathways allow bacteria to adapt to changing environments. For pathogenic bacteria, signaling pathways allow for timely expression of virulence factors and the repression of antivirulence factors within the mammalian host. As the bacteria exit the mammalian host, signaling pathways enable the expression of factors promoting survival in the environment and/or nonmammalian hosts. One such signaling pathway uses the dinucleotide cyclic-di-GMP (c-di-GMP), and many bacterial genomes encode numerous proteins that are responsible for synthesizing and degrading c-di-GMP...
October 8, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28984054/rna-uridylation-a-key-posttranscriptional-modification-shaping-the-coding-and-noncoding-transcriptome
#8
REVIEW
Caroline De Almeida, Hélène Scheer, Hélène Zuber, Dominique Gagliardi
RNA uridylation is a potent and widespread posttranscriptional regulator of gene expression. RNA uridylation has been detected in a range of eukaryotes including trypanosomes, animals, plants, and fungi, but with the noticeable exception of budding yeast. Virtually all classes of eukaryotic RNAs can be uridylated and uridylation can also tag viral RNAs. The untemplated addition of a few uridines at the 3' end of a transcript can have a decisive impact on RNA's fate. In rare instances, uridylation is an intrinsic step in the maturation of noncoding RNAs like for the U6 spliceosomal RNA or mitochondrial guide RNAs in trypanosomes...
October 5, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28975734/a-jack-of-all-trades-the-rna-binding-protein-vigilin
#9
REVIEW
Matthew Hk Cheng, Ralf-Peter Jansen
The vigilin family of proteins is evolutionarily conserved from yeast to humans and characterized by the proteins' 14 or 15 hnRNP K homology (KH) domains, typically associated with RNA-binding. Vigilin is the largest RNA-binding protein (RBP) in the KH domain-containing family and one of the largest RBP known to date. Since its identification 30 years ago, vigilin has been shown to bind over 700 mRNAs and has been associated with cancer progression and cardiovascular disease. We provide a brief historic overview of vigilin research and outline the proteins' different functions, focusing on maintenance of genome ploidy, heterochromatin formation, RNA export, as well as regulation of translation, mRNA transport, and mRNA stability...
October 4, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28971629/regulation-and-function-of-cmtr1-dependent-mrna-cap-methylation
#10
REVIEW
Francisco Inesta-Vaquera, Victoria H Cowling
mRNA is modified co-transcriptionally at the 5' end by the addition of an inverted guanosine cap structure which can be methylated at several positions. The mRNA cap recruits proteins involved in gene expression and identifies the transcript as being cellular or 'self' in the innate immune response. Methylation of the first transcribed nucleotide on the ribose 2'-O position is a prevalent cap modification which has roles in splicing, translation and provides protection against the innate immune response. In this review, we discuss the regulation and function of CMTR1, the first transcribed nucleotide ribose 2'-O methyltransferase, and the molecular interactions which mediate methylated 2'-O ribose function...
October 2, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28949076/rules-and-tools-to-predict-the-splicing-effects-of-exonic-and-intronic-mutations
#11
REVIEW
Kinji Ohno, Jun-Ichi Takeda, Akio Masuda
Development of next generation sequencing technologies has enabled detection of extensive arrays of germline and somatic single nucleotide variations (SNVs) in human diseases. SNVs affecting intronic GT-AG dinucleotides invariably compromise pre-mRNA splicing. Most exonic SNVs introduce missense/nonsense codons, but some affect auxiliary splicing cis-elements or generate cryptic GT-AG dinucleotides. Similarly, most intronic SNVs are silent, but some affect canonical and auxiliary splicing cis-elements or generate cryptic GT-AG dinucleotides...
September 26, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28929622/endonuclease-regnase-1-monocyte-chemotactic-protein-1-induced-protein-1-mcpip1-in-controlling-immune-responses-and-beyond
#12
REVIEW
Osamu Takeuchi
The activation of inflammatory cells is controlled at transcriptional and posttranscriptional levels. Posttranscriptional regulation modifies mRNA stability and translation, allowing for elaborate control of proteins required for inflammation, such as proinflammatory cytokines, prostaglandin synthases, cell surface co-stimulatory molecules, and even transcriptional modifiers. Such regulation is important for coordinating the initiation and resolution of inflammation, and is mediated by a set of RNA-binding proteins (RBPs), including Regnase-1, Roquin, Tristetraprolin (TTP), and AU-rich elements/poly(U)-binding/degradation factor 1 (AUF1)...
September 20, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28815931/organization-of-the-flavivirus-rna-replicase-complex
#13
REVIEW
Carolin Brand, Martin Bisaillon, Brian J Geiss
Flaviviruses, such as dengue, Japanese encephalitis, West Nile, yellow fever, and Zika viruses, are serious human pathogens that cause significant morbidity and mortality globally each year. Flaviviruses are single-stranded, positive-sense RNA viruses, and encode two multidomain proteins, NS3 and NS5, that possess all enzymatic activities required for genome replication and capping. NS3 and NS5 interact within virus-induced replication compartments to form the RNA genome replicase complex. Although the individual enzymatic activities of both proteins have been extensively studied and are well characterized, there are still gaps in our understanding of how they interact to efficiently coordinate their respective activities during positive-strand RNA synthesis and capping...
November 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28782243/the-la-and-related-rna-binding-proteins-larps-structures-functions-and-evolving-perspectives
#14
REVIEW
Richard J Maraia, Sandy Mattijssen, Isabel Cruz-Gallardo, Maria R Conte
La was first identified as a polypeptide component of ribonucleic protein complexes targeted by antibodies in autoimmune patients and is now known to be a eukaryote cell-ubiquitous protein. Structure and function studies have shown that La binds to a common terminal motif, UUU-3'-OH, of nascent RNA polymerase III (RNAP III) transcripts and protects them from exonucleolytic decay. For precursor-tRNAs, the most diverse and abundant of these transcripts, La also functions as an RNA chaperone that helps to prevent their misfolding...
November 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28762653/single-cell-transcriptomics-of-noncoding-rnas-and-their-cell-specificity
#15
REVIEW
Katerina A B Gawronski, Junhyong Kim
Recent developments of single cell transcriptome profiling methods have led to the realization that many seemingly homogeneous cells have surprising levels of expression variability. The biological implications of the high degree of variability is unclear but one possibility is that many genes are restricted in expression to small lineages of cells, suggesting the existence of many more cell types than previously estimated. Noncoding RNA (ncRNA) are thought to be key parts of gene regulatory processes and their single cell expression patterns may help to dissect the biological function of single cell variability...
November 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28815951/physics-based-all-atom-modeling-of-rna-energetics-and-structure
#16
REVIEW
Louis G Smith, Jianbo Zhao, David H Mathews, Douglas H Turner
The database of RNA sequences is exploding, but knowledge of energetics, structures, and dynamics lags behind. All-atom computational methods, such as molecular dynamics, hold promise for closing this gap. New algorithms and faster computers have accelerated progress in improving the reliability and accuracy of predictions. Currently, the methods can facilitate refinement of experimentally determined nuclear magnetic resonance and x-ray structures, but are 'unreliable' for predictions based only on sequence...
September 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28815950/ribosome-profiling-a-hi-def-monitor-for-protein-synthesis-at-the-genome-wide-scale
#17
(no author information available yet)
No abstract text is available yet for this article.
September 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28815949/microbes-and-rna-not-something-to-sneeze-at
#18
EDITORIAL
Jeffrey Wilusz
No abstract text is available yet for this article.
September 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28608481/discovery-and-function-of-transfer-rna-derived-fragments-and-their-role-in-disease
#19
REVIEW
Ana Raquel Soares, Manuel Santos
Until recently, transfer RNAs (tRNAs) were thought to function in protein translation only. However, recent findings demonstrate that both pre- and mature tRNAs can undergo endonucleolytic cleavage by different ribonucleases originating different types of small non-coding RNAs, known as tRNA-derived fragments (tRFs). tRFs are classified according to their origin and are implicated in various cellular processes, namely apoptosis, protein synthesis control, and RNA interference. Although their functions are still poorly understood, their mechanisms of action vary according to the tRF sub-type...
September 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28524625/mrna-decay-an-adaptation-tool-for-the-environmental-fungal-pathogen-cryptococcus-neoformans
#20
REVIEW
Amanda L M Bloom, Jay Leipheimer, John C Panepinto
Fungi are ubiquitous in the environment and humans constantly encounter them in the soil, air, water, and food. The vast majority of these interactions are inconsequential. However, in the context of immunodeficiency precipitated by HIV infection, hematologic malignancy, or transplantation, a small subset of fungi can cause devastating, systemic infection. The most deadly of the opportunistic environmental fungi, Cryptococcus neoformans, is estimated to cause hundreds of thousands of deaths per year, mostly in the context of HIV co-infection...
September 2017: Wiley Interdisciplinary Reviews. RNA
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