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Wiley Interdisciplinary Reviews. RNA

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https://www.readbyqxmd.com/read/28994236/mrna-transport-in-fungal-top-models
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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/28853213/advances-and-challenges-in-the-detection-of-transcriptome-wide-protein-rna-interactions
#8
REVIEW
Emily C Wheeler, Eric L Van Nostrand, Gene W Yeo
RNA binding proteins (RBPs) play key roles in determining cellular behavior by manipulating the processing of target RNAs. Robust methods are required to detect the numerous binding sites of RBPs across the transcriptome. RNA-immunoprecipitation followed by sequencing (RIP-seq) and crosslinking followed by immunoprecipitation and sequencing (CLIP-seq) are state-of-the-art methods used to identify the RNA targets and specific binding sites of RBPs. Historically, CLIP methods have been confounded with challenges such as the requirement for tens of millions of cells per experiment, low RNA yields resulting in libraries that contain a high number of polymerase chain reaction duplicated reads, and technical inconveniences such as radioactive labeling of RNAs...
August 29, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28840663/chromatin-associated-noncoding-rnas-in-development-and-inheritance
#9
REVIEW
Sreemukta Acharya, Mark Hartmann, Sylvia Erhardt
Noncoding RNAs (ncRNAs) have emerged as crucial players in chromatin regulation. Their diversity allows them to partake in the regulation of numerous cellular processes across species. During development, long and short ncRNAs act in conjunction with each other where long ncRNAs (lncRNAs) are best understood in establishing appropriate gene expression patterns, while short ncRNAs (sRNAs) are known to establish constitutive heterochromatin and suppress mobile elements. Additionally, increasing evidence demonstrates roles of sRNAs in several typically lncRNA-mediated processes such as dosage compensation, indicating a complex regulatory network of noncoding RNAs...
August 25, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28815931/organization-of-the-flavivirus-rna-replicase-complex
#10
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...
August 16, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28815924/urinary-micrornas-for-prostate-cancer-diagnosis-prognosis-and-treatment-response-are-we-there-yet
#11
REVIEW
Ovidiu Balacescu, Bogdan Petrut, Oana Tudoran, Dragos Feflea, Loredana Balacescu, Andrei Anghel, Ioan O Sirbu, Edward Seclaman, Catalin Marian
Prostate cancer (PCa) remains one of the leading causes of cancer-related deaths in men. Despite the tremendous progress in research over the years, a suitable minimally invasive PCa biomarker is yet to be discovered. The recent advances regarding the roles of microRNAs as biomarkers has allowed for their study in PCa as well, especially as blood-based markers. However, there are several studies that used urine as biological sample to evaluate microRNAs as biomarkers for PCa diagnosis, prognosis, and treatment response, which were reviewed herein...
August 16, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28792118/rna-mediated-signal-perception-in-pathogenic-bacteria
#12
REVIEW
Dmitriy Ignatov, Jörgen Johansson
Bacterial pathogens encounter several different environments during an infection, many of them possibly being detrimental. In order to sense its surroundings and adjust the gene expression accordingly, different regulatory schemes are undertaken. With these, the bacterium appropriately can differentiate between various environmental cues to express the correct virulence factor at the appropriate time and place. An attractive regulator device is RNA, which has an outstanding ability to alter its structure in response to external stimuli, such as metabolite concentration or alterations in temperature, to control its downstream gene expression...
August 9, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28791797/emerging-roles-of-hnrnpa1-in-modulating-malignant-transformation
#13
REVIEW
Rajat Roy, Yueyang Huang, Michael J Seckl, Olivier E Pardo
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are RNA-binding proteins associated with complex and diverse biological processes such as processing of heterogeneous nuclear RNAs (hnRNAs) into mature mRNAs, RNA splicing, transactivation of gene expression, and modulation of protein translation. hnRNPA1 is the most abundant and ubiquitously expressed member of this protein family and has been shown to be involved in multiple molecular events driving malignant transformation. In addition to selective mRNA splicing events promoting expression of specific protein variants, hnRNPA1 regulates the gene expression and translation of several key players associated with tumorigenesis and cancer progression...
August 8, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28762653/single-cell-transcriptomics-of-noncoding-rnas-and-their-cell-specificity
#14
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...
August 1, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28762650/ancient-and-modern-hints-of-a-core-post-transcriptional-network-driving-chemotherapy-resistance-in-ovarian-cancer
#15
REVIEW
Sarah Blagden, Mai Abdel Mouti, James Chettle
RNA-binding proteins (RBPs) and noncoding (nc)RNAs (such as microRNAs, long ncRNAs, and others) cooperate within a post-transcriptional network to regulate the expression of genes required for many aspects of cancer behavior including its sensitivity to chemotherapy. Here, using an RBP-centric approach, we explore the current knowledge surrounding contributers to post-transcriptional gene regulation (PTGR) in ovarian cancer and identify commonalities that hint at the existence of an evolutionarily conserved core PTGR network...
August 1, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28782243/the-la-and-related-rna-binding-proteins-larps-structures-functions-and-evolving-perspectives
#16
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/28815951/physics-based-all-atom-modeling-of-rna-energetics-and-structure
#17
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
#18
(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
#19
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
#20
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
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