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Wiley Interdisciplinary Reviews. RNA

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https://www.readbyqxmd.com/read/28815931/organization-of-the-flavivirus-rna-replicase-complex
#1
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
#2
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
#3
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
#4
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/28782243/the-la-and-related-rna-binding-proteins-larps-structures-functions-and-evolving-perspectives
#5
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...
August 7, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28762653/single-cell-transcriptomics-of-noncoding-rnas-and-their-cell-specificity
#6
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
#7
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/28660659/rna-structure-binding-and-coordination-in-arabidopsis
#8
REVIEW
Shawn W Foley, Marianne C Kramer, Brian D Gregory
From the moment of transcription, up through degradation, each RNA transcript is bound by an ever-changing cohort of RNA binding proteins. The binding of these proteins is regulated by both the primary RNA sequence, as well as the intramolecular RNA folding, or secondary structure, of the transcript. Thus, RNA secondary structure regulates many post-transcriptional processes. With the advent of next generation sequencing, several techniques have been developed to generate global landscapes of both RNA-protein interactions and RNA secondary structure...
June 28, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28589684/chimeric-rnas-in-cancer-and-normal-physiology
#9
REVIEW
Katarzyna Chwalenia, Loryn Facemire, Hui Li
Traditionally, chimeric RNAs were considered to be exclusive to cancer cells. When occasionally observed in normal samples, they were usually considered to be transcriptional 'noises,' or artifacts due to template switching during the reverse transcription and/or Polymerase chain reaction (PCR) steps of experimentation. However, with the advances being made in next generation sequencing technologies and software tools, as well as the accumulation of new experimental evidences, increasing numbers of chimeric transcripts are being identified in noncancerous tissues and cells...
June 7, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28815951/physics-based-all-atom-modeling-of-rna-energetics-and-structure
#10
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
#11
(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
#12
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
#13
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
#14
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
https://www.readbyqxmd.com/read/28371504/functional-diversity-of-arabidopsis-organelle-localized-rna-recognition-motif-containing-proteins
#15
REVIEW
Xiaowen Shi, Maureen R Hanson, Stephane Bentolila
RNA-Binding Proteins (RBPs) play key roles in plant gene expression and regulation. RBPs contain a variety of RNA-binding motifs, the most abundant and most widespread one in eukaryotes is the RNA recognition motif (RRM). Many nucleus-encoded RRM-containing proteins are transported into chloroplasts and/or mitochondria, and participate in various RNA-related processes in plant organelles. Loss of these proteins can have a detrimental effect on some critical processes such as photosynthesis and respiration, sometimes leading to lethality...
September 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28231639/cell-cycle-rna-regulons-coordinating-early-lymphocyte-development
#16
REVIEW
Alison Galloway, Martin Turner
Lymphocytes undergo dynamic changes in gene expression as they develop from progenitor cells lacking antigen receptors, to mature cells that are prepared to mount immune responses. While transcription factors have established roles in lymphocyte development, they act in concert with post-transcriptional and post-translational regulators to determine the proteome. Furthermore, the post-transcriptional regulation of RNA regulons consisting of mRNAs whose protein products act cooperatively allows RNA binding proteins to exert their effects at multiple points in a pathway...
September 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28130820/microrna-binding-proteins-specificity-and-function
#17
REVIEW
Richard W Zealy, Samuel P Wrenn, Sylvia Davila, Kyung-Won Min, Je-Hyun Yoon
microRNA (miRNA) and RNA-binding proteins (RBPs) have been studied widely in post-transcriptional gene regulation. Previous work has focused on defining how miRNA and RBPs modulate target mRNA decay and translation as well as investigating how they interplay each other. Emerging studies indicate that certain RBPs other than the AGO-family proteins directly interact with mature miRNAs. These findings implicate competitive binding of RBPs to target miRNAs, sequestration of miRNAs from AGO, promotion of AGO binding to miRNAs, and transfer of miRNAs from RBPs to AGO...
September 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28130830/rna-in-extracellular-vesicles
#18
REVIEW
Kyoung Mi Kim, Kotb Abdelmohsen, Maja Mustapic, Dimitrios Kapogiannis, Myriam Gorospe
Cells release a range of membrane-enclosed extracellular vesicles (EVs) into the environment. Among them, exosomes and microvesicles (collectively measuring 40-1000 nm in diameter) carry proteins, signaling lipids, and nucleic acids from donor cells to recipient cells, and thus have been proposed to serve as intercellular mediators of communication. EVs transport cellular materials in many physiologic processes, including differentiation, stem cell homeostasis, immune responses, and neuronal signaling. EVs are also increasingly recognized as having a direct role in pathologies such as cancer and neurodegeneration...
July 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28008714/bioinformatic-tools-for-analysis-of-clip-ribonucleoprotein-data
#19
REVIEW
Supriyo De, Myriam Gorospe
Investigating the interactions of RNA-binding proteins (RBPs) with RNAs is a complex task for molecular and computational biologists. The molecular biology techniques and the computational approaches to understand RBP-RNA (or ribonucleoprotein, RNP) interactions have advanced considerably over the past few years and numerous and diverse software tools have been developed to analyze these data. Accordingly, laboratories interested in RNP biology face the challenge of choosing adequately among the available software tools those that best address the biological problem they are studying...
July 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27863022/unwinding-the-twister-ribozyme-from-structure-to-mechanism
#20
REVIEW
Jennifer Gebetsberger, Ronald Micura
The twister ribozyme motif has been identified by bioinformatic means very recently. Currently, four crystal structures with ordered active sites together with a series of chemical and biochemical data provide insights into how this RNA accomplishes its efficient self-cleavage. Of particular interest for a mechanistic proposal are structural distinctions observed in the active sites that concern the conformation of the U-A cleavage site dinucleotide (in-line alignment of the attacking 2'-O nucleophile to the to-be-cleaved PO5' bond versus suboptimal alignments) as well as the presence/absence of Mg(2+) ions at the scissile phosphate...
May 2017: Wiley Interdisciplinary Reviews. RNA
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