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Wiley Interdisciplinary Reviews. RNA

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https://www.readbyqxmd.com/read/28097803/regulation-of-mrna-following-brain-ischemia-and-reperfusion
#1
REVIEW
Donald J DeGracia
There is growing appreciation that mRNA regulation plays important roles in disease and injury. mRNA regulation and ribonomics occur in brain ischemia and reperfusion (I/R) following stroke and cardiac arrest and resuscitation. It was recognized over 40 years ago that translation arrest (TA) accompanies brain I/R and is now recognized as part of the intrinsic stress responses triggered in neurons. However, neuron death correlates to a prolonged TA in cells fated to undergo delayed neuronal death (DND). Dysfunction of mRNA regulatory processes in cells fated to DND prevents them from translating stress-induced mRNAs such as heat shock proteins...
January 17, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28008720/the-exon-junction-complex-a-lifelong-guardian-of-mrna-fate
#2
REVIEW
Lauren A Woodward, Justin W Mabin, Pooja Gangras, Guramrit Singh
During messenger RNA (mRNA) biogenesis and processing in the nucleus, many proteins are imprinted on mRNAs assembling them into messenger ribonucleoproteins (mRNPs). Some of these proteins remain stably bound within mRNPs and have a long-lasting impact on their fate. One of the best-studied examples is the exon junction complex (EJC), a multiprotein complex deposited primarily 24 nucleotides upstream of exon-exon junctions as a consequence of pre-mRNA splicing. The EJC maintains a stable, sequence-independent, hold on the mRNA until its removal during translation in the cytoplasm...
December 23, 2016: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28008714/bioinformatic-tools-for-analysis-of-clip-ribonucleoprotein-data
#3
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...
December 23, 2016: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27990773/long-noncoding-rnas-in-the-p53-network
#4
REVIEW
Ritu Chaudhary, Ashish Lal
The tumor-suppressor protein p53 is activated in response to numerous cellular stresses including DNA damage. p53 functions primarily as a sequence-specific transcription factor that controls the expression of hundreds of protein-coding genes and noncoding RNAs, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs). While the role of protein-coding genes and miRNAs in mediating the effects of p53 has been extensively studied, the physiological function and molecular mechanisms by which p53-regulated lncRNAs act is beginning to be understood...
December 19, 2016: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27882692/current-progress-on-micrornas-based-therapeutics-in-neurodegenerative-diseases
#5
REVIEW
Patrícia Pereira, João A Queiroz, Ana Figueiras, Fani Sousa
MicroRNAs (miRNAs)-based therapy has recently emerged as a promising strategy in the treatments of neurodegenerative diseases. Thus, in this review, the most recent and important challenges and advances on the development of miRNA therapeutics for brain targeting are discussed. In particular, this review highlights current knowledge and progress in the field of manufacturing, recovery, isolation, purification, and analysis of these therapeutic oligonucleotides. Finally, the available miRNA delivery systems are reviewed and an analysis is presented in what concerns to the current challenges that have to be addressed to ensure their specificity and efficacy...
November 24, 2016: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27873472/perfect-timing-splicing-and-transcription-rates-in-living-cells
#6
REVIEW
Tara Alpert, Lydia Herzel, Karla M Neugebauer
An important step toward understanding gene regulation is the elucidation of the time necessary for the completion of individual steps. Measurement of reaction rates can reveal potential nodes for regulation. For example, measurements of in vivo transcription elongation rates reveal regulation by DNA sequence, gene architecture, and chromatin. Pre-mRNA splicing is regulated by transcription elongation rates and vice versa, yet the rates of RNA processing reactions remain largely elusive. Since the 1980s, numerous model systems and approaches have been used to determine the precise timing of splicing in vivo...
November 21, 2016: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27863022/unwinding-the-twister-ribozyme-from-structure-to-mechanism
#7
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...
November 14, 2016: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27863009/regulation-of-mrna-turnover-in-cystic-fibrosis-lung-disease
#8
REVIEW
Roopa Biswas, Parameet Kumar, Harvey B Pollard
Cystic fibrosis (CF) is an autosomal recessive disease due to mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, F508del-CFTR being the most frequent mutation. The CF lung is characterized by a hyperinflammatory phenotype and is regulated by multiple factors that coordinate its pathophysiology. In CF the expression of CFTR as well as proinflammatory genes are regulated at the level of messenger RNA (mRNA) stability, which subsequently affect translation. These mechanisms are mediated by inflammatory RNA-binding proteins as well as small endogenous noncoding microRNAs, in coordination with cellular signaling pathways...
November 13, 2016: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27863061/how-to-understand-atomistic-molecular-dynamics-simulations-of-rna-and-protein-rna-complexes
#9
REVIEW
Jiří Šponer, Miroslav Krepl, Pavel Banáš, Petra Kührová, Marie Zgarbová, Petr Jurečka, Marek Havrila, Michal Otyepka
We provide a critical assessment of explicit-solvent atomistic molecular dynamics (MD) simulations of RNA and protein/RNA complexes, written primarily for non-specialists with an emphasis to explain the limitations of MD. MD simulations can be likened to hypothetical single-molecule experiments starting from single atomistic conformations and investigating genuine thermal sampling of the biomolecules. The main advantage of MD is the unlimited temporal and spatial resolution of positions of all atoms in the simulated systems...
November 10, 2016: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27863087/posttranscriptional-coordination-of-splicing-and-mirna-biogenesis-in-plants
#10
REVIEW
Agata Stepien, Katarzyna Knop, Jakub Dolata, Michal Taube, Mateusz Bajczyk, Maria Barciszewska-Pacak, Andrzej Pacak, Artur Jarmolowski, Zofia Szweykowska-Kulinska
MicroRNAs (miRNAs) are short, single-stranded, noncoding RNAs that play a crucial role in basic physiological and morphological processes and in response to various stresses in eukaryotic organisms. However, the miRNA biogenesis, which is based on the action of complex protein machinery, varies between plants and animals, with the differences largely concerning the location of the process, the protein composition of the microprocessor, the mechanism of miRNA action on mRNA target, and the miRNA gene ( MIR ) structure...
November 9, 2016: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27659605/rna-binding-proteins-implicated-in-neurodegenerative-diseases
#11
REVIEW
Mark R Cookson
Gene expression is regulated at many levels, including after generation of the primary RNA transcript from DNA but before translation into protein. Such post-translational gene regulation occurs via the action of a multitude of RNA binding proteins and include varied actions from splicing to regulation of association with the translational machinery. Primary evidence that such processes might contribute to disease mechanisms in neurodegenerative disorders comes from the observation of mutations in RNA binding proteins, particularly in diseases in the amyotrophic lateral sclerosis-frontotemporal dementia spectrum and in some forms of ataxia and tremor...
January 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27465259/the-nuts-and-bolts-of-the-endogenous-spliceosome
#12
REVIEW
Ruth Sperling
The complex life of pre-mRNA from transcription to the production of mRNA that can be exported from the nucleus to the cytoplasm to encode for proteins entails intricate coordination and regulation of a network of processing events. Coordination is required between transcription and splicing and between several processing events including 5' and 3' end processing, splicing, alternative splicing and editing that are major contributors to the diversity of the human proteome, and occur within a huge and dynamic macromolecular machine-the endogenous spliceosome...
January 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27436689/evolutionary-clues-in-lncrnas
#13
REVIEW
Anne Nitsche, Peter F Stadler
The diversity of long non-coding RNAs (lncRNAs) in the human transcriptome is in stark contrast to the sparse exploration of their functions concomitant with their conservation and evolution. The pervasive transcription of the largely non-coding human genome makes the evolutionary age and conservation patterns of lncRNAs to a topic of interest. Yet it is a fairly unexplored field and not that easy to determine as for protein-coding genes. Although there are a few experimentally studied cases, which are conserved at the sequence level, most lncRNAs exhibit weak or untraceable primary sequence conservation...
January 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27425147/new-insights-into-decapping-enzymes-and-selective-mrna-decay
#14
REVIEW
Ewa Grudzien-Nogalska, Megerditch Kiledjian
Removal of the 5' end cap is a critical determinant controlling mRNA stability and efficient gene expression. Removal of the cap is exquisitely controlled by multiple direct and indirect regulators that influence association with the cap and the catalytic step. A subset of these factors directly stimulate activity of the decapping enzyme, while others influence remodeling of factors bound to mRNA and indirectly stimulate decapping. Furthermore, the components of the general decapping machinery can also be recruited by mRNA-specific regulatory proteins to activate decapping...
January 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27396578/transcending-the-prediction-paradigm-novel-applications-of-shape-to-rna-function-and-evolution
#15
REVIEW
Katrina M Kutchko, Alain Laederach
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) provides information on RNA structure at single-nucleotide resolution. It is most often used in conjunction with RNA secondary structure prediction algorithms as a probabilistic or thermodynamic restraint. With the recent advent of ultra-high-throughput approaches for collecting SHAPE data, the applications of this technology are extending beyond structure prediction. In this review, we discuss recent applications of SHAPE data in the transcriptomic context and how this new experimental paradigm is changing our understanding of these experiments and RNA folding in general...
January 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27345446/translating-the-epitranscriptome
#16
REVIEW
Thomas Philipp Hoernes, Matthias David Erlacher
RNA modifications are indispensable for the translation machinery to provide accurate and efficient protein synthesis. Whereas the importance of transfer RNA (tRNA) and ribosomal RNA (rRNA) modifications has been well described and is unquestioned for decades, the significance of internal messenger RNA (mRNA) modifications has only recently been revealed. Novel experimental methods have enabled the identification of thousands of modified sites within the untranslated and translated regions of mRNAs. Thus far, N(6) -methyladenosine (m(6) A), pseudouridine (Ψ), 5-methylcytosine (m(5) C) and N(1) -methyladenosine (m(1) A) were identified in eukaryal, and to some extent in prokaryal mRNAs...
January 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27324829/the-organization-and-regulation-of-mrna-protein-complexes
#17
REVIEW
Olivia S Rissland
In a eukaryotic cell, each messenger RNA (mRNA) is bound to a variety of proteins to form an mRNA-protein complex (mRNP). Together, these proteins impact nearly every step in the life cycle of an mRNA and are critical for the proper control of gene expression. In the cytoplasm, for instance, mRNPs affect mRNA translatability and stability and provide regulation of specific transcripts as well as global, transcriptome-wide control. mRNPs are complex, diverse, and dynamic, and so they have been a challenge to understand...
January 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27307117/posttranslational-control-of-hur-function
#18
REVIEW
Ioannis Grammatikakis, Kotb Abdelmohsen, Myriam Gorospe
The RNA-binding protein HuR (human antigen R) associates with numerous transcripts, coding and noncoding, and controls their splicing, localization, stability, and translation. Through its regulation of target transcripts, HuR has been implicated in cellular events including proliferation, senescence, differentiation, apoptosis, and the stress and immune responses. In turn, HuR influences processes such as cancer and inflammation. HuR function is primarily regulated through posttranslational modifications that alter its subcellular localization and its ability to bind target RNAs; such modifications include phosphorylation, methylation, ubiquitination, NEDDylation, and proteolytic cleavage...
January 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27301829/the-role-of-mrna-structure-in-bacterial-translational-regulation
#19
REVIEW
Michelle M Meyer
The characteristics of bacterial messenger RNAs (mRNAs) that influence translation efficiency provide many convenient handles for regulation of gene expression, especially when coupled with the processes of transcription termination and mRNA degradation. An mRNA's structure, especially near the site of initiation, has profound consequences for how readily it is translated. This property allows bacterial gene expression to be altered by changes to mRNA structure induced by temperature, or interactions with a wide variety of cellular components including small molecules, other RNAs (such as sRNAs and tRNAs), and RNA-binding proteins...
January 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27251431/hallmarks-of-cancer-and-au-rich-elements
#20
REVIEW
Khalid S A Khabar
Post-transcriptional control of gene expression is aberrant in cancer cells. Sustained stabilization and enhanced translation of specific mRNAs are features of tumor cells. AU-rich elements (AREs), cis-acting mRNA decay determinants, play a major role in the posttranscriptional regulation of many genes involved in cancer processes. This review discusses the role of aberrant ARE-mediated posttranscriptional processes in each of the hallmarks of cancer, including sustained cellular growth, resistance to apoptosis, angiogenesis, invasion, and metastasis...
January 2017: Wiley Interdisciplinary Reviews. RNA
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