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Wiley Interdisciplinary Reviews. RNA

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https://www.readbyqxmd.com/read/29655315/a-360%C3%A2-view-of-circular-rnas-from-biogenesis-to-functions
#1
REVIEW
Jeremy E Wilusz
The first circular RNA (circRNA) was identified more than 40 years ago, but it was only recently appreciated that circRNAs are common outputs of many eukaryotic protein-coding genes. Some circRNAs accumulate to higher levels than their associated linear mRNAs, especially in the nervous system, and have clear regulatory functions that result in organismal phenotypes. The pre-mRNA splicing machinery generates circRNAs via backsplicing reactions, which are often facilitated by intronic repeat sequences that base pair to one another and bring the intervening splice sites into close proximity...
April 14, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29633565/hfq-chaperone-brings-speed-dating-to-bacterial-srna
#2
REVIEW
Andrew Santiago-Frangos, Sarah A Woodson
Hfq is a ubiquitous, Sm-like RNA binding protein found in most bacteria and some archaea. Hfq binds small regulatory RNAs (sRNAs), facilitates base pairing between sRNAs and their mRNA targets, and directly binds and regulates translation of certain mRNAs. Because sRNAs regulate many stress response pathways in bacteria, Hfq is essential for adaptation to different environments and growth conditions. The chaperone activities of Hfq arise from multipronged RNA binding by three different surfaces of the Hfq hexamer...
April 6, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29624880/translation-initiation-by-cap-dependent-ribosome-recruitment-recent-insights-and-open-questions
#3
REVIEW
Nikolay E Shirokikh, Thomas Preiss
Gene expression universally relies on protein synthesis, where ribosomes recognize and decode the messenger RNA template by cycling through translation initiation, elongation, and termination phases. All aspects of translation have been studied for decades using the tools of biochemistry and molecular biology available at the time. Here, we focus on the mechanism of translation initiation in eukaryotes, which is remarkably more complex than prokaryotic initiation and is the target of multiple types of regulatory intervention...
April 6, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29582564/genetic-variants-in-mrna-untranslated-regions
#4
REVIEW
Maristella Steri, M Laura Idda, Michael B Whalen, Valeria Orrù
Genome Wide Association Studies (GWAS) have mapped thousands of genetic variants associated with complex disease risk and regulating quantitative traits, thus exploiting an unprecedented high-resolution genetic characterization of the human genome. A small fraction (3.7%) of the identified associations is located in untranslated regions (UTRs), and the molecular mechanism has been elucidated for few of them. Genetic variations at UTRs may modify regulatory elements affecting the interaction of the UTRs with proteins and microRNAs...
March 26, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29516680/cytoplasmic-functions-of-long-noncoding-rnas
#5
REVIEW
Ji Heon Noh, Kyoung Mi Kim, Waverly G McClusky, Kotb Abdelmohsen, Myriam Gorospe
Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides found throughout the cell that lack protein-coding function. Their functions are closely linked to their interaction with RNA-binding proteins (RBPs) and nucleic acids. Nuclear lncRNAs have been studied extensively, revealing complexes with structural and regulatory roles that enable gene organization and control transcription. Cytoplasmic lncRNAs are less well understood, but accumulating evidence indicates that they also form complexes with diverse structural and regulatory functions...
March 8, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29508942/intron-retention-in-viruses-and-cellular-genes-detention-border-controls-and-passports
#6
REVIEW
David Rekosh, Marie-Louise Hammarskjold
Intron retention (IR), where one or more introns remain in the RNA after splicing, was long thought to be rare in mammalian cells, albeit common in plants and some viruses. Largely due to the development of better methods for RNA analysis, it has now been recognized that IR is much more common than previously thought and that this mechanism is likely to play an important role in mammalian gene regulation. To date, most publications and reviews about IR have described the resulting mRNAs as "dead end" products, with no direct consequence for the proteome...
March 6, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29452455/complex-hur-function-in-pancreatic-cancer-cells
#7
REVIEW
Jonathan R Brody, Dan A Dixon
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers with dismal patient outcomes. The underlying core genetic drivers of disease have been identified in human tumor specimens and described in genetically engineered mouse models. These genetic drivers of PDAC include KRAS signaling, TP53 mutations, and genetic loss of the SMAD4 tumor suppressor protein. Beyond the known mutational landscape of PDAC genomes, alternative disrupted targets that extend beyond conventional genetic mutations have been elusive and understudied in the context of PDAC cell therapeutic resistance and survival...
February 16, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29424086/circadian-processes-in-the-rna-life-cycle
#8
REVIEW
Manon Torres, Denis Becquet, Jean-Louis Franc, Anne-Marie François-Bellan
The circadian clock drives daily rhythms of multiple physiological processes, allowing organisms to anticipate and adjust to periodic changes in environmental conditions. These physiological rhythms are associated with robust oscillations in the expression of at least 30% of expressed genes. While the ability for the endogenous timekeeping system to generate a 24-hr cycle is a cell-autonomous mechanism based on negative autoregulatory feedback loops of transcription and translation involving core-clock genes and their protein products, it is now increasingly evident that additional mechanisms also govern the circadian oscillations of clock-controlled genes...
February 9, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29423937/mutually-exclusive-alternative-splicing-of-pre-mrnas
#9
REVIEW
Yongfeng Jin, Haiyang Dong, Yang Shi, Lina Bian
Pre-mRNA alternative splicing is an important mechanism used to expand protein diversity in higher eukaryotes, and mutually exclusive splicing is a specific type of alternative splicing in which only one of the exons in a cluster is included in functional transcripts. The most extraordinary example of this is the Drosophila melanogaster Down's syndrome cell adhesion molecule gene (Dscam), which potentially encodes 38,016 different isoforms through mutually exclusive splicing. Mutually exclusive splicing is a unique and challenging model that can be used to elucidate the evolution, regulatory mechanism, and function of alternative splicing...
February 9, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29383855/therapeutic-applications-of-group-i-intron-based-trans-splicing-ribozymes
#10
REVIEW
Chang Ho Lee, Seung Ryul Han, Seong-Wook Lee
Since the breakthrough discovery of catalytic RNAs (ribozymes) in the early 1980s, valuable ribozyme-based gene therapies have been developed for incurable diseases ranging from genetic disorders to viral infections and cancers. Ribozymes can be engineered and used to downregulate or repair pathogenic genes via RNA cleavage mediated by trans-cleaving ribozymes or repair and reprograming mediated by trans-splicing ribozymes, respectively. Uniquely, trans-splicing ribozymes can edit target RNAs via simultaneous destruction and repair (and/or reprograming) to yield the desired therapeutic RNAs, thus selectively inducing therapeutic gene activity in cells expressing the target RNAs...
January 31, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29327503/noncoding-rnas-in-alzheimer-s-disease
#11
REVIEW
M Laura Idda, Rachel Munk, Kotb Abdelmohsen, Myriam Gorospe
Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the main cause of dementia among the elderly worldwide. Despite intense efforts to develop drugs for preventing and treating AD, no effective therapies are available as yet, posing a growing burden at the personal, medical, and socioeconomic levels. AD is characterized by the production and aggregation of amyloid β (Aβ) peptides derived from amyloid precursor protein (APP), the presence of hyperphosphorylated microtubule-associated protein Tau (MAPT), and chronic inflammation leading to neuronal loss...
March 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29322631/cold-inducible-rna-binding-protein-in-cancer-and-inflammation
#12
REVIEW
Daniel A Lujan, Joey L Ochoa, Rebecca S Hartley
RNA binding proteins (RBPs) play key roles in RNA dynamics, including subcellular localization, translational efficiency and metabolism. Cold-inducible RNA binding protein (CIRP) is a stress-induced protein that was initially described as a DNA damage-induced transcript (A18 hnRNP), as well as a cold-shock domain containing cold-stress response protein (CIRBP) that alters the translational efficiency of its target messenger RNAs (mRNAs). This review summarizes recent work on the roles of CIRP in the context of inflammation and cancer...
March 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29314657/molecular-and-genetic-interactions-of-the-rna-degradation-machineries-in-firmicute-bacteria
#13
REVIEW
Peter Redder
Correct balance between bacterial RNA degradation and synthesis is essential for controlling expression level of all RNAs. The RNA polymerase, which performs the RNA synthesis, is highly conserved across the bacterial domain. However, this is surprisingly not the case for the RNA degradation machinery, which is composed of different subunits and performs different enzymatic reactions, depending on the organism. In Escherichia coli, the RNA decay is performed by the degradosome complex, which forms around the membrane-associated endoribonuclease RNase E, and is stable enough to be purified without falling apart...
March 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29280295/emerging-roles-of-rna-binding-proteins-in-diabetes-and-their-therapeutic-potential-in-diabetic-complications
#14
REVIEW
Curtis A Nutter, Muge N Kuyumcu-Martinez
Diabetes is a debilitating health care problem affecting 422 million people around the world. Diabetic patients suffer from multisystemic complications that can cause mortality and morbidity. Recent advancements in high-throughput next-generation RNA-sequencing and computational algorithms led to the discovery of aberrant posttranscriptional gene regulatory programs in diabetes. However, very little is known about how these regulatory programs are mis-regulated in diabetes. RNA-binding proteins (RBPs) are important regulators of posttranscriptional RNA networks, which are also dysregulated in diabetes...
March 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29193740/viral-internal-ribosomal-entry-sites-four-classes-for-one-goal
#15
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...
March 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29152905/the-gait-translational-control-system
#16
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)...
March 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29124890/new-perspectives-on-telomerase-rna-structure-and-function
#17
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...
March 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29341438/natural-antisense-transcripts-in-diseases-from-modes-of-action-to-targeted-therapies
#18
REVIEW
Elżbieta Wanowska, Magdalena Regina Kubiak, Wojciech Rosikiewicz, Izabela Makałowska, Michał Wojciech Szcześniak
Antisense transcription is a widespread phenomenon in mammalian genomes, leading to production of RNAs molecules referred to as natural antisense transcripts (NATs). NATs apply diverse transcriptional and post-transcriptional regulatory mechanisms to carry out a wide variety of biological roles that are important for the normal functioning of living cells, but their dysfunctions can be associated with human diseases. In this review, we attempt to provide a molecular basis for the involvement of NATs in the etiology of human disorders such as cancers and neurodegenerative and cardiovascular diseases...
January 17, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29341429/trans-acting-translational-regulatory-rna-binding-proteins
#19
REVIEW
Robert F Harvey, Tom S Smith, Thomas Mulroney, Rayner M L Queiroz, Mariavittoria Pizzinga, Veronica Dezi, Eneko Villenueva, Manasa Ramakrishna, Kathryn S Lilley, Anne E Willis
The canonical molecular machinery required for global mRNA translation and its control has been well defined, with distinct sets of proteins involved in the processes of translation initiation, elongation and termination. Additionally, noncanonical, trans-acting regulatory RNA-binding proteins (RBPs) are necessary to provide mRNA-specific translation, and these interact with 5' and 3' untranslated regions and coding regions of mRNA to regulate ribosome recruitment and transit. Recently it has also been demonstrated that trans-acting ribosomal proteins direct the translation of specific mRNAs...
January 17, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29105333/rna-versatility-flexibility-and-thermostability-for-practice-in-rna-nanotechnology-and-biomedical-applications
#20
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...
January 2018: Wiley Interdisciplinary Reviews. RNA
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