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Wiley Interdisciplinary Reviews. RNA

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https://www.readbyqxmd.com/read/28524625/mrna-decay-an-adaptation-tool-for-the-environmental-fungal-pathogen-cryptococcus-neoformans
#1
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...
May 19, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28382748/insights-into-rna-structure-and-dynamics-from-recent-nmr-and-x-ray-studies-of-the-neurospora-varkud-satellite-ribozyme
#2
REVIEW
Pierre Dagenais, Nicolas Girard, Eric Bonneau, Pascale Legault
Despite the large number of noncoding RNAs and their importance in several biological processes, our understanding of RNA structure and dynamics at atomic resolution is still very limited. Like many other RNAs, the Neurospora Varkud satellite (VS) ribozyme performs its functions through dynamic exchange of multiple conformational states. More specifically, the VS ribozyme recognizes and cleaves its stem-loop substrate via a mechanism that involves several structural transitions within its stem-loop substrate...
April 6, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28371504/functional-diversity-of-arabidopsis-organelle-localized-rna-recognition-motif-containing-proteins
#3
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...
March 29, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28296064/box-c-d-small-nucleolar-rna-genes-and-the-prader-willi-syndrome-a-complex-interplay
#4
REVIEW
Jérôme Cavaillé
The nucleolus of mammalian cells contains hundreds of box C/D small nucleolar RNAs (SNORDs). Through their ability to base pair with ribosomal RNA precursors, most play important roles in the synthesis and/or activity of ribosomes, either by guiding sequence-specific 2'-O-methylations or by facilitating RNA folding and cleavages. A growing number of SNORD genes with elusive functions have been discovered recently. Intriguingly, the vast majority of them are located in two large, imprinted gene clusters at human chromosome region 15q11q13 (the SNURF-SNRPN domain) and at 14q32 (the DLK1-DIO3 domain) where they are expressed, respectively, only from the paternally and maternally inherited alleles...
March 13, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27863022/unwinding-the-twister-ribozyme-from-structure-to-mechanism
#5
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
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...
March 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27748060/developmental-regulation-of-rna-processing-by-rbfox-proteins
#7
REVIEW
John G Conboy
The Rbfox genes encode an ancient family of sequence-specific RNA binding proteins (RBPs) that are critical developmental regulators in multiple tissues including skeletal muscle, cardiac muscle, and brain. The hallmark of Rbfox proteins is a single high-affinity RRM domain, highly conserved from insects to humans, that binds preferentially to UGCAUG motifs at diverse regulatory sites in pre-mRNA introns, mRNA 3'UTRs, and pre-miRNAs hairpin structures. Versatile regulatory circuits operate on Rbfox pre-mRNA and mRNA to ensure proper expression of Rbfox1 protein isoforms, which then act on the broader transcriptome to regulate alternative splicing networks, mRNA stability and translation, and microRNA processing...
March 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27704722/posttranscriptional-regulation-of-intestinal-epithelial-integrity-by-noncoding-rnas
#8
REVIEW
Jun-Yao Wang, Lan Xiao, Jian-Ying Wang
Maintenance of the gut epithelial integrity under stressful environments requires epithelial cells to rapidly elicit changes in gene expression patterns to regulate their survival, adapt to stress, and keep epithelial homeostasis. Disruption of the intestinal epithelial integrity occurs commonly in patients with various critical illnesses, leading to the translocation of luminal toxic substances and bacteria to the blood stream. Recently, noncoding RNAs (ncRNAs) have emerged as a novel class of master regulators of gene expression and are fundamentally involved in many aspects of gut mucosal regeneration, protection, and epithelial barrier function...
March 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27620010/auf1-regulation-of-coding-and-noncoding-rna
#9
REVIEW
Elizabeth J F White, Aerielle E Matsangos, Gerald M Wilson
AUF1 is a family of four RNA-binding proteins (RBPs) generated by alternative pre-messenger RNA (pre-mRNA) splicing, with canonical roles in controlling the stability and/or translation of mRNA targets based on recognition of AU-rich sequences within mRNA 3' untranslated regions. However, recent studies identifying AUF1 target sites across the transcriptome have revealed that these canonical functions are but a subset of its roles in posttranscriptional regulation of gene expression. In this review, we describe recent developments in our understanding of the RNA-binding properties of AUF1 together with their biochemical implications and roles in directing mRNA decay and translation...
March 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27612318/emerging-roles-and-context-of-circular-rnas
#10
REVIEW
Amaresh C Panda, Ioannis Grammatikakis, Rachel Munk, Myriam Gorospe, Kotb Abdelmohsen
Circular RNAs (circRNAs) represent a large class of noncoding RNAs (ncRNAs) that have recently emerged as regulators of gene expression. They have been shown to suppress microRNAs, thereby increasing the translation and stability of the targets of such microRNAs. In this review, we discuss the emerging functions of circRNAs, including RNA transcription, splicing, turnover, and translation. We also discuss other possible facets of circRNAs that can influence their function depending on the cell context, such as circRNA abundance, subcellular localization, interacting partners (RNA, DNA, and proteins), dynamic changes in interactions following stimulation, and potential circRNA translation...
March 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27531497/extracellular-rna-in-aging
#11
REVIEW
Douglas F Dluzen, Nicole Noren Hooten, Michele K Evans
Since the discovery of extracellular RNA (exRNA) in circulation and other bodily fluids, there has been considerable effort to catalog and assess whether exRNAs can be used as markers for health and disease. A variety of exRNA species have been identified including messenger RNA and noncoding RNA such as microRNA (miRNA), small nucleolar RNA, transfer RNA, and long noncoding RNA. Age-related changes in exRNA abundance have been observed, and it is likely that some of these transcripts play a role in aging. In this review, we summarize the current state of exRNA profiling in various body fluids and discuss age-related changes in exRNA abundance that have been identified in humans and other model organisms...
March 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27440103/modulating-splicing-with-small-molecular-inhibitors-of-the-spliceosome
#12
REVIEW
Kerstin A Effenberger, Veronica K Urabe, Melissa S Jurica
Small molecule inhibitors that target components of the spliceosome have great potential as tools to probe splicing mechanism and dissect splicing regulatory networks in cells. These compounds also hold promise as drug leads for diseases in which splicing regulation plays a critical role, including many cancers. Because the spliceosome is a complicated and dynamic macromolecular machine comprised of many RNA and protein components, a variety of compounds that interfere with different aspects of spliceosome assembly is needed to probe its function...
March 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28231639/cell-cycle-rna-regulons-coordinating-early-lymphocyte-development
#13
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...
February 23, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28188674/microexons-discovery-regulation-and-function
#14
REVIEW
Dmytro Ustianenko, Sebastien M Weyn-Vanhentenryck, Chaolin Zhang
The importance of RNA splicing in numerous cellular processes is well established. However, an underappreciated aspect is the ability of the spliceosome to recognize a set of very small (3-30 nucleotide, 1-10 amino acid) exons named microexons. Despite their small size, microexons and their regulation through alternative splicing have now been shown to play critical roles in protein and system function. Here we review the discovery of microexons over time and the mechanisms by which their splicing is regulated, including recent progress made through deep RNA sequencing...
February 11, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28130835/structures-of-rna-repeats-associated-with-neurological-diseases
#15
REVIEW
Leszek Błaszczyk, Wojciech Rypniewski, Agnieszka Kiliszek
All RNA molecules possess a 'propensity' to fold into complex secondary and tertiary structures. Although they are composed of only four types of nucleotides, they show an enormous structural richness which reflects their diverse functions in the cell. However, in some cases the folding of RNA can have deleterious consequences. Aberrantly expanded, repeated RNA sequences can exhibit gain-of-function abnormalities and become pathogenic, giving rise to many incurable neurological diseases. Most RNA repeats form long hairpin structures whose stem consists of noncanonical base pairs interspersed among Watson-Crick pairs...
January 28, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28130830/rna-in-extracellular-vesicles
#16
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...
January 28, 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...
January 28, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28120379/mrna-localization-as-a-rheostat-to-regulate-subcellular-gene-expression
#18
REVIEW
Nevraj S Kejiou, Alexander F Palazzo
It is currently believed that certain messenger RNAs (mRNAs) are localized to distinct subcellular regions to efficiently target their encoded proteins. However, this simplistic model does not explain why in certain scenarios mRNA localization is dispensable for proper protein distribution. In other cases, mRNA localization is accompanied by translational silencing and degradation by the localization machinery. Here we propose that in certain scenarios mRNAs are localized so that they can either be stabilized and translated, or silenced and degraded, in response to the needs of the subcellular locale...
January 24, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28097803/regulation-of-mrna-following-brain-ischemia-and-reperfusion
#19
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/27659605/rna-binding-proteins-implicated-in-neurodegenerative-diseases
#20
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
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