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Wiley Interdisciplinary Reviews. RNA

journal
https://www.readbyqxmd.com/read/30109918/regulation-of-cytoplasmic-rna-stability-lessons-from-drosophila
#1
REVIEW
Benjamin P Towler, Sarah F Newbury
The process of RNA degradation is a critical level of regulation contributing to the control of gene expression. In the last two decades a number of studies have shown the specific and targeted nature of RNA decay and its importance in maintaining homeostasis. The key players within the pathways of RNA decay are well conserved with their mutation or disruption resulting in distinct phenotypes as well as human disease. Model organisms including Drosophila melanogaster have played a substantial role in elucidating the mechanisms conferring control over RNA stability...
August 15, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/30101566/dynamic-rna-holo-editosomes-with-subcomplex-variants-insights-into-the-control-of-trypanosome-editing
#2
REVIEW
Jorge Cruz-Reyes, Blaine H M Mooers, Pawan K Doharey, Joshua Meehan, Shelly Gulati
RNA editing causes massive remodeling of the mitochondrial mRNA transcriptome in trypanosomes and related kinetoplastid protozoa. This type of editing involves the specific insertion or deletion of uridylates (U) directed by small noncoding guide RNAs (gRNAs). Because U-insertion exceeds U-deletion by a factor of 10, editing increases the nascent mRNA size by up to 55%. In Trypanosoma brucei, the editing apparatus uses ~40 proteins and >1,200 gRNAs to create the functional open reading frame in 12 mRNAs...
August 12, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/30091184/unconventional-rna-binding-proteins-step-intothe-virus-host-battlefront
#3
REVIEW
Manuel Garcia-Moreno, Aino I Järvelin, Alfredo Castello
The crucial participation of cellular RNA-binding proteins (RBPs) in virtually all steps of virus infection has been known for decades. However, most of the studies characterizing this phenomenon have focused on well-established RBPs harboring classical RNA-binding domains (RBDs). Recent proteome-wide approaches have greatly expanded the census of RBPs, discovering hundreds of proteins that interact with RNA through unconventional RBDs. These domains include protein-protein interaction platforms, enzymatic cores, and intrinsically disordered regions...
August 9, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/30074293/antisense-and-yet-sensitive-copy-number-control-of-rolling-circle-replicating-plasmids-by-small-rnas
#4
REVIEW
Radoslaw Pluta, Manuel Espinosa
Bacterial plasmids constitute a wealth of shared DNA amounting to about 20% of the total prokaryotic pangenome. Plasmids replicate autonomously and control their replication by maintaining a fairly constant number of copies within a given host. Plasmids should acquire a good fitness to their hosts so that they do not constitute a genetic load. Here we review some basic concepts in plasmid biology, pertaining to the control of replication and distribution of plasmid copies among daughter cells. A particular class of plasmids is constituted by those that replicate by the rolling circle mode (rolling circle-replicating [RCR]-plasmids)...
August 3, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29989343/regulation-of-translation-initiation-factor-eif2b-at-the-hub-of-the-integrated-stress-response
#5
REVIEW
Graham D Pavitt
Phosphorylation of the translation initiation factor eIF2 is one of the most widely used and well-studied mechanisms cells use to respond to diverse cellular stresses. Known as the integrated stress response (ISR), the control pathway uses modulation of protein synthesis to reprogram gene expression and restore homeostasis. Here the current knowledge of the molecular mechanisms of eIF2 activation and its control by phosphorylation at a single-conserved phosphorylation site, serine 51 are discussed with a major focus on the regulatory roles of eIF2B and eIF5 where a current molecular view of ISR control of eIF2B activity is presented...
July 10, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29921017/rna-methylation-in-nuclear-pre-mrna-processing
#6
REVIEW
Helena Covelo-Molares, Marek Bartosovic, Stepanka Vanacova
Eukaryotic RNA can carry more than 100 different types of chemical modifications. Early studies have been focused on modifications of highly abundant RNA, such as ribosomal RNA and transfer RNA, but recent technical advances have made it possible to also study messenger RNA (mRNA). Subsequently, mRNA modifications, namely methylation, have emerged as key players in eukaryotic gene expression regulation. The most abundant and widely studied internal mRNA modification is N6 -methyladenosine (m6 A), but the list of mRNA chemical modifications continues to grow as fast as interest in this field...
June 19, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29911349/tales-around-the-clock-poly-a-tails-in-circadian-gene-expression
#7
REVIEW
Rafailia A A Beta, Nikolaos A A Balatsos
Circadian rhythms are ubiquitous time-keeping processes in eukaryotes with a period of ~24 hr. Light is perhaps the main environmental cue (zeitgeber) that affects several aspects of physiology and behaviour, such as sleep/wake cycles, orientation of birds and bees, and leaf movements in plants. Temperature can serve as the main zeitgeber in the absence of light cycles, even though it does not lead to rhythmicity through the same mechanism as light. Additional cues include feeding patterns, humidity, and social rhythms...
June 17, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29888550/high-throughput-sequencing-revolution-reveals-conserved-fundamentals-of-u-indel-editing
#8
REVIEW
Sara L Zimmer, Rachel M Simpson, Laurie K Read
Among Euglenozoans, mitochondrial RNA editing occurs in the diplonemids and in the kinetoplastids that include parasitic trypanosomes. Yet U-indel editing, in which open reading frames (ORFs) on mRNAs are generated by insertion and deletion of uridylates in locations dictated by guide RNAs, appears confined to kinetoplastids. The nature of guide RNA and edited mRNA populations has been cursorily explored in a surprisingly extensive number of species over the years, although complete sets of fully edited mRNAs for most kinetoplast genomes are largely missing...
June 11, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29869837/polya-tracks-polybasic-peptides-poly-translational-hurdles
#9
REVIEW
Laura L Arthur, Sergej Djuranovic
The abundance of messenger RNA (mRNA) is one of the major determinants of protein synthesis. As such, factors that influence mRNA stability often contribute to gene regulation. Polyadenylation of the 3' end of mRNA transcripts, the poly(A) tail, has long been recognized as one of these regulatory elements given its influence on translation efficiency and mRNA stability. Unwanted translation of the poly(A) tail signals to the cell an aberrant polyadenylation event or the lack of stop codons, which makes this sequence an important element in translation fidelity and mRNA surveillance response...
June 5, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29869836/ataxin-2-a-versatile-posttranscriptional-regulator-and-its-implication-in-neural-function
#10
REVIEW
Jongbo Lee, Minjong Kim, Taichi Q Itoh, Chunghun Lim
Ataxin-2 (ATXN2) is a eukaryotic RNA-binding protein that is conserved from yeast to human. Genetic expansion of a poly-glutamine tract in human ATXN2 has been implicated in several neurodegenerative diseases, likely acting through gain-of-function effects. Emerging evidence, however, suggests that ATXN2 plays more direct roles in neural function via specific molecular and cellular pathways. ATXN2 and its associated protein complex control distinct steps in posttranscriptional gene expression, including poly-A tailing, RNA stabilization, microRNA-dependent gene silencing, and translational activation...
June 5, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29851258/the-evolution-of-posttranscriptional-regulation
#11
REVIEW
Bernhard Schaefke, Wei Sun, Yi-Sheng Li, Liang Fang, Wei Chen
"DNA makes RNA makes protein." After transcription, mRNAs undergo a series of intertwining processes to be finally translated into functional proteins. The "posttranscriptional" regulation (PTR) provides cells an extended option to fine-tune their proteomes. To meet the demands of complex organism development and the appropriate response to environmental stimuli, every step in these processes needs to be finely regulated. Moreover, changes in these regulatory processes are important driving forces underlying the evolution of phenotypic differences across different species...
May 31, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29790280/cas9-versus-cas12a-cpf1-structure-function-comparisons-and-implications-for-genome-editing
#12
REVIEW
Daan C Swarts, Martin Jinek
Cas9 and Cas12a are multidomain CRISPR-associated nucleases that can be programmed with a guide RNA to bind and cleave complementary DNA targets. The guide RNA sequence can be varied, making these effector enzymes versatile tools for genome editing and gene regulation applications. While Cas9 is currently the best-characterized and most widely used nuclease for such purposes, Cas12a (previously named Cpf1) has recently emerged as an alternative for Cas9. Cas9 and Cas12a have distinct evolutionary origins and exhibit different structural architectures, resulting in distinct molecular mechanisms...
May 22, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29790275/suppressor-of-clathrin-deficiency-scd6-an-emerging-rgg-motif-translation-repressor
#13
REVIEW
Debadrita Roy, Purusharth I Rajyaguru
Translation control plays a key role in variety of cellular processes. Translation initiation factors augment translation, whereas translation repressor proteins inhibit translation. Different repressors act by distinct mechanisms to accomplish the repression process. Although messenger RNAs (mRNAs) can be repressed at various steps of translation, most repressors have been reported to target the initiation step. We focus on one such translation repressor, an Arginine-Glycine-Glycine (RGG)-motif containing protein Scd6...
May 22, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29726113/targeting-rna-in-mammalian-systems-with-small-molecules
#14
REVIEW
Anita Donlic, Amanda E Hargrove
The recognition of RNA functions beyond canonical protein synthesis has challenged the central dogma of molecular biology. Indeed, RNA is now known to directly regulate many important cellular processes, including transcription, splicing, translation, and epigenetic modifications. The misregulation of these processes in disease has led to an appreciation of RNA as a therapeutic target. This potential was first recognized in bacteria and viruses, but discoveries of new RNA classes following the sequencing of the human genome have invigorated exploration of its disease-related functions in mammals...
July 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29693319/alternative-splicing-defects-in-cancer-splicing-regulators-and-their-downstream-targets-guiding-the-way-to-novel-cancer-therapeutics
#15
REVIEW
Laura M Urbanski, Nathan Leclair, Olga Anczuków
Defects in alternative splicing are frequently found in human tumors and result either from mutations in splicing-regulatory elements of specific cancer genes or from changes in the regulatory splicing machinery. RNA splicing regulators have emerged as a new class of oncoproteins and tumor suppressors, and contribute to disease progression by modulating RNA isoforms involved in the hallmark cancer pathways. Thus, dysregulation of alternative RNA splicing is fundamental to cancer and provides a potentially rich source of novel therapeutic targets...
July 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29655315/a-360%C3%A2-view-of-circular-rnas-from-biogenesis-to-functions
#16
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...
July 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29633565/hfq-chaperone-brings-speed-dating-to-bacterial-srna
#17
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...
July 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29624880/translation-initiation-by-cap-dependent-ribosome-recruitment-recent-insights-and-open-questions
#18
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...
July 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29582564/genetic-variants-in-mrna-untranslated-regions
#19
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...
July 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29722158/larp1-on-top-of-ribosome-production
#20
REVIEW
Bruno D Fonseca, Roni M Lahr, Christian K Damgaard, Tommy Alain, Andrea J Berman
The ribosome is an essential unit of all living organisms that commands protein synthesis, ultimately fuelling cell growth (accumulation of cell mass) and cell proliferation (increase in cell number). The eukaryotic ribosome consists of 4 ribosomal RNAs (rRNAs) and 80 ribosomal proteins (RPs). Despite its fundamental role in every living organism, our present understanding of how higher eukaryotes produce the various ribosome components is incomplete. Uncovering the mechanisms utilized by human cells to generate functional ribosomes will likely have far-reaching implications in human disease...
May 2, 2018: Wiley Interdisciplinary Reviews. RNA
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