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Wiley Interdisciplinary Reviews. RNA

journal
https://read.qxmd.com/read/30864256/the-tandem-zinc-finger-rna-binding-domain-of-members-of-the-tristetraprolin-protein-family
#1
REVIEW
Wi S Lai, Melissa L Wells, Lalith Perera, Perry J Blackshear
Tristetraprolin (TTP), the prototype member of the protein family of the same name, was originally discovered as the product of a rapidly inducible gene in mouse cells. Development of a knockout (KO) mouse established that absence of the protein led to a severe inflammatory syndrome, due in part to elevated levels of tumor necrosis factor (TNF). TTP was found to bind directly and with high affinity to specific AU-rich sequences in the 3'-untranslated region of the TNF mRNA. This initial binding led to promotion of TNF mRNA decay and inhibition of its translation...
March 12, 2019: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30848101/writing-a-wrong-coupled-rna-polymerase-ii-transcription-and-rna-quality-control
#2
REVIEW
Sarah A Peck, Katlyn D Hughes, Jose F Victorino, Amber L Mosley
Processing and maturation of precursor RNA species is coupled to RNA polymerase II transcription. Co-transcriptional RNA processing helps to ensure efficient and proper capping, splicing, and 3' end processing of different RNA species to help ensure quality control of the transcriptome. Many improperly processed transcripts are not exported from the nucleus, are restricted to the site of transcription, and are in some cases degraded, which helps to limit any possibility of aberrant RNA causing harm to cellular health...
March 7, 2019: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30843375/the-cellular-landscape-of-mid-size-noncoding-rna
#3
REVIEW
Vincent Boivin, Laurence Faucher-Giguère, Michelle Scott, Sherif Abou-Elela
Noncoding RNA plays an important role in all aspects of the cellular life cycle, from the very basic process of protein synthesis to specialized roles in cell development and differentiation. However, many noncoding RNAs remain uncharacterized and the function of most of them remains unknown. Mid-size noncoding RNAs (mncRNAs), which range in length from 50 to 400 nucleotides, have diverse regulatory functions but share many fundamental characteristics. Most mncRNAs are produced from independent promoters although others are produced from the introns of other genes...
March 6, 2019: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30816016/tissue-specific-mechanisms-of-alternative-polyadenylation-testis-brain-and-beyond-2018-update
#4
REVIEW
Clinton C MacDonald
Alternative polyadenylation (APA) is how genes choose different sites for 3' end formation for mRNAs during transcription. APA often occurs in a tissue- or developmental stage-specific manner that can significantly affect gene activity by changing the protein product generated, the stability of the transcript, its localization within the cell, or its translatability. Despite the important regulatory effects that APA has on tissue-specific gene expression, only a few examples have been characterized mechanistically...
February 27, 2019: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30793528/stress-induced-mrnp-granules-form-and-function-of-processing-bodies-and-stress-granules
#5
REVIEW
Anna R Guzikowski, Yang S Chen, Brian M Zid
In response to stress, cells must quickly reprogram gene expression to adapt and survive. This is achieved in part by altering levels of mRNAs and their translation into proteins. Recently, the formation of two stress-induced messenger ribonucleoprotein (mRNP) assemblies named stress granules and processing bodies has been postulated to directly impact gene expression during stress. These assemblies sequester and concentrate specific proteins and RNAs away from the larger cytoplasm during stress, thereby providing a layer of posttranscriptional gene regulation with the potential to directly impact mRNA levels, protein translation, and cell survival...
February 21, 2019: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30788906/computational-approaches-for-circular-rna-analysis
#6
REVIEW
Tobias Jakobi, Christoph Dieterich
Circular RNAs (circRNAs) are a recent addition to the expanding universe of RNA species and originate through back-splicing events from linear primary transcripts. CircRNAs show specific expression profiles with regards to cell type and developmental stage. Importantly, only few circRNAs have been functionally characterized to date. The detection of circRNAs from RNA sequencing data is a complex computational workflow that, depending on tissue and condition typically yields candidate sets of hundreds or thousands of circRNA candidates...
February 20, 2019: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30773852/splicing-and-cancer-challenges-and-opportunities
#7
REVIEW
Patricia P Coltri, Maria G P Dos Santos, Guilherme H G da Silva
Cancer arises from alterations in several metabolic processes affecting proliferation, growth, replication and death of cells. A fundamental challenge in the study of cancer biology is to uncover molecular mechanisms that lead to malignant cellular transformation. Recent genomic analyses revealed that many molecular alterations observed in cancers come from modifications in the splicing process, including mutations in pre-mRNA regulatory sequences, mutations in spliceosome components, and altered ratio of specific splicing regulators...
February 17, 2019: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30761752/mimicry-deception-and-competition-the-life-of-competing-endogenous-rnas
#8
REVIEW
Marc P Grüll, Eric Massé
Since their discovery, small regulatory RNAs (sRNAs) were thought to be regulated exclusively at the transcriptional level. However, accumulating data from recent reports indicate that posttranscriptional signals can also modulate the function and stability of sRNAs. One of these posttranscriptional signals are competing endogenous RNAs (ceRNAs). Commonly called RNA sponges, ceRNAs can effectively sequester sRNAs and prevent them from binding their cognate target messenger RNAs (mRNAs). Subsequently, they prevent sRNA-dependent regulation of translation and stability of mRNA targets...
February 13, 2019: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30729694/rnas-in-the-spliceosome-insight-from-cryoem-structures
#9
REVIEW
Lingdi Zhang, Anne Vielle, Sara Espinosa, Rui Zhao
Pre-mRNA splicing is catalyzed by the spliceosome, a multimegadalton RNA-protein complex. The spliceosome undergoes dramatic compositional and conformational changes through the splicing cycle, forming at least 10 distinct complexes. Recent high-resolution cryoEM structures of various spliceosomal complexes revealed unprecedented details of this large molecular machine. This review highlights insight into the structure and function of the spliceosomal RNA components obtained from these new structures, with a focus on the yeast spliceosome...
February 6, 2019: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30560575/on-the-edge-of-degradation-autophagy-regulation-by-rna-decay
#10
REVIEW
Elizabeth Delorme-Axford, Daniel J Klionsky
Cells must dynamically adapt to altered environmental conditions, particularly during times of stress, to ensure their ability to function effectively and survive. The macroautophagy/autophagy pathway is highly conserved across eukaryotic cells and promotes cell survival during stressful conditions. In general, basal autophagy occurs at a low level to sustain cellular homeostasis and metabolism. However, autophagy is robustly upregulated in response to nutrient deprivation, pathogen infection and increased accumulation of potentially toxic protein aggregates and superfluous organelles...
December 17, 2018: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30548404/structure-and-function-of-rnt1p-an-alternative-to-rnai-for-targeted-rna-degradation
#11
REVIEW
Sherif Abou Elela, Xinhua Ji
The double-stranded RNA-binding protein (dsRBP) family controls RNA editing, stability, and function in all eukaryotes. The central feature of this family is the recognition of a generic RNA duplex using highly conserved double-stranded RNA-binding domain (dsRBD) that recognizes the characteristic distance between the minor grooves created by the RNA helix. Variations on this theme that confer species and functional specificities have been reported but most dsRBPs retain their capacity to bind generic dsRNA...
December 11, 2018: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30506978/the-ddx5-dbp2-subfamily-of-dead-box-rna-helicases
#12
REVIEW
Zheng Xing, Wai Kit Ma, Elizabeth J Tran
The mammalian DEAD-box RNA helicase DDX5, its paralog DDX17, and their orthologs in Saccharomyces cerevisiae and Drosophila melanogaster, namely Dbp2 and Rm62, define a subfamily of DEAD-box proteins. Members from this subfamily share highly conserved protein sequences and cellular functions. They are involved in multiple steps of RNA metabolism including mRNA processing, microRNA processing, ribosome biogenesis, RNA decay, and regulation of long noncoding RNA activities. The DDX5/Dbp2 subfamily is also implicated in transcription regulation, cellular signaling pathways, and energy metabolism...
December 2, 2018: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30485688/the-evolution-of-rna-structural-probing-methods-from-gels-to-next-generation-sequencing
#13
REVIEW
Elodie Mailler, Jean-Christophe Paillart, Roland Marquet, Redmond P Smyth, Valerie Vivet-Boudou
RNA molecules are important players in all domains of life and the study of the relationship between their multiple flexible states and the associated biological roles has increased in recent years. For several decades, chemical and enzymatic structural probing experiments have been used to determine RNA structure. During this time, there has been a steady improvement in probing reagents and experimental methods, and today the structural biologist community has a large range of tools at its disposal to probe the secondary structure of RNAs in vitro and in cells...
November 28, 2018: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30479000/diverse-roles-of-rna-binding-proteins-in-cancer-traits-and-their-implications-in-gastrointestinal-cancers
#14
REVIEW
Kiyoshi Masuda, Yuki Kuwano
Gene expression patterns in cancer cells are strongly influenced by posttranscriptional mechanisms. RNA-binding proteins (RBPs) play key roles in posttranscriptional gene regulation; they can interact with target mRNAs in a sequence- and structure-dependent manner, and determine cellular behavior by manipulating the processing of these mRNAs. Numerous RBPs are aberrantly deregulated in many human cancers and hence, affect the functioning of mRNAs that encode proteins, implicated in carcinogenesis. Here, we summarize the key roles of RBPs in posttranscriptional gene regulation, describe RBPs disrupted in cancer, and lastly focus on RBPs that are responsible for implementing cancer traits in the digestive tract...
November 26, 2018: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30406965/maturation-of-pre-40s-particles-in-yeast-and-humans
#15
REVIEW
Emilie Cerezo, Célia Plisson-Chastang, Anthony K Henras, Simon Lebaron, Pierre-Emmanuel Gleizes, Marie-Françoise O'Donohue, Yves Romeo, Yves Henry
The synthesis of ribosomal subunits in eukaryotes requires the interplay of numerous maturation and assembly factors (AFs) that intervene in the insertion of ribosomal proteins within pre-ribosomal particles, the ribosomal subunit precursors, as well as in pre-ribosomal RNA (rRNA) processing and folding. Here, we review the intricate nuclear and cytoplasmic maturation steps of pre-40S particles, the precursors to the small ribosomal subunits, in both yeast and human cells, with particular emphasis on the timing and mechanisms of AF association with and dissociation from pre-40S particles and the roles of these AFs in the maturation process...
November 8, 2018: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30118183/glycogen-synthase-kinase-3-and-alternative-splicing
#16
REVIEW
Xiaolei Liu, Peter S Klein
Glycogen synthase kinase-3 (GSK-3) is a highly conserved negative regulator of receptor tyrosine kinase, cytokine, and Wnt signaling pathways. Stimulation of these pathways inhibits GSK-3 to modulate diverse downstream effectors that include transcription factors, nutrient sensors, glycogen synthesis, mitochondrial function, circadian rhythm, and cell fate. GSK-3 also regulates alternative splicing in response to T-cell receptor activation, and recent phosphoproteomic studies have revealed that multiple splicing factors and regulators of RNA biosynthesis are phosphorylated in a GSK-3-dependent manner...
November 2018: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30109918/regulation-of-cytoplasmic-rna-stability-lessons-from-drosophila
#17
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...
November 2018: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30101566/dynamic-rna-holo-editosomes-with-subcomplex-variants-insights-into-the-control-of-trypanosome-editing
#18
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...
November 2018: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30091184/unconventional-rna-binding-proteins-step-into-the-virus-host-battlefront
#19
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...
November 2018: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30074293/antisense-and-yet-sensitive-copy-number-control-of-rolling-circle-replicating-plasmids-by-small-rnas
#20
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)...
November 2018: Wiley Interdisciplinary Reviews. RNA
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