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RNA biogenesis

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https://www.readbyqxmd.com/read/28098827/shared-sulfur-mobilization-routes-for-trna-thiolation-and-molybdenum-cofactor-biosynthesis-in-prokaryotes-and-eukaryotes
#1
REVIEW
Silke Leimkühler, Martin Bühning, Lena Beilschmidt
Modifications of transfer RNA (tRNA) have been shown to play critical roles in the biogenesis, metabolism, structural stability and function of RNA molecules, and the specific modifications of nucleobases with sulfur atoms in tRNA are present in pro- and eukaryotes. Here, especially the thiomodifications xm⁵s²U at the wobble position 34 in tRNAs for Lys, Gln and Glu, were suggested to have an important role during the translation process by ensuring accurate deciphering of the genetic code and by stabilization of the tRNA structure...
January 14, 2017: Biomolecules
https://www.readbyqxmd.com/read/28098260/hepatitis-b-virus-x-protein-is-capable-of-down-regulating-protein-level-of-host-antiviral-protein-apobec3g
#2
Ruidong Chen, Xue Zhao, Yongxiang Wang, Youhua Xie, Jing Liu
The apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) family proteins bind RNA and single-stranded DNA, and create C-to-U base modifications through cytidine deaminase activity. APOBEC3G restricts human immunodeficiency virus 1 (HIV-1) infection by creating hypermutations in proviral DNA, while HIV-1-encoded vif protein antagonizes such restriction by targeting APOBEC3G for degradation. APOBEC3G also inhibits hepatitis B virus (HBV): APOBEC3G co-expression inhibits HBV replication and evidences exist indicating APOBEC3G-mediated HBV hypermutations in patients...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28096332/human-nf-%C3%AE%C2%BAb-repressing-factor-acts-as-a-stress-regulated-switch-for-ribosomal-rna-processing-and-nucleolar-homeostasis-surveillance
#3
Marta Coccia, Antonio Rossi, Anna Riccio, Edoardo Trotta, Maria Gabriella Santoro
The nucleolus, a dynamic nuclear compartment long regarded as the cell ribosome factory, is emerging as an important player in the regulation of cell survival and recovery from stress. In larger eukaryotes, the stress-induced transcriptional response is mediated by a family of heat-shock transcription factors. Among these, HSF1, considered the master regulator of stress-induced transcriptional responses, controls the expression of cytoprotective heat shock proteins (HSPs), molecular chaperones/cochaperones constituting a major component of the cell protein quality control machinery essential to circumvent stress-induced degradation and aggregation of misfolded proteins...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28095716/circrnas-a-regulator-of-cellular-stress
#4
Joseph W Fischer, Anthony K L Leung
Circular RNAs (CircRNAs) were first identified as a viroid and later found to also be an endogenous RNA splicing product in eukaryotes. In recent years, a series of RNA-sequencing analyses from a diverse range of eukaryotes have shed new light on these eukaryotic circRNAs, revealing dynamic expression patterns in various developmental stages and physiological conditions. In this review, we focus on circRNAs implicated in stress response pathways and explore potential mechanisms underlying their regulation. To date, circRNAs have been shown to act as scaffolds in the assembly of protein complexes, sequester proteins from native subcellular localization, activate transcription of parental genes, inhibit RNA-protein interactions, and function as regulators of microRNA activity...
January 17, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28095296/diverse-role-of-survival-motor-neuron-protein
#5
REVIEW
Ravindra N Singh, Matthew D Howell, Eric W Ottesen, Natalia N Singh
The multifunctional Survival Motor Neuron (SMN) protein is required for the survival of all organisms of the animal kingdom. SMN impacts various aspects of RNA metabolism through the formation and/or interaction with ribonucleoprotein (RNP) complexes. SMN regulates biogenesis of small nuclear RNPs, small nucleolar RNPs, small Cajal body-associated RNPs, signal recognition particles and telomerase. SMN also plays an important role in DNA repair, transcription, pre-mRNA splicing, histone mRNA processing, translation, selenoprotein synthesis, macromolecular trafficking, stress granule formation, cell signaling and cytoskeleton maintenance...
January 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28089091/characteristics-and-processing-of-pol-iv-dependent-transcripts-in-arabidopsis
#6
Hsuan Yu Kuo, Elise L Jacobsen, Yanping Long, Xinyuan Chen, Jixian Zhai
RNAi is a highly conserved machinery in eukaryotes for transcriptional or post-transcriptional silencing. In plants, RNA-directed DNA Methylation (RdDM) pathway deploys small interfering RNAs (siRNAs) to target DNA methylation. This process is initiated by the plant-specific RNA polymerase IV (Pol IV) to produce RNA precursors that are later processed into siRNAs. Until recently, characterization of Pol IV transcript had been difficult due to its presumed rapid turnover. This review summarizes five recent reports on Pol IV-dependent RNAs that explore the biogenesis and features of Pol IV transcripts, as well as alternative dicer-independent processing of Pol IV products...
December 30, 2016: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28087943/rna-interference-in-fungi-retention-and-loss
#7
Francisco E Nicolás, Victoriano Garre
RNA interference (RNAi) is a mechanism conserved in eukaryotes, including fungi, that represses gene expression by means of small noncoding RNAs (sRNAs) of about 20 to 30 nucleotides. Its discovery is one of the most important scientific breakthroughs of the past 20 years, and it has revolutionized our perception of the functioning of the cell. Initially described and characterized in Neurospora crassa, the RNAi is widespread in fungi, suggesting that it plays important functions in the fungal kingdom. Several RNAi-related mechanisms for maintenance of genome integrity, particularly protection against exogenous nucleic acids such as mobile elements, have been described in several fungi, suggesting that this is the main function of RNAi in the fungal kingdom...
December 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/28087842/novel-determinants-of-mammalian-primary-microrna-processing-revealed-by-systematic-evaluation-of-hairpin-containing-transcripts-and-human-genetic-variation
#8
Christine Anne Roden, Jonathan Gaillard, Shaveta Kanoria, William Rennie, Syndi Barish, Jijun Cheng, Wen Pan, Jun Liu, Chris Cotsapas, Ye Ding, Jun Lu
Mature microRNAs (miRNAs) are processed from hairpin-containing primary miRNAs (pri-miRNAs). However, rules that distinguish pri-miRNAs from other hairpin-containing transcripts in the genome are incompletely understood. By developing a computational pipeline to systematically evaluate 30 structural and sequence features of mammalian RNA hairpins, we report several new rules that are preferentially utilized in miRNA hairpins and govern efficient pri-miRNA processing. We propose that a hairpin stem length of 36+/-3nt is optimal for pri-miRNA processing...
January 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28076796/ribosomal-proteins-rpl22-and-rpl22l1-control-morphogenesis-by-regulating-pre-mrna-splicing
#9
Yong Zhang, Monique N O'Leary, Suraj Peri, Minshi Wang, Jikun Zha, Simon Melov, Dietmar J Kappes, Qing Feng, Jennifer Rhodes, Paul S Amieux, David R Morris, Brian K Kennedy, David L Wiest
Most ribosomal proteins (RP) are regarded as essential, static components that contribute only to ribosome biogenesis and protein synthesis. However, emerging evidence suggests that RNA-binding RP are dynamic and can influence cellular processes by performing "extraribosomal," regulatory functions involving binding to select critical target mRNAs. We report here that the RP, Rpl22, and its highly homologous paralog Rpl22-Like1 (Rpl22l1 or Like1) play critical, extraribosomal roles in embryogenesis. Indeed, they antagonistically control morphogenesis through developmentally regulated localization to the nucleus, where they modulate splicing of the pre-mRNA encoding smad2, an essential transcriptional effector of Nodal/TGF-β signaling...
January 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/28073919/trub1-is-the-predominant-pseudouridine-synthase-acting-on-mammalian-mrna-via-a-predictable-and-conserved-code
#10
Modi Safra, Ronit Nir, Daneyal Farouq, Schraga Schwartz
Following synthesis, RNA can be modified with over 100 chemically distinct modifications, which can potentially regulate RNA expression post-transcriptionally. Pseudouridine (Ψ) was recently established to be widespread and dynamically regulated on yeast mRNA, but less is known about Ψ presence, regulation and biogenesis in mammalian mRNA. Here, we sought to characterize the Ψ landscape on mammalian mRNA, to identify the main Ψ-synthases (PUSs) catalyzing Ψ formation, and to understand the factors governing their specificity towards selected targets...
January 10, 2017: Genome Research
https://www.readbyqxmd.com/read/28069438/ribosomal-protein-pno40-mediates-nucleolar-sequestration-of-sr-family-splicing-factors-and-its-overexpression-impairs-mrna-metabolism
#11
Yen-Ming Lin, Pao-Hsien Chu, Yun-Zhu Li, Pin Ouyang
The nucleolus acts as a key stress sensor and responds to changes in cellular growth rate and metabolic activity. In addition to its major role as the site of ribosome biogenesis, high-throughput proteomic analyses of purified nucleoli have highlighted the multi-functional nature of these organelles, and several SR family splicing factors, including SRSF1 and SRSF2, have been detected in human nucleolar proteome analysis. Here we provide evidence that pNO40, a 60s ribosomal protein associated with nucleoli, acts as a mediator for recruitment of SR family splicing factors into nucleoli...
January 6, 2017: Cellular Signalling
https://www.readbyqxmd.com/read/28069422/identification-of-ecdysteroid-receptor-mediated-signaling-pathways-in-the-hepatopancreas-of-the-red-swamp-crayfish-procambarus-clarkii
#12
Baojian Zhu, Lin Tang, Yingying Yu, Huimin Yu, Lei Wang, Cen Qian, Guoqing Wei, Chaoliang Liu
The hepatopancreas of crustaceans plays an important role in lipid and carbohydrate metabolism, digestion of food, and biogenesis. In this study, the hepatopancreas transcriptome from the red crayfish Procambarus clarkii was characterized for the first time using high-throughput sequencing, producing approximately 41.4 million reads were obtained. After de novo assembly, 57,363 unigenes with an average length of 725bp were identified, Gene Ontology analysis categorized 22,580 as being involved in biological processes, among which metabolic process and cellular process groups were the most highly enriched...
January 6, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28062837/principles-of-60s-ribosomal-subunit-assembly-emerging-from-recent-studies-in-yeast
#13
REVIEW
Salini Konikkat, John L Woolford
Ribosome biogenesis requires the intertwined processes of folding, modification, and processing of ribosomal RNA, together with binding of ribosomal proteins. In eukaryotic cells, ribosome assembly begins in the nucleolus, continues in the nucleoplasm, and is not completed until after nascent particles are exported to the cytoplasm. The efficiency and fidelity of ribosome biogenesis are facilitated by >200 assembly factors and ∼76 different small nucleolar RNAs. The pathway is driven forward by numerous remodeling events to rearrange the ribonucleoprotein architecture of pre-ribosomes...
January 15, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28062495/therapeutic-targeting-of-rna-polymerase-i-with-the-small-molecule-cx-5461-for-prevention-of-arterial-injury-induced-neointimal-hyperplasia
#14
Qing Ye, Shu Pang, Wenjing Zhang, Xiaotong Guo, Jianli Wang, Yongtao Zhang, Yang Liu, Xiao Wu, Fan Jiang
OBJECTIVE: RNA polymerase I (Pol I)-dependent rRNA synthesis is a determinant factor in ribosome biogenesis and thus cell proliferation. The importance of dysregulated Pol I activity in cardiovascular disease, however, has not been recognized. Here, we tested the hypothesis that specific inhibition of Pol I might prevent arterial injury-induced neointimal hyperplasia. APPROACH AND RESULTS: CX-5461 is a novel selective Pol I inhibitor. Using this tool, we demonstrated that local inhibition of Pol I blocked balloon injury-induced neointima formation in rat carotid arteries in vivo...
January 5, 2017: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/28061332/in%C3%A2-vivo-cleavage-map-illuminates-the-central-role-of-rnase-e-in-coding-and-non-coding-rna-pathways
#15
Yanjie Chao, Lei Li, Dylan Girodat, Konrad U Förstner, Nelly Said, Colin Corcoran, Michał Śmiga, Kai Papenfort, Richard Reinhardt, Hans-Joachim Wieden, Ben F Luisi, Jörg Vogel
Understanding RNA processing and turnover requires knowledge of cleavages by major endoribonucleases within a living cell. We have employed TIER-seq (transiently inactivating an endoribonuclease followed by RNA-seq) to profile cleavage products of the essential endoribonuclease RNase E in Salmonella enterica. A dominating cleavage signature is the location of a uridine two nucleotides downstream in a single-stranded segment, which we rationalize structurally as a key recognition determinant that may favor RNase E catalysis...
January 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28060464/rna-polymerase-ii-components-and-rrn7-form-a-pre-initiation-complex-on-the-homold-box-to-promote-ribosomal-protein-gene-expression-in-schizosaccharomyces-pombe
#16
Matías Montes, Sandra Moreira-Ramos, Diego A Rojas, Fabiola Urbina, Norbert F Käufer, Edio Maldonado
In Schizosaccharomyces pombe, ribosomal protein gene (RPG) promoters contain a TATA box analog, the HomolD box, which is bound by the Rrn7 protein. Despite the importance of ribosome biogenesis for cell survival, the mechanisms underlying RPG transcription remain unknown. In this study, we found that components of the RNA polymerase II (RNAPII) system, consisting of the initiation or general transcription factors (GTFs) TFIIA, IIB, IIE, TBP and the RNAPII holoenzyme, interacted directly with Rrn7 in vitro and were able to form a pre-initiation complex (PIC) on the HomolD box...
January 6, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28054357/linking-amyotrophic-lateral-sclerosis-and-spinal-muscular-atrophy-through-rna-transcriptome-homeostasis-a-genomics-perspective
#17
REVIEW
Margarida Gama-Carvalho, Marina L Garcia-Vaquero, Francisco R Pinto, Florence Besse, Joachim Weis, Aaron Voigt, Jörg B Schulz, Javier De Las Rivas
In this review we present our most recent understanding of key biomolecular processes that underlie two motor neuron degenerative disorders, Amyotrophic Lateral Sclerosis (ALS) and Spinal Muscular Atrophy (SMA). We focus on the role of four multifunctional proteins involved in RNA metabolism (TDP-43, FUS, SMN and Senataxin) that play a causal role in these diseases. Recent results have led to a novel scenario of intricate connections between these four proteins, bringing transcriptome homeostasis into the spotlight as a common theme in motor neuron degeneration...
January 5, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28053119/short-intron-derived-ncrnas
#18
Florent Hubé, Damien Ulveling, Alain Sureau, Sabrina Forveille, Claire Francastel
Introns represent almost half of the human genome, although they are eliminated from transcripts through RNA splicing. Yet, different classes of non-canonical miRNAs have been proposed to originate directly from intron splicing. Here, we considered the alternative splicing of introns as an interesting source of miRNAs, compatible with a developmental switch. We report computational prediction of new Short Intron-Derived ncRNAs (SID), defined as precursors of smaller ncRNAs like miRNAs and snoRNAs produced directly by splicing, and tested their dependence on each key factor in canonical or alternative miRNAs biogenesis (Drosha, DGCR8, DBR1, snRNP70, U2AF65, PRP8, Dicer, Ago2)...
January 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28053100/heat-shock-protein-90-ensures-efficient-mumps-virus-replication-by-assisting-with-viral-polymerase-complex-formation
#19
Hiroshi Katoh, Toru Kubota, Yuichiro Nakatsu, Maino Tahara, Minoru Kidokoro, Makoto Takeda
: Paramyxoviral RNAs are synthesized by a viral RNA-dependent RNA polymerase (RdRp) consisting of the large (L) protein and its cofactor phosphoprotein (P protein). The L protein is a multifunctional protein that catalyzes RNA synthesis, mRNA capping and mRNA polyadenylation. Growing evidence shows that the stability of several paramyxovirus L proteins is regulated by heat shock protein 90 (Hsp90). In this study, we demonstrated that Hsp90 activity was important for mumps virus (MuV) replication...
January 4, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28052353/temporal-and-spatial-regulation-of-mrna-export-single-particle-rna-imaging-provides-new-tools-and-insights
#20
Stephanie Heinrich, Carina Patrizia Derrer, Azra Lari, Karsten Weis, Ben Montpetit
The transport of messenger RNAs (mRNAs) from the nucleus to cytoplasm is an essential step in the gene expression program of all eukaryotes. Recent technological advances in the areas of RNA-labeling, microscopy, and sequencing are leading to novel insights about mRNA biogenesis and export. This includes quantitative single molecule imaging (SMI) of RNA molecules in live cells, which is providing knowledge of the spatial and temporal dynamics of the export process. As this information becomes available, it leads to new questions, the reinterpretation of previous findings, and revised models of mRNA export...
January 4, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
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