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https://www.readbyqxmd.com/read/28213527/advancing-viral-rna-structure-prediction-measuring-the-thermodynamics-of-pyrimidine-rich-internal-loops
#1
Andy Phan, Katherine Mailey, Jessica Sakai, Xiaobo Gu, Susan J Schroeder
Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased towards small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with more than 6 nucleotides that occur frequently in viral RNA...
February 17, 2017: RNA
https://www.readbyqxmd.com/read/28209633/gene-expression-control-by-bacillus-anthracis-purine-riboswitches
#2
Marion Kirchner, Sabine Schneider
In all kingdoms of life, cellular replication relies on the presence of nucleosides and nucleotides, the building blocks of nucleic acids and the main source of energy. In bacteria, the availability of metabolites sometimes directly regulates the expression of enzymes and proteins involved in purine salvage, biosynthesis and uptake through riboswitches. Riboswitches are located in bacterial mRNAs and can control gene expression by conformational changes in response to ligand binding. We have established an inverse reporter gene system in Bacillus subtilis that allows us to monitor riboswitch-controlled gene expression...
February 16, 2017: RNA
https://www.readbyqxmd.com/read/28209632/high-resolution-profiling-of-nmd-targets-in-yeast-reveals-translational-fidelity-as-a-basis-for-substrate-selection
#3
Alper Celik, Richard Baker, Feng He, Allan Jacobson
Nonsense-mediated mRNA decay (NMD) plays an important role in eukaryotic gene expression yet the scope and the defining features of NMD-targeted transcripts remain elusive. To address these issues, we re-evaluated the genome-wide expression of annotated transcripts in yeast cells harboring deletions of the UPF1, UPF2, or UPF3 genes. Our new RNA-Seq analyses confirm previous results of microarray studies, but also uncover hundreds of new NMD-regulated transcripts that had escaped previous detection, including many intron-containing pre-mRNAs and several non-coding RNAs...
February 16, 2017: RNA
https://www.readbyqxmd.com/read/28202710/practical-data-handling-pipeline-improves-performance-of-qpcr-based-circulating-mirna-measurements
#4
Maurice W J de Ronde, Jan M Ruijter, David Lanfear, Antoni Bayes-Genis, Maayke Kok, Esther Creemers, Yigal M Pinto, Sara-Joan Pinto-Sietsma
BACKGROUND: Since numerous miRNAs have been shown to be present in the circulation, these so-called circulating miRNAs have emerged as potential biomarkers for disease. However, results of qPCR studies on circulating miRNA biomarkers vary greatly and many experiments cannot be reproduced. Missing data in qPCR experiments often occur due to off-target amplification, non-analyzable qPCR curves and discordance between replicates. The low concentration of most miRNAs leads to most, but not all missing data...
February 15, 2017: RNA
https://www.readbyqxmd.com/read/28202709/understanding-in-line-probing-experiments-by-modeling-cleavage-of-non-reactive-rna-nucleotides
#5
Vojtech Mlynsky, Giovanni Bussi
Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural datasets for a variety of RNAs and are used to characterize conformational changes in riboswitches. However, the structural determinants that lead to differential reactivities in unpaired nucleotides have not been investigated yet. In this work we used a combination of theoretical approaches, i...
February 15, 2017: RNA
https://www.readbyqxmd.com/read/28193673/structure-of-the-escherichia-coli-proq-rna-chaperone-protein
#6
Grecia Gonzalez, Steven Hardwick, Sarah L Maslen, J Mark Skehel, Erik Holmqvist, Jörg Vogel, Alex Bateman, Ben Luisi, R William Broadhurst
The protein ProQ has recently been identified as a global RNA chaperone in Salmonella, and a similar role is anticipated for its numerous homologues in divergent bacterial species. We report the solution structure of Escherichia coli ProQ, revealing an N-terminal FinO-like domain, a C-terminal domain that unexpectedly has a Tudor-domain fold commonly found in eukaryotes, and an elongated bridging intra-domain linker that is flexible but nonetheless incompressible. Structure based sequence analysis suggests that the Tudor domain was acquired through horizontal gene transfer and gene fusion to the ancestral FinO-like domain...
February 13, 2017: RNA
https://www.readbyqxmd.com/read/28193672/translation-of-poly-a-tails-leads-to-precise-mrna-cleavage
#7
Nicholas R Guydosh, Rachel Green
Translation of poly(A) tails leads to mRNA cleavage but the mechanism and global pervasiveness of this "nonstop/no-go" decay process is not understood. Here we performed ribosome profiling (in a yeast strain lacking exosome function) of short 15-18 nt mRNA footprints to identify ribosomes stalled at 3' ends of mRNA decay intermediates. In this background, we found mRNA cleavage extending hundreds of nucleotides upstream of ribosome stalling in poly(A) and predominantly in one reading frame. These observations suggest that decay-triggering endonucleolytic cleavage is closely associated with the ribosome...
February 13, 2017: RNA
https://www.readbyqxmd.com/read/28159804/lariat-capping-as-a-tool-to-study-5-cap-functions-of-individual-yeast-mrna-species-in-vivo
#8
Nicolai Krogh, Max Pietschmann, Manfred Schmid, Torben Heick Jensen, Henrik Nielsen
The 5' cap structure of eukaryotic mRNA is critical for its processing, transport, translation and stability. The many functions of the cap and the fact that most, if not all, mRNA carries the same type of cap makes it difficult to analyse cap function in vivo at individual steps of gene expression. We have used the lariat capping ribozyme (LCrz) from the myxomycete Didymium to replace the mRNA m7G cap of a single reporter mRNA species with a tiny lariat in which the first and the third nucleotide are joined by a 2', 5' phosphodiester bond...
February 3, 2017: RNA
https://www.readbyqxmd.com/read/28153948/extremely-fast-and-incredibly-close-co-transcriptional-splicing-in-budding-yeast
#9
Edward W J Wallace, Jean D Beggs
RNA splicing, an essential part of eukaryotic pre-messenger RNA processing, can be simultaneous with transcription by RNA polymerase II. Here, we compare and review independent next-generation sequencing methods that jointly quantify transcription and splicing in budding yeast. For many yeast transcripts, splicing is fast, taking place within seconds of intron transcription, while polymerase is within a few dozens of nucleotides of the 3' splice site. Ribosomal protein transcripts are spliced particularly fast and co-transcriptionally...
February 2, 2017: RNA
https://www.readbyqxmd.com/read/28148825/unravelling-mg2-rna-binding-with-atomistic-molecular-dynamics
#10
Richard A Cunha, Giovanni Bussi
Interaction with divalent cations is of paramount importance for RNA structural stability and function. We here report a detailed molecular dynamics study of all the possible binding sites for Mg(2+) on a RNA duplex, including both direct (inner sphere) and indirect (outer sphere) binding. In order to tackle sampling issues, we develop a modified version of bias-exchange metadynamics which allows us to simultaneously compute affinities with previously unreported statistical accuracy. Results correctly reproduce trends observed in crystallographic databases...
February 1, 2017: RNA
https://www.readbyqxmd.com/read/28148824/biochemical-and-genetic-functional-dissection-of-the-p38-viral-suppressor-of-rna-silencing
#11
Taichiro Iki, Marie-Aude Tschopp, Olivier Voinnet
Phytoviruses encode viral suppressors of RNA-silencing (VSRs) to counteract the plant antiviral silencing response, which relies on virus-derived small interfering (si)RNAs processed by Dicer RNaseIII enzymes and subsequently loaded into ARGONAUTE (AGO) effector proteins. Here, a tobacco cell-free system was engineered to recapitulate the key steps of antiviral RNA-silencing and, in particular, the most upstream double-stranded (ds)RNA processing reaction, not kinetically investigated thus far in the context of plant VSR studies...
February 1, 2017: RNA
https://www.readbyqxmd.com/read/28143889/the-structure-of-an-e-coli-trnafmet-a1-u72-variant-shows-an-unusual-conformation-of-the-a1-u72-base-pair
#12
Auriane Monestier, Alexey Aleksandrov, Pierre-Damien Coureux, Michel Panvert, Yves Mechulam, Emmanuelle Schmitt
Translation initiation in eukaryotes and archaea involves a methionylated initiator tRNA delivered to the ribosome in a ternary complex with e/aIF2 and GTP. Eukaryotic and archaeal initiator tRNAs contain a highly conserved A1-U72 base pair at the top of the acceptor stem. The importance of this base pair to discriminate initiator tRNAs from elongator tRNAs has been established previously using genetics and biochemistry. However, no structural data illustrating how the A1-U72 base pair participates in the accurate selection of the initiator tRNAs by the translation initiation systems are available...
January 31, 2017: RNA
https://www.readbyqxmd.com/read/28138061/pseudouridine-and-n-6-methyladenosine-modifications-weaken-puf-protein-rna-interactions
#13
Pavanapuresan P Vaidyanathan, Ishraq AlSadhan, Dawn K Merriman, Hashim Al-Hashimi, Daniel Herschlag
RNA modifications are ubiquitous in biology, with over 100 distinct modifications. While the vast majority were identified and characterized on abundant non-coding RNA such as tRNA and rRNA, the advent of sensitive sequencing-based approaches has led to the discovery of extensive and regulated modification of eukaryotic messenger RNAs as well. The two most abundant mRNA modifications -pseudouridine (Ψ) and N-6 methyladenosine (m6A)- affect diverse cellular processes including mRNA splicing, localization, translation, and decay and modulate RNA structure...
January 30, 2017: RNA
https://www.readbyqxmd.com/read/28138060/rna-puzzles-round-iii-3d-rna-structure-prediction-of-five-riboswitches-and-one-ribozyme
#14
Zhichao Miao, Ryszard W Adamiak, Maciej Antczak, Robert T Batey, Alexander J Becka, Marcin Biesiada, Michał J Boniecki, Janusz Bujnicki, Shi-Jie Chen, Clarence Yu Cheng, Fang-Chieh Chou, Adrian R Ferré-D'Amaré, Rhiju Das, Wayne K Dawson, Ding Feng, Nikolay V Dokholyan, Stanisław Dunin-Horkawicz, Caleb Geniesse, Kalli Kappel, Wipapat Kladwang, Andrey Krokhotin, Grzegorz E Łach, François Major, Thomas H Mann, Marcin Magnus, Katarzyna Pachulska-Wieczorek, Dinshaw J Patel, Joseph A Piccirilli, Mariusz Popenda, Katarzyna J Purzycka, Aiming Ren, Greggory M Rice, John Santalucia, Joanna Sarzynska, Marta Szachniuk, Arpit Tandon, Jeremiah J Trausch, Siqi Tian, Jian Wang, Kevin M Weeks, Benfeard Williams, Yi Xiao, Xiaojun Xu, Dong Zhang, Tomasz Zok, Eric Westhof
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF) and one set describes large conformational changes between ligand-free and ligand-bound states; the Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme...
January 30, 2017: RNA
https://www.readbyqxmd.com/read/28115596/osmium-tetroxide-as-a-probe-of-rna-structure
#15
Jing Zhang, Danbin Li, Jun Zhang, Dongrong Chen, Alastair I H Murchie
Structured RNAs have a central role in cellular function. The capability of structured RNAs to adopt fixed architectural structures or undergo dynamic conformational changes contributes to their diverse role in the regulation of gene expression. Although numerous biophysical and biochemical tools have been developed to study structured RNAs, there is a continuing need for the development of new methods for the investigation of RNA structures, especially methods that allow RNA structure to be studied in solution close to its native cellular conditions...
January 23, 2017: RNA
https://www.readbyqxmd.com/read/28108520/rna-binding-specificity-landscape-of-the-pentatricopeptide-repeat-protein-ppr10
#16
Rafael G Miranda, Margarita Rojas, Michael P Montgomery, Kyle P Gribbin, Alice Barkan
Pentatricopeptide repeat (PPR) proteins comprise a large family of helical repeat proteins that influence gene expression in mitochondria and chloroplasts. PPR tracts can bind RNA via a modular one repeat-one nucleotide mechanism in which the nucleotide is specified by the identities of several amino acids in each repeat. This mode of recognition, the so-called PPR code, offers opportunities for the prediction of native PPR binding sites and the design of proteins to bind specified RNAs. However, a deep understanding of the parameters that dictate the affinity and specificity of PPR-RNA interactions is necessary to realize these goals...
January 20, 2017: RNA
https://www.readbyqxmd.com/read/28096519/the-nuclear-poly-a-binding-protein-of-mammals-but-not-of-fission-yeast-participates-in-mrna-polyadenylation
#17
Uwe Kühn, Juliane Buschmann, Elmar Wahle
The nuclear poly(A) binding protein (PABPN1) has been suggested, on the basis of biochemical evidence, to play a role in mRNA polyadenylation by strongly increasing the processivity of poly(A) polymerase. While experiments in metazoans have tended to support such a role, the results were not unequivocal, and genetic data show that the S. pombe orthologue of PABPN1, Pab2, is not involved in mRNA polyadenylation. The specific model that PABPN1 increases the rate of poly(A) tail elongation has never been examined in vivo...
January 17, 2017: RNA
https://www.readbyqxmd.com/read/28096518/structural-basis-for-guanidine-sensing-by-the-ykkc-family-of-riboswitches
#18
Robert A Battaglia, Ian R Price, Ailong Ke
Regulation of gene expression by cis-encoded riboswitches is a prevalent theme in bacteria. Of the hundreds of riboswitch families identified, the majority of them remain as orphans, without a clear ligand assignment. The ykkC orphan family was recently characterized as guanidine-sensing riboswitches. Herein we present a 2.04 Å crystal structure of the guanidine-bound ykkC riboswitch from Dickeya dadantii. The riboswitch folds into a boot-shaped structure, with a co-axially stacked P1/P2 stem forming the boot, and a 3'-P3 stem-loop forming the heel...
January 17, 2017: RNA
https://www.readbyqxmd.com/read/28096517/the-nucleoside-analog-clitocine-is-a-potent-and-efficacious-readthrough-agent
#19
Westley J Friesen, Christopher R Trotta, Yuki Tomizawa, Jin Zhuo, Briana Johnson, Jairo Sierra, Bijoyita Roy, Marla Weetall, Jean Hedrick, Josephine Sheedy, James Takasugi, Young-Choon Moon, Suresh Babu, Ramil Baiazitov, John D Leszyk, Thomas W Davis, Stuart W Peltz, Ellen M Welch
Nonsense mutations resulting in a premature stop codon in an open reading frame occur in critical tumor suppressor genes in a large number of the most common forms of cancers and are known to cause or contribute to the progression of disease. Low molecular weight compounds that induce readthrough of nonsense mutations offer a new means of treating patients with genetic disorders or cancers resulting from nonsense mutations. We have identified the nucleoside analog clitocine as a potent and efficacious suppressor of nonsense mutations...
January 17, 2017: RNA
https://www.readbyqxmd.com/read/28069890/apobec1-complementation-factor-a1cf-is-not-required-for-c-to-u-rna-editing-in-vivo
#20
Elizabeth M Snyder, Christopher McCarty, Adrienne Mehalow, Karen Svenson, Stephen Murray, Ron Korstanje, Robert E Braun
Editing of the human and murine ApoB mRNA by APOBEC1, the catalytic enzyme of the protein complex that catalyzes C-to-U RNA editing, creates an internal stop codon within the APOB coding sequence, generating two protein isoforms. It has been long held that APOBEC1-mediated editing activity is dependent on the RNA binding protein A1CF. The importance of A1CF in adult tissues has been unclear as a previously reported null allele displays embryonic lethality. This work aimed to address the function of A1CF in adult mouse tissues using a conditional A1cf allele...
January 9, 2017: RNA
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