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Miguel A Sanz, Esther Gonzalez-Almela, Manuel Garcia Moreno, Ana I Marina, Luis Carrasco
Non-canonical translation, and particularly initiation on non-AUG codons, are frequently used by viral and cellular mRNAs during virus infection and disease, but these are generally poorly understood processes. The Sindbis virus (SINV) subgenomic mRNA (sgRNA) constitutes a unique model system to analyze the translation of a capped viral mRNA without the participation of several initiation factors. Accordingly, this messenger can direct protein synthesis following a scanning mechanism in the absence of active eukaryotic translation initiation factor eIF2, eIF4G and eIF4A...
January 18, 2019: RNA
Yoon Ki Kim, Lynne E Maquat
Nonsense-mediated mRNA decay (NMD), which is arguably the best-characterized translation-dependent regulatory pathway in mammals, selectively degrades mRNAs as a means of post-transcriptional gene control. Control can be for the purpose of ensuring the quality of gene expression. Alternatively, control can facilitate the adaptation of cells to changes in their environment. Key to NMD, no matter what its purpose, is the ATP-dependent RNA helicase upstream frameshift 1 (UPF1), without which NMD fails to occur...
January 17, 2019: RNA
Zeljka Trepotec, Johannes Geiger, Christian Plank, Manish Kumar Aneja, Carsten Rudolph
Extensive research in the past decade has brought mRNA closer to the clinical realization of its therapeutic potential. One common structural feature for all cellular messenger RNAs is a poly(A) tail, which can either be brought in co-transcriptionally via the DNA template (plasmid or PCR based) or added to the mRNA in a post-transcriptional enzymatic process. Plasmids containing poly(A) regions recombine in E.coli, resulting in extensive shortening of the poly(A) tail. Using a segmented poly(A) approach, we could significantly reduce recombination of plasmids in E...
January 15, 2019: RNA
Lin Huang, Jia Wang, Timothy J Wilson, David M J Lilley
We have designed structure-based ligands for the guanidine-II riboswitch that bind with enhanced affinity, exploiting the twin binding sites created by loop-loop interaction. We synthesized diguanidine species, comprising two guanidino groups covalently connected by Cn linkers where n = 4 or 5. Calorimetric and fluorescent analysis shows that these ligands bind with a ten-fold higher affinity to the riboswitch compared to guanidine. We determined X-ray crystal structures of the riboswitch bound to the new ligands, showing that the guanidino groups are bound to both nucleobases and backbone within the binding pockets, analogously to guanidine binding...
January 4, 2019: RNA
Dooyoung Lee, Daechan Park, June Hyun Park, Chanseok Shin
The 3' ends of metazoan microRNAs (miRNAs) are initially defined by the RNase III enzymes during maturation, but subsequently experience extensive modifications by several enzymatic activities. For example, terminal nucleotidyltransferases (TNTases) elongate miRNAs by adding one or a few nucleotides to their 3' ends, which occasionally leads to differential regulation of miRNA stability or function. However, the catalytic entities that shorten miRNAs and the molecular consequences of such shortening are less well understood, especially in vertebrates...
December 27, 2018: RNA
Philippe le Mercier, Daniel Kolakofsky
A primary property of paramyxovirus bipartite promoters is to ensure that their RNA genomes are imprinted with a hexamer phase via their association with nucleoproteins, in part because this phase as well the editing sequence itself controls paramyxovirus mRNA editing. The question then arises whether a similar mechanism operates for filoviruses that also contain bipartite promoters that are governed by the "rule of six", even though these genomes need not, nor given Ebola virus biology, always be of hexamer RNA length...
December 26, 2018: RNA
Charles J Daniels, Lien B Lai, Tien-Hao Chen, Venkat Gopalan
RNase P, an essential housekeeping endonuclease needed for 5'-processing of tRNAs, exists in two distinct forms: one with an RNA- and the other with a protein-based active site. The notion that the protein form of RNase P exists only in eukaryotes has been upended by the recent discovery of a protein-only variant in bacteria and archaea. The use of these two divergent scaffolds, shaped by convergent evolution, in all three domains of life inspires questions relating to the ancestral form of RNase P, as well as their origins and function(s) in vivo...
December 21, 2018: RNA
Meghan S Warden, Kai Cai, Gabriel Cornilescu, Jordan E Burke, Komala Ponniah, Samuel E Butcher, Steven M Pascal
A presumed RNA cloverleaf (5'CL), located at the 5'-most end of the non-coding region of the enterovirus genome, is the primary established site for initiation of genomic replication. Stem loop B (SLB) and stem loop D (SLD), the two largest stem loops within the 5'CL, serve as recognition sites for protein interactions that are essential for replication. Here we present the solution structure of rhinovirus serotype 14 5'CL using a combination of nuclear magnetic resonance spectroscopy and small-angle X-ray scattering...
December 21, 2018: RNA
Livia V Bayer, Omar S Omar, Diana P Bratu, Irina E Catrina
Molecular beacons are nucleic acid oligomers labeled with a fluorophore and a quencher that fold in a hairpin-shaped structure, which fluoresce only when bound to their target RNA. They are used for the visualization of endogenous mRNAs in live cells. Here, we report a Python program ( PinMol ) that designs molecular beacons best suited for live cell imaging by using structural information from secondary structures of the target RNA, predicted via energy minimization approaches. PinMol takes into account the accessibility of the targeted regions, as well as the inter- and intramolecular interactions of each selected probe...
December 20, 2018: RNA
Sjors van der Horst, Berend Snel, Johannes Hanson, Sjef Smeekens
Eukaryotic mRNAs contain a 5' leader preceding the main open reading frame (mORF) and, depending on the species, 20-50% of eukaryotic mRNAs harbor an upstream ORF (uORF) in the 5' leader. An unknown fraction of these uORFs encode sequence conserved peptides (conserved peptide uORFs, CPuORFs). Most experimentally validated CPuORFs demonstrated to regulate the translation of the downstream main ORF, usually in a metabolite concentration dependent manner. To this end, comparative genomic approaches have been used to identify novel CPuORFs, by comparing AUG initiating uORF sequences of the Arabidopsis genome or Arabidopsis ESTs...
December 19, 2018: RNA
Hossein Amiri, Harry F Noller
Protein synthesis in all organisms proceeds by stepwise translocation of the ribosome along messenger RNAs (mRNAs), during which the helicase activity of the ribosome unwinds encountered structures in the mRNA. This activity is known to occur near the mRNA tunnel entrance, which is lined by ribosomal proteins uS3, uS4, and uS5. However, the mechanism(s) of mRNA unwinding by the ribosome and the possible role of these proteins in the helicase activity are not well understood. Here, we present a crystal structure of the Escherichia coli ribosome in which single-stranded mRNA is observed beyond the tunnel entrance, interacting in an extended conformation with a positively-charged patch on ribosomal protein uS3 immediately outside the entrance...
December 14, 2018: RNA
Alan L Jiao, Roberto Perales, Neil T Umbreit, Jeffrey R Haswell, Mary E Piper, Brian D Adams, David Pellman, Scott Kennedy, Frank J Slack
The accurate inheritance of genetic material is a basic necessity in all domains of life and an unexpectedly large number of RNA processing factors are required for mitotic progression and genome stability. NRDE2 (nuclear RNAi defective-2) is an evolutionarily conserved protein originally discovered for its role in nuclear RNA interference (RNAi) and heritable gene silencing in Caenorhabditis elegans (C. elegans). The function of the human NRDE2 gene remains poorly understood. Here we show that human NRDE2 is an essential protein required for suppressing intron retention in a subset of pre-mRNAs containing short, GC-rich introns with relatively weak 5' and 3' splice sites...
December 11, 2018: RNA
Thomas J Lopdell, Victoria Hawkins, Christine Couldrey, Kathryn Tiplady, Stephen R Davis, Russell G Snell, Bevin L Harris, Mathew D Littlejohn
Post-transcriptional RNA editing may regulate transcript expression and diversity in cells, with potential impacts on various aspects of physiology and environmental adaptation. A small number of recent genome-wide studies in Drosophila , mouse, and human have shown that RNA editing can be genetically modulated, highlighting loci that quantitatively impact editing of transcripts. The potential gene expression and physiological consequences of these RNA editing quantitative trait loci (edQTL), however, are almost entirely unknown...
December 10, 2018: RNA
Manisha Deogharia, Shaoni Mukhopadhyay, Archi Joardar, Ramesh Gupta
The nearly conserved U54 of tRNA is mostly converted to a version of ribothymidine (T) in Bacteria and eukaryotes and to a version of pseudouridine (Ψ) in Archaea. Conserved U55 is nearly always modified to Ψ55 in all organisms. Orthologs of TrmA and TruB that produce T54 and Ψ55 respectively, in Bacteria and eukaryotes are absent in Archaea. Pus10 produces both Ψ54 and Ψ55 in Archaea. Pus10 orthologs are found in nearly all sequenced archaeal and most eukaryal genomes, but not in yeast and bacteria. This coincides with the presence of Ψ54 in most archaeal tRNAs and some animal tRNAs, but its absence from yeast and bacteria...
December 7, 2018: RNA
Teppei Morita, Hiroji Aiba
The RNA chaperone Hfq plays a critical role in sRNA-mediated gene regulation in enteric bacteria. The major role of Hfq is to stimulate base-pairing between sRNAs and target mRNAs by binding both RNAs through three RNA-binding surfaces. To understand the post-transcriptional network exerted by Hfq and its associated sRNAs, it is important to know how the cellular concentration of Hfq is regulated. While an early study showed that hfq translation is repressed by Hfq, the detailed mechanism and biological significance of the hfq autoregulation remain to be studied...
November 28, 2018: RNA
Katherine A Pillman, Gregory J Goodall, Cameron P Bracken, Michael P Gantier
Most microRNAs (miRNAs) are expressed as a mix of length isoforms (referred to as isomiRs). IsomiR stoichiometry can be differentially impacted upon cell stimulation, as recently evidenced by our group in the context of immune responses induced by type-I interferon (IFN). Here, we revisit published RNA-Seq datasets of human and mouse macrophages stimulated with bacterial products, at the isomiR level. We demonstrate that for several miRNAs, macrophage stimulation induces changes in isomiR stoichiometry. Critically, we find that changes in miRNA expression can be misinterpreted when miRNAs are quantified by RT-qPCR, as primers directed against canonical miRNA sequences may not equally target the different isomiRs that are regulated endogenously...
November 28, 2018: RNA
Jingxuan Liu, June Qin, Anna Borodovsky, Timothy Racie, Adam Castoreno, Mark Schlegel, Martin Maier, Tracy Zimmerman, Kevin Fitzgerald, James Butler, Akin Akinc
BACKGROUND: Hereditary angioedema (HAE) is a genetic disorder mostly caused by mutations in the C1 esterase inhibitor gene (C1INH) that results in poor control of contact pathway activation and excess bradykinin generation. Bradykinin increases vascular permeability and is ultimately responsible for the episodes of swelling characteristic of HAE. OBJECTIVE: We hypothesized that the use of RNA interference (RNAi) to reduce plasma Factor XII (FXII), which initiates the contact pathway signaling cascade, would reduce contact pathway activation and prevent excessive bradykinin generation...
November 21, 2018: RNA
Olke C Uhlenbeck
No abstract text is available yet for this article.
November 14, 2018: RNA
Quan Zou, Pengwei Xing, Leyi Wei, Bin Liu
N6-methyladenosine (m6A) refers to methylation modification of the adenosine nucleotide acid at the nitrogen-6 position. Many conventional computational methods for identifying N6-methyladenosine sites are limited by the small amount of data available. Taking advantage of the thousands of m6A sites detected by high-throughput sequencing, it is now possible to discover the characteristics of m6A sequences using deep learning techniques. To the best of our knowledge, our work is the first attempt to use word embedding and deep neural networks for m6A prediction from mRNA sequences...
November 13, 2018: RNA
Sandro Bottaro, Giovanni Bussi, Giovanni Pinamonti, Sabine Reißer, Wouter Boomsma, Kresten Lindorff-Larsen
RNA molecules are highly dynamic systems characterized by a complex interplay between sequence, structure, dynamics, and function. Molecular simulations can potentially provide powerful insights into the nature of these relationships. The analysis of structures and molecular trajectories of nucleic acids can be non-trivial because it requires processing very high-dimensional data that are not easy to visualize and interpret. Here we introduce Barnaba, a Python library aimed at facilitating the analysis of nucleic acids structures and molecular simulations...
November 12, 2018: RNA
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