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Structure of 3'-PO4/5'-OH RNA ligase RtcB in complex with a 5'-OH oligonucleotide RNA (IF 4.32) Pub Date : 2021-02-22 Ankan Banerjee; Yehuda Goldgur; Stewart Shuman
RtcB enzymes comprise a widely distributed family of manganese- and GTP-dependent RNA repair enzymes that join 2',3'-cyclic phosphate ends to 5'-OH ends via RtcB-(histidinyl-N)–GMP, RNA 3'-phosphate, and RNA3'pp5'G intermediates. RtcB can ligate either 5'-OH RNA or 5'-OH DNA strands in vitro. The nucleic acid contacts of RtcB are uncharted. Here we report a 2.7 Å crystal structure of Pyrococcus horikoshii
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Revisiting tRNA chaperones: New players in an ancient game RNA (IF 4.32) Pub Date : 2021-02-16 Jennifer Porat; Ute Kothe; Mark A. Bayfield
tRNAs undergo an extensive maturation process including post-transcriptional modifications that influence secondary and tertiary interactions. Precursor and mature tRNAs lacking key modifications are often recognized as aberrant and subsequently targeted for decay, illustrating the importance of modifications in promoting structural integrity. tRNAs also rely on tRNA chaperones to promote the folding
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A method for colocalizing lineage tracing reporter and RNAscope signals on skeletal tissue section RNA (IF 4.32) Pub Date : 2021-03-01 Huiliang Yang; Liang Wang; Kathleen Turajane; Lijun Wang; Wentian Yang
Fluorescent reporters have been widely used in modern biology as a powerful tool in cell lineage tracing during development and in studying the pathogenesis of diseases. RNAscope is a recently developed RNA in situ hybridization method with high specificity and sensitivity. Combined application of these two techniques on skeletal tissue is technically challenging and has not been explored; the reporter
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RNA structure probing to characterize RNA–protein interactions on low abundance pre-mRNA in living cells RNA (IF 4.32) Pub Date : 2021-03-01 Jodi L. Bubenik; Melissa Hale; Ona McConnell; Eric T. Wang; Maurice S. Swanson; Robert C. Spitale; J. Andrew Berglund
In vivo RNA structure analysis has become a powerful tool in molecular biology, largely due to the coupling of an increasingly diverse set of chemical approaches with high-throughput sequencing. This has resulted in a transition from single target to transcriptome-wide approaches. However, these methods require sequencing depths that preclude studying low abundance targets, which are not sufficiently
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Ancient microRNA profiles of 14,300-yr-old canid samples confirm taxonomic origin and provide glimpses into tissue-specific gene regulation from the Pleistocene RNA (IF 4.32) Pub Date : 2021-03-01 Bastian Fromm; Marcel Tarbier; Oliver Smith; Emilio Mármol-Sánchez; Love Dalén; M. Tom P. Gilbert; Marc R. Friedländer
DNA sequencing is the current key technology for historic or ancient biological samples and has led to many exciting discoveries in the field of paleogenomics. However, functional insights into tissue identity, cellular composition, or gene regulation cannot be gained from DNA. Recent analyses have shown that, under favorable conditions, RNA can also be sequenced from ancient samples, enabling studies
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Roadblock-qPCR: a simple and inexpensive strategy for targeted measurements of mRNA stability RNA (IF 4.32) Pub Date : 2021-03-01 Maegan J. Watson; Yeonwoo Park; Carson C. Thoreen
The stability of mRNAs is fundamental to determining expression level and dynamics. Nonetheless, current approaches for measuring transcript half-lives (e.g., transcription shutoff) are generally toxic or technically complex. Here we describe an alternative strategy for targeted measurements of endogenous mRNA stability that is simple, inexpensive, and nontoxic. Cells are first metabolically labeled
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CtIP-mediated alternative mRNA splicing fine-tunes the DNA damage response RNA (IF 4.32) Pub Date : 2021-03-01 Rosario Prados-Carvajal; Guillermo Rodríguez-Real; Gabriel Gutierrez-Pozo; Pablo Huertas
In order to survive to the exposure of DNA damaging agents, cells activate a complex response that coordinates the cellular metabolism, cell cycle progression, and DNA repair. Among many other events, recent evidence has described global changes in mRNA splicing in cells treated with genotoxic agents. Here, we explore further this DNA damage-dependent alternative splicing. Indeed, we show that both
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mRNA spindle localization and mitotic translational regulation by CPEB1 and CPEB4 RNA (IF 4.32) Pub Date : 2021-03-01 Rosa Pascual; Carolina Segura-Morales; Manja Omerzu; Nicolás Bellora; Eulàlia Belloc; Chiara Lara Castellazzi; Oscar Reina; Eduardo Eyras; Madelon M. Maurice; Alba Millanes-Romero; Raúl Méndez
Transition through cell cycle phases requires temporal and spatial regulation of gene expression to ensure accurate chromosome duplication and segregation. This regulation involves dynamic reprogramming of gene expression at multiple transcriptional and posttranscriptional levels. In transcriptionally silent oocytes, the CPEB-family of RNA-binding proteins coordinates temporal and spatial translation
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Transcription-dependent enrichment of the yeast FACT complex influences nucleosome dynamics on the RNA polymerase III-transcribed genes RNA (IF 4.32) Pub Date : 2021-03-01 Ashutosh Shukla; Pratibha Bhalla; Pooja Kiran Potdar; Preethi Jampala; Purnima Bhargava
The FACT (FAcilitates Chromatin Transactions) complex influences transcription initiation and enables passage of RNA polymerase (Pol) II through gene body nucleosomes during elongation. In the budding yeast, ∼280 noncoding RNA genes highly transcribed in vivo by Pol III are found in the nucleosome-free regions bordered by positioned nucleosomes. The downstream nucleosome dynamics was found to regulate
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Mitochondrial misreading in skeletal muscle accelerates metabolic aging and confers lipid accumulation and increased inflammation RNA (IF 4.32) Pub Date : 2021-03-01 Dimitri Shcherbakov; Stefan Duscha; Reda Juskeviciene; Lisa M. Restelli; Stephan Frank; Endre Laczko; Erik C. Böttger
We have recently reported on an experimental model of mitochondrial mistranslation conferred by amino acid exchange V338Y in mitochondrial ribosomal protein MrpS5. Here we used a combination of RNA-seq and metabolic profiling of homozygous transgenic Mrps5V338Y/V338Y mice to analyze the changes associated with the V338Y mutation in postmitotic skeletal muscle. Metabolome analysis demonstrated enhanced
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Deflating the RNA Mg2+ bubble: stereochemistry to the rescue! RNA (IF 4.32) Pub Date : 2021-03-01 Pascal Auffinger; Eric Ennifar; Luigi D'Ascenzo
Proper evaluation of the ionic structure of biomolecular systems through X-ray and cryo-EM techniques remains challenging but is essential for advancing our understanding of the underlying structure/activity/solvent relationships. However, numerous studies overestimate the number of Mg2+ in deposited structures due to assignment errors finding their origin in improper consideration of stereochemical
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The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation RNA (IF 4.32) Pub Date : 2021-03-01 Antonin Tidu; Aurélie Janvier; Laure Schaeffer; Piotr Sosnowski; Lauriane Kuhn; Philippe Hammann; Eric Westhof; Gilbert Eriani; Franck Martin
SARS-CoV-2 coronavirus is responsible for the Covid-19 pandemic. In the early phase of infection, the single-strand positive RNA genome is translated into nonstructural proteins (NSP). One of the first proteins produced during viral infection, NSP1, binds to the host ribosome and blocks the mRNA entry channel. This triggers translation inhibition of cellular translation. Despite the presence of NSP1
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Transcriptional profiling of fission yeast RNA polymerase II CTD mutants RNA (IF 4.32) Pub Date : 2021-02-12 Angad Garg; Ana M Sanchez; Beate Schwer; Stewart Shuman
The carboxyl-terminal domain (CTD) of RNA polymerase II (Pol2) consists of tandem repeats of a consensus heptapeptide Y1 S2 P3 T4 S5 P6 S7 . The CTD recruits numerous proteins that drive or regulate gene expression. The trafficking of CTD-interacting proteins is orchestrated by remodeling CTD primary structure via Ser/Thr/Tyr phosphorylation and proline cis-trans isomerization, which collectively inscribe
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U2AF2 binds IL7R exon 6 ectopically and represses its inclusion RNA (IF 4.32) Pub Date : 2021-02-10 Geraldine Schott; Gaddiel Galarza-Muñoz; Noe Trevino; Xiaoting Chen; Matthew Weirauch; Simon G. Gregory; Shelton S. Bradrick; Mariano A. Garcia-Blanco
Interleukin 7 receptor α-chain is crucial for the development and maintenance of T cells and is genetically associated with autoimmune disorders including multiple sclerosis (MS), a demyelinating disease of the CNS. Exon 6 of IL7R encodes for the transmembrane domain of the receptor and is regulated by alternative splicing: inclusion or skipping of IL7R exon 6 results in membrane-bound or soluble IL7R
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Saccharomyces cerevisiae Ecm2 Modulates the Catalytic Steps of pre-mRNA Splicing RNA (IF 4.32) Pub Date : 2021-02-05 Clarisse van der Feltz; Brandon Nikolai; Charles Schneider; Joshua C. Paulson; Xingyang Fu; Aaron A. Hoskins
Genetic, biochemical, and structural studies have elucidated the molecular basis for spliceosome catalysis. Splicing is RNA catalyzed and the essential snRNA and protein factors are well-conserved. However, little is known about how non-essential components of the spliceosome contribute to the reaction and modulate the activities of the fundamental core machinery. Ecm2 is a non-essential yeast splicing
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Activity and substrate specificity of Candida, Aspergillus, and Coccidioides Tpt1: essential tRNA splicing enzymes and potential anti-fungal targets RNA (IF 4.32) Pub Date : 2021-01-28 Swathi Dantuluri; Beate Schwer; Leonora Abdullahu; Masad J. Damha; Stewart Shuman
The enzyme Tpt1 is an essential agent of fungal tRNA splicing that removes an internal RNA 2'-PO4 generated by fungal tRNA ligase. Tpt1 performs a two-step reaction in which: (i) the 2'-PO4 attacks NAD+ to form an RNA-2'-phospho-(ADP-ribose) intermediate; and (ii) transesterification of the ADP-ribose O2'' to the RNA 2'-phosphodiester yields 2'-OH RNA and ADP-ribose-1'',2''-cyclic phosphate. Because
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Optimization of a bacterial three-hybrid assay through in vivo titration of an RNA-DNA adapter-protein RNA (IF 4.32) Pub Date : 2021-01-26 Clara D Wang; Rachel Mansky; Hannah LeBlanc; Chandra M Gravel; Katherine E Berry
Non-coding RNAs regulate gene expression in every domain of life. In bacteria, small RNAs (sRNAs) regulate gene expression in response to stress and are often assisted by RNA-chaperone proteins, such as Hfq. We have recently developed a bacterial three-hybrid (B3H) assay that detects the strong binding interactions of certain E. coli sRNAs with proteins Hfq and ProQ. Despite the promise of this system
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Dynamic association of human Ebp1 with the ribosome RNA (IF 4.32) Pub Date : 2021-01-21 Varun Bhaskar; Jessica Desogus; Alexandra Graff-Meyer; Andreas D. Schenk; Simone Cavadini; Jeffrey A. Chao
Ribosomes are the macromolecular machines at the heart of protein synthesis, however, their function can be modulated by a variety of additional protein factors that directly interact with them. Here, we report the cryo-EM structure of human Ebp1 (p48 isoform) bound to the human 80S ribosome at 3.3 Å resolution. Ebp1 binds in the vicinity of the peptide exit tunnel on the 80S ribosome and this binding
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The emerging structural complexity of G-quadruplex RNAs RNA (IF 4.32) Pub Date : 2021-01-22 Michael Banco; Adrian Ferre-D'Amare
G-quadruplexes (G4s) are four-stranded nucleic acid structures that arise from the stacking of G-quartets, cyclic arrangements of four guanines engaged in Hoogsteen base pairing. Until recently, most RNA G4 structures were thought to conform to a sequence pattern in which guanines stacking within the G4 would also be contiguous in sequence (e.g., four successive guanine trinucleotide tracts separated
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High-resolution structure of eukaryotic Fibrillarin interacting with Nop56 N-terminal domain RNA (IF 4.32) Pub Date : 2021-01-22 Simone Hoefler; Peer Lukat; Wulf Blankenfeldt; Teresa Carlomagno
Ribosomal RNA (rRNA) carries extensive 2’-O-methyl marks at functionally important sites. This simple chemical modification is thought to confer stability, promote RNA folding and contribute to generate a heterogenous ribosome population with a yet-uncharacterized function. 2’-O-methylation occurs both in archaea and eukaryotes and is accomplished by the Box C/D RNP enzyme in an RNA-guided manner.
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Inducible nuclear import by TetR aptamer-controlled 3′ splice site selection RNA (IF 4.32) Pub Date : 2021-02-01 Adam A. Mol; Marc Vogel; Beatrix Suess
Correct cellular localization is essential for the function of many eukaryotic proteins and hence cell physiology. Here, we present a synthetic genetic device that allows the control of nuclear and cytosolic localization based on controlled alternative splicing in human cells. The device is based on the fact that an alternative 3′ splice site is located within a TetR aptamer that in turn is positioned
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An open interface in the pre-80S ribosome coordinated by ribosome assembly factors Tsr1 and Dim1 enables temporal regulation of Fap7 RNA (IF 4.32) Pub Date : 2021-02-01 Jay Rai; Melissa D. Parker; Haina Huang; Stefan Choy; Homa Ghalei; Matthew C. Johnson; Katrin Karbstein; M. Elizabeth Stroupe
During their maturation, nascent 40S subunits enter a translation-like quality control cycle, where they are joined by mature 60S subunits to form 80S-like ribosomes. While these assembly intermediates are essential for maturation and quality control, how they form, and how their structure promotes quality control, remains unknown. To address these questions, we determined the structure of an 80S-like
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Posttranscriptional modifications at the 37th position in the anticodon stem–loop of tRNA: structural insights from MD simulations RNA (IF 4.32) Pub Date : 2021-02-01 Preethi Seelam Prabhakar; Nathania A. Takyi; Stacey D. Wetmore
Transfer RNA (tRNA) is the most diversely modified RNA. Although the strictly conserved purine position 37 in the anticodon stem–loop undergoes modifications that are phylogenetically distributed, we do not yet fully understand the roles of these modifications. Therefore, molecular dynamics simulations are used to provide molecular-level details for how such modifications impact the structure and function
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RNA partitioning into stress granules is based on the summation of multiple interactions RNA (IF 4.32) Pub Date : 2021-02-01 Tyler Matheny; Briana Van Treeck; Thao Ngoc Huynh; Roy Parker
Stress granules (SGs) are stress-induced RNA–protein assemblies formed from a complex transcriptome of untranslating ribonucleoproteins (RNPs). Although RNAs can be either enriched or depleted from SGs, the rules that dictate RNA partitioning into SGs are unknown. We demonstrate that the SG-enriched NORAD RNA is sufficient to enrich a reporter RNA within SGs through the combined effects of multiple
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Cold-inducible RNA binding protein promotes breast cancer cell malignancy by regulating Cystatin C levels RNA (IF 4.32) Pub Date : 2021-02-01 Alberto Indacochea; Santiago Guerrero; Macarena Ureña; Ferrán Araujo; Olga Coll; Matilde E. LLeonart; Fátima Gebauer
Cold-inducible RNA binding protein (CIRBP) is a stress-responsive protein that promotes cancer development and inflammation. Critical to most CIRBP functions is its capacity to bind and posttranscriptionally modulate mRNA. However, a transcriptome-wide analysis of CIRBP mRNA targets in cancer has not yet been performed. Here, we use an ex vivo breast cancer model to identify CIRBP targets and mechanisms
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siRNA potency enhancement via chemical modifications of nucleotide bases at the 5′-end of the siRNA guide strand RNA (IF 4.32) Pub Date : 2021-02-01 Fumikazu Shinohara; Taiji Oashi; Toshimasa Harumoto; Tomoyuki Nishikawa; Yuki Takayama; Hikaru Miyagi; Yuichi Takahashi; Takahiro Nakajima; Takashi Sawada; Yasuo Koda; Asana Makino; Atsuko Sato; Kaori Hamaguchi; Michihiko Suzuki; Junichiro Yamamoto; Yukihide Tomari; Jun-Ichi Saito
Small interfering RNAs (siRNAs) can be utilized not only as functional biological research tools but also as therapeutic agents. For the clinical use of siRNA as drugs, various chemical modifications have been used to improve the activity of siRNA drugs, and further chemical modifications are expected to improve the utility of siRNA therapeutics. As the 5′ nucleobase of the guide strand affects the
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Expansion segments in bacterial and archaeal 5S ribosomal RNAs RNA (IF 4.32) Pub Date : 2021-02-01 Victor G. Stepanov; George E. Fox
The large ribosomal RNAs of eukaryotes frequently contain expansion sequences that add to the size of the rRNAs but do not affect their overall structural layout and are compatible with major ribosomal function as an mRNA translation machine. The expansion of prokaryotic ribosomal RNAs is much less explored. In order to obtain more insight into the structural variability of these conserved molecules
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Mechanistic analysis of the enhanced RNAi activity by 6-mCEPh-purine at the 5′ end of the siRNA guide strand RNA (IF 4.32) Pub Date : 2021-02-01 Vincent Brechin; Fumikazu Shinohara; Jun-ichi Saito; Hervé Seitz; Yukihide Tomari
A key approach for improving siRNA efficacy is chemical modifications. Through an in silico screening of modifications at the 5′-end nucleobase of the guide strand, an adenine-derived compound called 6-(3-(2-carboxyethyl)phenyl)-purine (6-mCEPh-purine) was identified to improve the RNAi activity in cultured human cells and in vivo mouse models. Nevertheless, it remains unclear how this chemical modification
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Insertions of codons encoding basic amino acids in H7 hemagglutinins of influenza A viruses occur by recombination with RNA at hotspots near snoRNA binding sites RNA (IF 4.32) Pub Date : 2021-02-01 Alexander P. Gultyaev; Monique I. Spronken; Mathis Funk; Ron A.M. Fouchier; Mathilde Richard
The presence of multiple basic amino acids in the protease cleavage site of the hemagglutinin (HA) protein is the main molecular determinant of virulence of highly pathogenic avian influenza (HPAI) viruses. Recombination of HA RNA with other RNA molecules of host or virus origin is a dominant mechanism of multibasic cleavage site (MBCS) acquisition for H7 subtype HA. Using alignments of HA RNA sequences
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Neocles B. Leontis (1955 – 2020) RNA (IF 4.32) Pub Date : 2021-01-15 Peter B Moore; Anton Petrov; Eric Westhof; Craig L Zirbel
None
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Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs) RNA (IF 4.32) Pub Date : 2021-01-14 Vairavan Lakshmanan; Sujith T N; Dhiru Bansal; Shivaprasad V Padubidri; Dasaradhi Palakodeti; Srikar Krishna
tRNA-derived fragments (tRFs) have recently gained a lot of scientific interest due to their diverse regulatory roles in several cellular processes. However, their function in dynamic biological process such as development and regeneration remains unexplored. Here, we show that tRFs are dynamically expressed during planarian regeneration suggesting a possible role for these small RNAs in the regulation
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Alternative RNA degradation pathways by the exonuclease Pop2p from Saccharomyces Cerevisiae RNA (IF 4.32) Pub Date : 2021-01-06 Xuan Ye; Armend Axhemi; Eckhard Jankowsky
The 3’ to 5’ exonuclease Pop2p (Caf1p) is part of the CCR4-NOT deadenylation complex that removes poly(A) tails from mRNAs in cells. Pop2p is structurally conserved in eukaryotes, but S. cerevisiae Pop2p harbors non-canonical amino acids in its catalytic center. The enzymatic properties of S. cerevisiae Pop2p are not well defined. Here we characterize the RNA exonuclease activity of recombinant S.
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Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome RNA (IF 4.32) Pub Date : 2021-01-04 Isioma I.I. Enwerem; Nathan D. Elrod; Chung-Te Chang; Ai Lin; Ping Ji; Jennifer A. Bohn; Yevgen Levdansky; Eric J Wagner; Eugene Valkov; Aaron Goldstrohm
Pumilio paralogs, PUM1 and PUM2, are sequence-specific RNA-binding proteins that are essential for vertebrate development and neurological functions. PUM1&2 negatively regulate gene expression by accelerating degradation of specific mRNAs. Here, we determined the repression mechanism and impact of human PUM1&2 on the transcriptome. We identified subunits of the CCR4-NOT (CNOT) deadenylase complex required
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A mark of disease: how mRNA modifications shape genetic and acquired pathologies RNA (IF 4.32) Pub Date : 2020-12-29 Eliana Destefanis; Gülben Avşar; Paula Groza; Antonia Romitelli; Serena Torrini; Pınar Pir; Silvestro Giovanni Conticello; Francesca Aguilo; Erik Dassi
RNA modifications have recently emerged as a widespread and complex facet of gene expression regulation. Counting more than 170 distinct chemical modifications with far-reaching implications for RNA fate, they are collectively referred to as the epitranscriptome. These modifications can occur in all RNA species, including messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs). In mRNAs, the deposition
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Circulating SNORD57 rather than piR-54265 is a promising biomarker for colorectal cancer: common pitfalls in the study of somatic piRNAs in cancer RNA (IF 4.32) Pub Date : 2020-12-29 Juan Pablo Tosar; Maria Rosa Garcia-Silva; Alfonso Cayota
There is increasing interest among cancer researchers in the study of Piwi-interacting RNAs (piRNAs), a group of small RNAs important for maintaining genome stability in the germline. Aberrant expression of piRNAs in cancer could imply an involvement of these regulatory RNAs in neoplastic transformation. On top of that, it could enable early cancer diagnosis based on RNA analysis in liquid biopsies
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Identification of m6A residues at single-nucleotide resolution using eCLIP and an accessible custom analysis pipeline RNA (IF 4.32) Pub Date : 2020-12-29 Justin T. Roberts; Allison M. Porman; Aaron M. Johnson
Methylation at the N6 position of adenosine (m6A) is one of the most abundant RNA modifications found in eukaryotes, however accurate detection of specific m6A nucleotides within transcripts has been historically challenging due to m6A and unmodified adenosine having virtually indistinguishable chemical properties. While previous strategies such as methyl-RNA immunoprecipitation and sequencing (MeRIP-Seq)
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Disease-associated mutations in mitochondrial precursor tRNAs affect binding, m1R9 methylation and tRNA processing by mtRNase P RNA (IF 4.32) Pub Date : 2020-12-30 Agnes Karasik; Catherine A. Wilhelm; Carol A. Fierke; Markos Koutmos
Mitochondrial diseases linked to mutations in mitochondrial (mt) tRNA sequences are common. However, the contributions of these tRNA mutations to the development of diseases is mostly unknown. Mutations may affect interactions with (mt)tRNA maturation enzymes or protein synthesis machinery leading to mitochondrial dysfunction. In human mitochondria, in most cases the first step of tRNA processing is
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Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET RNA (IF 4.32) Pub Date : 2020-12-29 Sunny SCY Jeng; Robert J. Trachman III; Florian Weissenboek; Lynda Troung; Katie Link; Mette B Jepsen; Jay Knutson; Ebbe Andersen; Adrian R Ferré-D'Amaré; Peter J Unrau
To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Förster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor-acceptor pairs. Angle-dependent FRET measurements have proven
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PAR-TERRA is the main contributor to telomeric repeat-containing RNA transcripts in normal and cancer mouse cells RNA (IF 4.32) Pub Date : 2021-01-01 Nikenza Viceconte; Axelle Loriot; Patrícia Lona Abreu; Marion Scheibe; Albert Fradera Sola; Falk Butter; Charles De Smet; Claus M. Azzalin; Nausica Arnoult; Anabelle Decottignies
Telomeric repeat-containing RNA (TERRA) molecules play important roles at telomeres, from heterochromatin regulation to telomerase activity control. In human cells, TERRA is transcribed from subtelomeric promoters located on most chromosome ends and associates with telomeres. The origin of mouse TERRA molecules is, however, unclear, as transcription from the pseudoautosomal PAR locus was recently suggested
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A second riboswitch class for the enzyme cofactor NAD+ RNA (IF 4.32) Pub Date : 2021-01-01 Shanker S.S. Panchapakesan; Lukas Corey; Sarah N. Malkowski; Gadareth Higgs; Ronald R. Breaker
A bacterial noncoding RNA motif almost exclusively associated with pnuC genes was uncovered using comparative sequence analysis. Some PnuC proteins are known to transport nicotinamide riboside (NR), which is a component of the ubiquitous and abundant enzyme cofactor nicotinamide adenine dinucleotide (NAD+). Thus, we speculated that the newly found “pnuC motif” RNAs might function as aptamers for a
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A systematic evaluation of bioinformatics tools for identification of long noncoding RNAs RNA (IF 4.32) Pub Date : 2021-01-01 You Duan; Wanting Zhang; Yingyin Cheng; Mijuan Shi; Xiao-Qin Xia
High-throughput RNA sequencing unveiled the complexity of transcriptome and significantly increased the records of long noncoding RNAs (lncRNAs), which were reported to participate in a variety of biological processes. Identification of lncRNAs is a key step in lncRNA analysis, and a bunch of bioinformatics tools have been developed for this purpose in recent years. While these tools allow us to identify
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Mammalian nuclear TRUB1, mitochondrial TRUB2, and cytoplasmic PUS10 produce conserved pseudouridine 55 in different sets of tRNA RNA (IF 4.32) Pub Date : 2021-01-01 Shaoni Mukhopadhyay; Manisha Deogharia; Ramesh Gupta
Most mammalian cytoplasmic tRNAs contain ribothymidine (T) and pseudouridine (Ψ) at positions 54 and 55, respectively. However, some tRNAs contain Ψ at both positions. Several Ψ54-containing tRNAs function as primers in retroviral DNA synthesis. The Ψ54 of these tRNAs is produced by PUS10, which can also synthesize Ψ55. Two other enzymes, TRUB1 and TRUB2, can also produce Ψ55. By nearest-neighbor analyses
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Mutations in domain IV of elongation factor EF-G confer −1 frameshifting RNA (IF 4.32) Pub Date : 2021-01-01 Dustin Niblett; Charlotte Nelson; Calvin S. Leung; Gillian Rexroad; Jake Cozy; Jie Zhou; Laura Lancaster; Harry F. Noller
A recent crystal structure of a ribosome complex undergoing partial translocation in the absence of elongation factor EF-G showed disruption of codon–anticodon pairing and slippage of the reading frame by −1, directly implicating EF-G in preservation of the translational reading frame. Among mutations identified in a random screen for dominant-lethal mutations of EF-G were a cluster of six that map
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Different tertiary interactions create the same important 3D features in a distinct flavivirus xrRNA RNA (IF 4.32) Pub Date : 2021-01-01 Rachel A. Jones; Anna-Lena Steckelberg; Quentin Vicens; Matthew J. Szucs; Benjamin M. Akiyama; Jeffrey S. Kieft
During infection by a flavivirus (FV), cells accumulate noncoding subgenomic flavivirus RNAs (sfRNAs) that interfere with several antiviral pathways. These sfRNAs are formed by structured RNA elements in the 3′ untranslated region (UTR) of the viral genomic RNA, which block the progression of host cell exoribonucleases that have targeted the viral RNA. Previous work on these exoribonuclease-resistant
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Structural diversity and phylogenetic distribution of valyl tRNA-like structures in viruses RNA (IF 4.32) Pub Date : 2021-01-01 Madeline E. Sherlock; Erik W. Hartwick; Andrea MacFadden; Jeffrey S. Kieft
Viruses commonly use specifically folded RNA elements that interact with both host and viral proteins to perform functions important for diverse viral processes. Examples are found at the 3′ termini of certain positive-sense ssRNA virus genomes where they partially mimic tRNAs, including being aminoacylated by host cell enzymes. Valine-accepting tRNA-like structures (TLSVal) are an example that share
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Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem–loop RNAs and their implications for functional cellular assays RNA (IF 4.32) Pub Date : 2021-01-01 Megan L. Kelly; Chia-Chieh Chu; Honglue Shi; Laura R. Ganser; Hal P. Bogerd; Kelly Huynh; Yuze Hou; Bryan R. Cullen; Hashim M. Al-Hashimi
Identifying small molecules that selectively bind an RNA target while discriminating against all other cellular RNAs is an important challenge in RNA-targeted drug discovery. Much effort has been directed toward identifying drug-like small molecules that minimize electrostatic and stacking interactions that lead to nonspecific binding of aminoglycosides and intercalators to many stem–loop RNAs. Many
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The virtual circular genome model for primordial RNA replication RNA (IF 4.32) Pub Date : 2021-01-01 Lijun Zhou; Dian Ding; Jack W. Szostak
We propose a model for the replication of primordial protocell genomes that builds upon recent advances in the nonenzymatic copying of RNA. We suggest that the original genomes consisted of collections of oligonucleotides beginning and ending at all possible positions on both strands of one or more virtual circular sequences. Replication is driven by feeding with activated monomers and by the activation
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RNA: Reviewers for Volume 26, 2020 RNA (IF 4.32) Pub Date : 2020-12-01
The editors wish to thank the following individuals whose efforts in reviewing papers for RNA in the past year are greatly appreciated.
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Single-pass transcription by T7 RNA polymerase. RNA (IF 4.32) Pub Date : 2020-12-01 Luiz F M Passalacqua,Armine I Dingilian,Andrej Luptak
RNA molecules can be conveniently synthesized in vitro by the T7 RNA polymerase (T7 RNAP). In some experiments, such as cotranscriptional biochemical analyses, continuous synthesis of RNA is not desired. Here, we propose a method for a single-pass transcription that yields a single transcript per template DNA molecule using the T7 RNAP system. We hypothesized that stalling the polymerase downstream
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Chemical shifts-based similarity restraints improve accuracy of RNA structures determined via NMR. RNA (IF 4.32) Pub Date : 2020-12-01 Chad Lawrence,Alexander V Grishaev
Determination of structure of RNA via NMR is complicated in large part by the lack of a precise parameterization linking the observed chemical shifts to the underlying geometric parameters. In contrast to proteins, where numerous high-resolution crystal structures serve as coordinate templates for this mapping, such models are rarely available for smaller oligonucleotides accessible via NMR, or they
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Solution structure and RNA-binding of a minimal ProQ-homolog from Legionella pneumophila (Lpp1663) RNA (IF 4.32) Pub Date : 2020-12-01 Carina Immer; Carolin Hacker; Jens Wöhnert
Small regulatory RNAs (sRNAs) play an important role for posttranscriptional gene regulation in bacteria. sRNAs recognize their target messenger RNAs (mRNAs) by base-pairing, which is often facilitated by interactions with the bacterial RNA-binding proteins Hfq or ProQ. The FinO/ProQ RNA-binding protein domain was first discovered in the bacterial repressor of conjugation, FinO. Since then, the functional
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Termi-Luc: a versatile assay to monitor full-protein release from ribosomes. RNA (IF 4.32) Pub Date : 2020-12-01 Denis Susorov,Shawn Egri,Andrei A Korostelev
Termination of protein biosynthesis is an essential step of gene expression, during which a complete functional protein is released from the ribosome. Premature or inefficient termination results in truncated, nonfunctional, or toxic proteins that may cause disease. Indeed, more than 10% of human genetic diseases are caused by nonsense mutations leading to premature termination. Efficient and sensitive
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Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy RNA (IF 4.32) Pub Date : 2020-12-01 Dushyant Jahagirdar; Vikash Jha; Kaustuv Basu; Josue Gomez-Blanco; Javier Vargas; Joaquin Ortega
It is only after recent advances in cryo-electron microscopy that it is now possible to describe at high-resolution structures of large macromolecules that do not crystalize. Purified 30S subunits interconvert between an “active” and “inactive” conformation. The active conformation was described by crystallography in the early 2000s, but the structure of the inactive form at high resolution remains
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Physiologic RNA targets and refined sequence specificity of coronavirus EndoU RNA (IF 4.32) Pub Date : 2020-12-01 Rachel Ancar; Yize Li; Eveline Kindler; Daphne A. Cooper; Monica Ransom; Volker Thiel; Susan R. Weiss; Jay R. Hesselberth; David J. Barton
Coronavirus EndoU inhibits dsRNA-activated antiviral responses; however, the physiologic RNA substrates of EndoU are unknown. In this study, we used mouse hepatitis virus (MHV)-infected bone marrow–derived macrophage (BMM) and cyclic phosphate cDNA sequencing to identify the RNA targets of EndoU. EndoU targeted viral RNA, cleaving the 3′ side of pyrimidines with a strong preference for U↓A and C↓A
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The origin of the high stability of 3'-terminal uridine tetrads. The contributions of hydrogen bonding, stacking interactions and steric factors evaluated using modified oligonucleotide analogs. RNA (IF 4.32) Pub Date : 2020-12-01 Witold Andralojc,Karol Pasternak,Joanna Sarzynska,Karolina Zielinska,Ryszard Kierzek,Zofia Gdaniec
RNA G-quadruplexes fold almost exclusively into parallel-stranded structures and thus display much less structural diversity than their DNA counterparts. However, also among RNA G-quadruplexes peculiar structural elements can be found which are capable of reshaping the physico-chemical properties of the folded structure. A striking example is provided by a uridine tetrad (U-tetrad) placed on the 3′-terminus
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Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea RNA (IF 4.32) Pub Date : 2020-12-01 Philippe Wolff; Claire Villette; Julie Zumsteg; Dimitri Heintz; Laura Antoine; Béatrice Chane-Woon-Ming; Louis Droogmans; Henri Grosjean; Eric Westhof
To improve and complete our knowledge of archaeal tRNA modification patterns, we have identified and compared the modification pattern (type and location) in tRNAs of three very different archaeal species, Methanococcus maripaludis (a mesophilic methanogen), Pyrococcus furiosus (a hyperthermophile thermococcale), and Sulfolobus acidocaldarius (an acidophilic thermophilic sulfolobale). Most abundant
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NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal-ventral patterning. RNA (IF 4.32) Pub Date : 2020-12-01 Om S Rathore,Rui D Silva,Mariana Ascensao-Ferreira,Ricardo Matos,Celia Carvalho,Bruno Marques,Margarida N Tiago,Pedro Prudencio,Raquel P Andrade,Jean-Yves Roignant,Nuno L Barbosa-Morais,Rui Goncalo Martinho
The NineTeen Complex (NTC), also known as pre-mRNA-processing factor 19 (Prp19) complex, regulates distinct spliceosome conformational changes necessary for splicing. During Drosophila midblastula transition, splicing is particularly sensitive to mutations in NTC-subunit Fandango, which suggests differential requirements of NTC during development. We show that NTC-subunit Salsa, the Drosophila ortholog
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The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2'-O-Me sites. RNA (IF 4.32) Pub Date : 2020-12-01 Sowmya Ramachandran,Nicolai Krogh,Tor Erik Jørgensen,Steinar Daae Johansen,Henrik Nielsen,Igor Babiak
During zebrafish development, an early type of rRNA is gradually replaced by a late type that is substantially different in sequence. We applied RiboMeth-seq to rRNA from developmental stages for profiling of 2′-O-Me, to learn if changes in methylation pattern were a component of the shift. We compiled a catalog of 2′-O-Me sites and cognate box C/D guide RNAs comprising 98 high-confidence sites, including