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Corrigendum: Phosphorylation of SRSF1 by SRPK1 regulates alternative splicing of tumor-related Rac1b in colorectal cells RNA (IF 4.5) Pub Date : 2024-04-01 Vânia Gonçalves, Andreia Henriques, Joana Pereira, Ana Neves Costa, Mary Pat Moyer, Luís Ferreira Moita, Margarida Gama-Carvalho, Paulo Matos, Peter Jordan
RNA 20: 474–482 (2014)
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Chemi-Northern: a versatile chemiluminescent northern blot method for analysis and quantitation of RNA molecules RNA (IF 4.5) Pub Date : 2024-04-01 Katherine M. McKenney, Robert P. Connacher, Elise B. Dunshee, Aaron C. Goldstrohm
This report describes a chemiluminescence-based detection method for RNAs on northern blots, designated Chemi-Northern. This approach builds on the simplicity and versatility of northern blotting, while dispensing of the need for expensive and cumbersome radioactivity. RNAs are first separated by denaturing gel electrophoresis, transferred to a nylon membrane, and then hybridized to a biotinylated
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Histone lysine demethylase KDM5B facilitates proliferation and suppresses apoptosis in human acute myeloid leukemia cells through the miR-140-3p/BCL2 axis RNA (IF 4.5) Pub Date : 2024-04-01 Jiaojuan Huang, Shuiling Jin, Rongqun Guo, Wei Wu, Chengxuan Yang, Yali Qin, Qingchuan Chen, Ximiao He, Jing Qu, Zhenhua Yang
The histone lysine demethylase KDM5B is frequently up-regulated in various human cancer cells. However, its expression and functional role in human acute myeloid leukemia (AML) cells remain unclear. Here, we found that the expression level of KDM5B is high in primary human AML cells. We have demonstrated that knocking down KDM5B leads to apoptosis and impairs proliferation in primary human AML and
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T helper cells exhibit a dynamic and reversible 3′-UTR landscape RNA (IF 4.5) Pub Date : 2024-04-01 Denis Seyres, Oliver Gorka, Ralf Schmidt, Romina Marone, Mihaela Zavolan, Lukas T. Jeker
3′ untranslated regions (3′ UTRs) are critical elements of messenger RNAs, as they contain binding sites for RNA-binding proteins (RBPs) and microRNAs that affect various aspects of the RNA life cycle including transcript stability and cellular localization. In response to T cell receptor activation, T cells undergo massive expansion during the effector phase of the immune response and dynamically
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Spliceosomal helicases DDX41/SACY-1 and PRP22/MOG-5 both contribute to proofreading against proximal 3′ splice site usage RNA (IF 4.5) Pub Date : 2024-04-01 Kenneth Osterhoudt, Orazio Bagno, Sol Katzman, Alan M. Zahler
RNA helicases drive necessary rearrangements and ensure fidelity during the pre-mRNA splicing cycle. DEAD-box helicase DDX41 has been linked to human disease and has recently been shown to interact with DEAH-box helicase PRP22 in the spliceosomal C* complex, yet its function in splicing remains unknown. Depletion of DDX41 homolog SACY-1 from somatic cells has been previously shown to lead to changes
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Turn-on RNA Mango Beacons for trans-acting fluorogenic nucleic acid detection RNA (IF 4.5) Pub Date : 2024-04-01 Amir Abdolahzadeh, Quiana R. Ang, Jana R. Caine, Shanker Shyam S. Panchapakesan, Shinta Thio, Razvan Cojocaru, Peter J. Unrau
The Mango I and II RNA aptamers have been widely used in vivo and in vitro as genetically encodable fluorogenic markers that undergo large increases in fluorescence upon binding to their ligand, TO1-Biotin. However, while studying nucleic acid sequences, it is often desirable to have trans-acting probes that induce fluorescence upon binding to a target sequence. Here, we rationally design three types
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Direct and indirect control of Rho-dependent transcription termination by the Escherichia coli lysC riboswitch RNA (IF 4.5) Pub Date : 2024-04-01 Tithi Ghosh, Shirin Jahangirnejad, Adrien Chauvier, Anne M. Stringer, Alexey P. Korepanov, Jean Phillippe Côté, Joseph T. Wade, Daniel A. Lafontaine
Bacterial riboswitches are molecular structures that play a crucial role in controlling gene expression to maintain cellular balance. The Escherichia coli lysC riboswitch has been previously shown to regulate gene expression through translation initiation and mRNA decay. Recent research suggests that lysC gene expression is also influenced by Rho-dependent transcription termination. Through a series
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Characterization of tRNA splicing enzymes RNA ligase and tRNA 2′-phosphotransferase from the pathogenic fungi Mucorales RNA (IF 4.5) Pub Date : 2024-04-01 Shreya Ghosh, Swathi Dantuluri, Agata Jacewicz, Ana M. Sanchez, Leonora Abdullahu, Masad J. Damha, Beate Schwer, Stewart Shuman
Fungal Trl1 is an essential trifunctional tRNA splicing enzyme that heals and seals tRNA exons with 2′,3′-cyclic-PO4 and 5′-OH ends. Trl1 is composed of C-terminal cyclic phosphodiesterase and central polynucleotide kinase end-healing domains that generate the 3′-OH,2′-PO4 and 5′-PO4 termini required for sealing by an N-terminal ATP-dependent ligase domain. Trl1 enzymes are present in many human fungal
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Fungi of the order Mucorales express a “sealing-only” tRNA ligase RNA (IF 4.5) Pub Date : 2024-04-01 Khondakar Sayef Ahammed, Ambro van Hoof
Some eukaryotic pre-tRNAs contain an intron that is removed by a dedicated set of enzymes. Intron-containing pre-tRNAs are cleaved by tRNA splicing endonuclease, followed by ligation of the two exons and release of the intron. Fungi use a “heal and seal” pathway that requires three distinct catalytic domains of the tRNA ligase enzyme, Trl1. In contrast, humans use a “direct ligation” pathway carried
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betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions RNA (IF 4.5) Pub Date : 2024-04-01 Mariana Ascensão-Ferreira, Rita Martins-Silva, Nuno Saraiva-Agostinho, Nuno L. Barbosa-Morais
Next-generation RNA sequencing allows alternative splicing (AS) quantification with unprecedented resolution, with the relative inclusion of an alternative sequence in transcripts being commonly quantified by the proportion of reads supporting it as percent spliced-in (PSI). However, PSI values do not incorporate information about precision, proportional to the respective AS events’ read coverage.
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The molecular language of RNA 5′ ends: guardians of RNA identity and immunity RNA (IF 4.5) Pub Date : 2024-04-01 Rodolfo Gamaliel Avila-Bonilla, Sara Macias
RNA caps are deposited at the 5′ end of RNA polymerase II transcripts. This modification regulates several steps of gene expression, in addition to marking transcripts as self to enable the innate immune system to distinguish them from uncapped foreign RNAs, including those derived from viruses. Specialized immune sensors, such as RIG-I and IFITs, trigger antiviral responses upon recognition of uncapped
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A scalable and cost-efficient rRNA depletion approach to enrich RNAs for molecular biology investigations RNA (IF 4.5) Pub Date : 2024-03-14 Amrita Singh, Amy Xue, Justin Tai, Faith Mbadugha, Prisca Obi, Romario Mascarenhas, Antariksh Tyagi, Adamo Siena, Y. Grace Chen
Transcriptomics analyses play pivotal roles in understanding the complex regulatory networks that govern cellular processes. The abundance of rRNAs, which account for 80-90% of total RNA in eukaryotes, limits the detection and investigation of other transcripts. While mRNAs and long non-coding RNAs have polyA(+) tails that are often used for positive selection, investigations of polyA(-) RNAs, such
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Quantification of tRNA m1A modification by templated-ligation qPCR RNA (IF 4.5) Pub Date : 2024-03-12 Wen Zhang, Hankui Chen, Marek Sobczyk, Daniel Krochmal, Christopher D. Katanski, Mahdi Assari, Amy Chen, Yichen Hou, Qing Dai, Tao Pan
N1-methyladenosine (m1A) is a widespread modification in all eukaryotic, many archaeal, and some bacterial tRNAs. M1A is generally located in the T loop of cytosolic tRNA and between acceptor and D stems of mitochondrial tRNAs, it is involved in tertiary interaction that stabilizes tRNA. Human tRNA m1A levels are dynamically regulated that fine-tune translation and can also serve as biomarkers for
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Localization of RNAs to the Mitochondria – Mechanisms and Functions RNA (IF 4.5) Pub Date : 2024-03-06 Surbhi Sharma, Furqan M Fazal
The mammalian mitochondrial proteome comprises over 1000 proteins, with the majority translated from nuclear-encoded messenger RNAs (mRNAs). Mounting evidence suggests many of these mRNAs are localized to the outer mitochondrial membrane (OMM) in a pre-or co-translational state. Upon reaching the mitochondrial surface, these mRNAs are locally translated to produce proteins that are co-translationally
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A Role for SNU66 in Maintaining 5’ Splice Site Identity During Spliceosome Assembly RNA (IF 4.5) Pub Date : 2024-03-05 Kenna Sarka, Sol Katzman, Alan M. Zahler
In spliceosome assembly, the 5’ splice site is initially recognized by U1snRNA. U1 leaves the spliceosome during the assembly process, therefore other factors contribute to maintenance of 5’ splice site identity as it is loaded into the catalytic site. Recent structural data suggest that human tri-snRNP 27K (SNRP27) M141 and SNU66 H734 interact to stabilize the U4/U6 quasi-pseudo knot at the base of
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Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast RNA (IF 4.5) Pub Date : 2024-03-05 Sara ANDJUS, Ugo SZACHNOWSKI, Nicolas VOGT, Stamatia GIOFTSIDI, Isabelle HATIN, David CORNU, Chris PAPADOPOULOS, Anne LOPES, Olivier NAMY, Maxime WERY, Antonin MORILLON
Despite being predicted to lack coding potential, cytoplasmic long non-coding (lnc)RNAs can associate with ribosomes. However, the landscape and biological relevance of lncRNAs translation remains poorly studied. In yeast, cytoplasmic Xrn1-sensitive lncRNAs (XUTs) are targeted by the Nonsense-Mediated mRNA Decay (NMD), suggesting a translation-dependent degradation process. Here, we report that XUTs
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Novel RNA molecular bioengineering technology efficiently produces functional miRNA agents RNA (IF 4.5) Pub Date : 2024-03-01 Gavin M. Traber, Colleen Yi, Neelu Batra, Meijuan Tu, Aiming Yu
Genome-derived microRNAs (miRNA or miR) govern posttranscriptional gene regulation and play important roles in various cellular processes and disease progression. While chemo-engineered miRNA mimics or biosimilars made in vitro are widely available and used, miRNA agents produced in vivo are emerging to closely recapitulate natural miRNA species for research. Our recent works have demonstrated the
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High-throughput quantitation of protein-RNA UV-crosslinking efficiencies as a predictive tool for high confidence identification of RNA binding proteins RNA (IF 4.5) Pub Date : 2024-02-29 Johncarlo Kristofich, Christopher Nicchitta
UV-crosslinking has proven to be an invaluable tool for the identification of RNA-protein interactomes. The paucity of methods for distinguishing background from bona fide RNA-protein interactions however makes attribution of RNA binding function on UV-crosslinking alone challenging. To address this need, we previously reported an RNA binding protein (RBP) confidence scoring metric, (RCS), incorporating
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Rational design of oligonucleotides for enhanced in vitro transcription of small RNA RNA (IF 4.5) Pub Date : 2024-02-29 Teppei Matsuda, Hiroyuki Hori, Ryota Yamagami
All kinds of RNA molecules can be produced by in vitro transcription using T7 RNA polymerase using DNA templates obtained by solid-phase chemical synthesis, primer extension, PCR or DNA cloning. The oligonucleotide design, however, is a challenge to non-experts as this relies on a set of rules that have been established empirically over time. Here, we describe a Python program to facilitate the Rational
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A comparative analysis of peptide-delivered antisense antibiotics employing diverse nucleotide mimics RNA (IF 4.5) Pub Date : 2024-02-27 Chandradhish Ghosh, Linda Popella, V. Dhamodharan, Jakob Jung, Julia Dietzsch, Lars Barquist, Claudia Höbartner, Jörg Vogel
Antisense oligomer (ASO)-based antibiotics that target mRNAs of essential bacterial genes have great potential for counteracting antimicrobial resistance and for precision microbiome editing. To date, the development of such antisense antibiotics has primarily focused on using phosphorodiamidate morpholino (PMO) and peptide nucleic acid (PNA) backbones, largely ignoring the growing number of chemical
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High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules RNA (IF 4.5) Pub Date : 2024-02-21 Jerricho Tipo, Keerthi Gottipati, Kyung H Choi
Flaviviruses such as Zika (ZIKV) and dengue virus (DENV) are positive-sense RNA viruses belonging to Flaviviridae. The flavivirus genome contains a 5’ end stem-loop promoter sequence known as stem-loop A (SLA) that is recognized by the flavivirus polymerase NS5 during viral RNA synthesis and 5’ guanosine cap methylation. The crystal structures of ZIKV and DENV SLAs show a well-defined fold, consisting
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AptaDB: a comprehensive database integrating aptamer–target interactions RNA (IF 4.5) Pub Date : 2024-03-01 Long Chen, Zhuohang Yu, Zengrui Wu, Moran Zhou, Yimeng Wang, Xinxin Yu, Weihua Li, Guixia Liu, Yun Tang
Aptamers have emerged as research hotspots of the next generation due to excellent performance benefits and application potentials in pharmacology, medicine, and analytical chemistry. Despite the numerous aptamer investigations, the lack of comprehensive data integration has hindered the development of computational methods for aptamers and the reuse of aptamers. A public access database named AptaDB
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2023 Recipients of the RNA Journal Prize RNA (IF 4.5) Pub Date : 2024-03-01 Javier Caceres, Eric Phizicky
RNA is pleased to announce the 2023 recipients of the RNA Journal Prize. This prize, initiated in 2021 and sponsored by the RNA Society, is awarded annually to two outstanding papers published in RNA during the year in any RNA-related research area.
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SCARPET: site-specific quantification of methylated and nonmethylated adenosines reveals m6A stoichiometry RNA (IF 4.5) Pub Date : 2024-03-01 Aashiq H. Mirza, Yaron Bram, Robert E. Schwartz, Samie R. Jaffrey
m6A has different stoichiometry at different positions in different mRNAs. However, the exact stoichiometry of m6A is difficult to measure. Here, we describe SCARPET (site-specific cleavage and radioactive-labeling followed by purification, exonuclease digestion, and thin-layer chromatography), a simple and streamlined biochemical assay for quantifying m6A at any specific site in any mRNA. SCARPET
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An easy tool to monitor the elemental steps of in vitro translation via gel electrophoresis of fluorescently labeled small peptides RNA (IF 4.5) Pub Date : 2024-03-01 Valeriya I. Marina, Medina Bidzhieva, Andrey G. Tereshchenkov, Dmitry Orekhov, Vladislava E. Sagitova, Nataliya V. Sumbatyan, Vadim N. Tashlitsky, Artem S. Ferberg, Tinashe P. Maviza, Pavel Kasatsky, Olga Tolicheva, Alena Paleskava, Vladimir I. Polshakov, Ilya A. Osterman, Olga A. Dontsova, Andrey L. Konevega, Petr V. Sergiev
Several methods are available to visualize and assess the kinetics and efficiency of elemental steps of protein biosynthesis. However, each of these methods has its own limitations. Here, we present a novel, simple and convenient tool for monitoring stepwise in vitro translation initiated by BODIPY-Met-tRNA. Synthesis and release of very short, 1–7 amino acids, BODIPY-labeled peptides, can be monitored
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CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone mRNA processing RNA (IF 4.5) Pub Date : 2024-03-01 Abdulrahman A. Alahmari, Aditi H. Chaubey, Venkata S. Jonnakuti, Arwen A. Tisdale, Carla D. Schwarz, Abigail C. Cornwell, Kathryn E. Maraszek, Emily J. Paterson, Minsuh Kim, Swati Venkat, Eduardo Cortes Gomez, Jianmin Wang, Katerina V. Gurova, Hari Krishna Yalamanchili, Michael E. Feigin
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited effective treatment options, potentiating the importance of uncovering novel drug targets. Here, we target cleavage and polyadenylation specificity factor 3 (CPSF3), the 3′ endonuclease that catalyzes mRNA cleavage during polyadenylation and histone mRNA processing. We find that CPSF3 is highly expressed in PDAC and is associated
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Examining the capacity of human U1 snRNA variants to facilitate pre-mRNA splicing RNA (IF 4.5) Pub Date : 2024-03-01 Jason Wong, Ryan Yellamaty, Christina Gallante, Ethan Lawrence, William Martelly, Shalini Sharma
The human U1 snRNA is encoded by a multigene family consisting of transcribed variants and defective pseudogenes. Many variant U1 (vU1) snRNAs have been demonstrated to not only be transcribed but also processed by the addition of a trimethylated guanosine cap, packaged into snRNPs, and assembled into spliceosomes; however, their capacity to facilitate pre-mRNA splicing has, so far, not been tested
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Genome-wide kinetic profiling of pre-mRNA 3′ end cleavage RNA (IF 4.5) Pub Date : 2024-03-01 Leslie Torres-Ulloa, Ezequiel Calvo-Roitberg, Athma A. Pai
Cleavage and polyadenylation is necessary for the formation of mature mRNA molecules. The rate at which this process occurs can determine the temporal availability of mRNA for subsequent function throughout the cell and is likely tightly regulated. Despite advances in high-throughput approaches for global kinetic profiling of RNA maturation, genome-wide 3′ end cleavage rates have never been measured
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Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA RNA (IF 4.5) Pub Date : 2024-03-01 Aileen C. Button, Simone D. Hall, Ethan L. Ashley, Colleen A. McHugh
XIST noncoding RNA promotes the initiation of X chromosome silencing by recruiting the protein SPEN to one X chromosome in female mammals. The SPEN protein is also called SHARP (SMRT and HDAC-associated repressor protein) and MINT (Msx-2 interacting nuclear target) in humans. SPEN recruits N-CoR2 and HDAC3 to initiate histone deacetylation on the X chromosome, leading to the formation of repressive
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LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function RNA (IF 4.5) Pub Date : 2024-03-01 Benjamin M. Lewis, Chae Yun Cho, Hsuan-Lin Her, Orel Mizrahi, Tony Hunter, Gene W. Yeo
Mitochondria-associated RNA-binding proteins (RBPs) have emerged as key contributors to mitochondrial biogenesis and homeostasis. With few examples known, we set out to identify RBPs that regulate nuclear-encoded mitochondrial mRNAs (NEMmRNAs). Our systematic analysis of RNA targets of 150 RBPs identified RBPs with a preference for binding NEMmRNAs, including LARP4, a La RBP family member. We show
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Diversity and modularity of tyrosine-accepting tRNA-like structures RNA (IF 4.5) Pub Date : 2024-03-01 Madeline E. Sherlock, Conner J. Langeberg, Jeffrey S. Kieft
Certain positive-sense single-stranded RNA viruses contain elements at their 3′ termini that structurally mimic tRNAs. These tRNA-like structures (TLSs) are classified based on which amino acid is covalently added to the 3′ end by host aminoacyl-tRNA synthetase. Recently, a cryoEM reconstruction of a representative tyrosine-accepting tRNA-like structure (TLSTyr) from brome mosaic virus (BMV) revealed
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RlmQ: a newly discovered rRNA modification enzyme bridging RNA modification and virulence traits in Staphylococcus aureus RNA (IF 4.5) Pub Date : 2024-03-01 Roberto Bahena-Ceron, Chloé Teixeira, Jose R. Jaramillo Ponce, Philippe Wolff, Florence Couzon, Pauline François, Bruno P. Klaholz, François Vandenesch, Pascale Romby, Karen Moreau, Stefano Marzi
rRNA modifications play crucial roles in fine-tuning the delicate balance between translation speed and accuracy, yet the underlying mechanisms remain elusive. Comparative analyses of the rRNA modifications in taxonomically distant bacteria could help define their general, as well as species-specific, roles. In this study, we identified a new methyltransferase, RlmQ, in Staphylococcus aureus responsible
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A tRNA-specific function for tRNA methyltransferase Trm10 is associated with a new tRNA quality control mechanism in Saccharomyces cerevisiae RNA (IF 4.5) Pub Date : 2024-02-01 Isobel E. Bowles, Jane E. Jackman
In Saccharomyces cerevisiae, a single homolog of the tRNA methyltransferase Trm10 performs m1G9 modification on 13 different tRNAs. Here we provide evidence that the m1G9 modification catalyzed by S. cerevisiae Trm10 plays a biologically important role for one of these tRNA substrates, tRNATrp. Overexpression of tRNATrp (and not any of 38 other elongator tRNAs) rescues growth hypersensitivity of the
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Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain RNA (IF 4.5) Pub Date : 2024-02-01 Oarteze Hunter, Jason Talkish, Jen Quick-Cleveland, Haller Igel, Asako Tan, Scott Kuersten, Sol Katzman, John Paul Donohue, Melissa S. Jurica, Manuel Ares, Jr
Intron branchpoint (BP) recognition by the U2 snRNP is a critical step of splicing, vulnerable to recurrent cancer mutations and bacterial natural product inhibitors. The BP binds a conserved pocket in the SF3B1 (human) or Hsh155 (yeast) U2 snRNP protein. Amino acids that line this pocket affect the binding of splicing inhibitors like Pladienolide-B (Plad-B), such that organisms differ in their sensitivity
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Analysis of programmed frameshifting during translation of prfB in Flavobacterium johnsoniae RNA (IF 4.5) Pub Date : 2024-02-01 Fawwaz M. Naeem, Bryan T. Gemler, Zakkary A. McNutt, Ralf Bundschuh, Kurt Fredrick
Ribosomes of Bacteroidia fail to recognize Shine–Dalgarno (SD) sequences due to sequestration of the 3′ tail of the 16S rRNA on the 30S platform. Yet in these organisms, the prfB gene typically contains the programmed +1 frameshift site with its characteristic SD sequence. Here, we investigate prfB autoregulation in Flavobacterium johnsoniae, a member of the Bacteroidia. We find that the efficiency
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Balanced cell division is secured by two different regulatory sites in OxyS RNA RNA (IF 4.5) Pub Date : 2024-02-01 Maya Elgrably-Weiss, Fayyaz Hussain, Jens Georg, Bushra Shraiteh, Shoshy Altuvia
The hydrogen peroxide-induced small RNA OxyS has been proposed to originate from the 3′ UTR of a peroxide mRNA. Unexpectedly, phylogenetic OxyS targetome predictions indicate that most OxyS targets belong to the category of “cell cycle,” including cell division and cell elongation. Previously, we reported that Escherichia coli OxyS inhibits cell division by repressing expression of the essential transcription
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3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations RNA (IF 4.5) Pub Date : 2024-02-01 Irene K. Beckmann, Maria Waldl, Sebastian Will, Ivo L. Hofacker
The structure of an RNA, and even more so its interactions with other RNAs, provide valuable information about its function. Secondary structure-based tools for RNA–RNA interaction predictions provide a quick way to identify possible interaction targets and structures. However, these tools ignore the effect of steric hindrance on the tertiary (3D) structure level, and do not consider whether a suitable
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The Bacillus subtilis ywbD gene encodes RlmQ, the 23S rRNA methyltransferase forming m7G2574 in the A-site of the peptidyl transferase center RNA (IF 4.5) Pub Date : 2024-02-01 Philippe Wolff, Geoffray Labar, Antony Lechner, Dany Van Elder, Romuald Soin, Cyril Gueydan, Véronique Kruys, Louis Droogmans, Martine Roovers
Ribosomal RNA contains many posttranscriptionally modified nucleosides, particularly in the functional parts of the ribosome. The distribution of these modifications varies from one organism to another. In Bacillus subtilis, the model organism for Gram-positive bacteria, mass spectrometry experiments revealed the presence of 7-methylguanosine (m7G) at position 2574 of the 23S rRNA, which lies in the
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Tributaries of the 2023 Nobel Prize in Physiology or Medicine, and lessons learned RNA (IF 4.5) Pub Date : 2024-02-01 Thoru Pederson
Almost without exception, scientific breakthroughs are not epistemological orphans. Historians of science have developed a body of scholarship on this, and the cases arising in our era continue to confirm the phenomenon. The work by Katalin Karikó and Drew Weissman that proved foundational for the subsequent development of mRNA vaccines for COVID-19 had its antecedent roots yet is also a striking example
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Tribute to Yoshiro Shimura (1932–2023) RNA (IF 4.5) Pub Date : 2024-02-01
On September 27, 2023, Dr. Yoshiro Shimura died of old age in Kyoto, Japan. He was born and grew up in Yamanashi prefecture, near Tokyo. He entered the Department of Botany at Kyoto University and received an MS degree in plant physiology. He then moved to Rutgers University in New Jersey and obtained his PhD in microbiology and molecular biology under the supervision of Professor Henry J. Vogel (Shimura
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Corrigendum: NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal–ventral patterning RNA (IF 4.5) Pub Date : 2024-01-01 Om Singh Rathore, Rui D. Silva, Mariana Ascensão-Ferreira, Ricardo Matos, Célia Carvalho, Bruno Marques, Margarida N. Tiago, Pedro Prudêncio, Raquel P. Andrade, Jean-Yves Roignant, Nuno L. Barbosa-Morais, Rui Gonçalo Martinho
RNA 26: 1935–1956 (2020)
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Tho2 is critical for the recruitment of Rrp6 to chromatin in response to perturbed mRNP biogenesis RNA (IF 4.5) Pub Date : 2024-01-01 Valentin Beauvais, Kévin Moreau, Bojan Žunar, Nadège Hervouet-Coste, Ana Novačić, Aurélia Le Dantec, Michael Primig, Christine Mosrin-Huaman, Igor Stuparević, A. Rachid Rahmouni
The eukaryotic THO complex coordinates the assembly of so-called messenger RNA–ribonucleoprotein particles (mRNPs), a process that involves cotranscriptional coating of nascent mRNAs with proteins. Once formed, mRNPs undergo a quality control step that marks them either for active transport to the cytoplasm, or Rrp6/RNA exosome-mediated degradation in the nucleus. However, the mechanism behind the
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Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging RNA (IF 4.5) Pub Date : 2024-01-01 Anjana Krishnan, Lizna M. Ali, Suresha G. Prabhu, Vineeta N. Pillai, Akhil Chameettachal, Valérie Vivet-Boudou, Serena Bernacchi, Farah Mustafa, Roland Marquet, Tahir A. Rizvi
The retroviral Gag precursor plays a central role in the selection and packaging of viral genomic RNA (gRNA) by binding to virus-specific packaging signal(s) (psi or ψ). Previously, we mapped the feline immunodeficiency virus (FIV) ψ to two discontinuous regions within the 5′ end of the gRNA that assumes a higher order structure harboring several structural motifs. To better define the region and structural
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Impact on splicing in Saccharomyces cerevisiae of random 50-base sequences inserted into an intron RNA (IF 4.5) Pub Date : 2024-01-01 Molly Perchlik, Alexander Sasse, Sara Mostafavi, Stanley Fields, Josh T. Cuperus
Intron splicing is a key regulatory step in gene expression in eukaryotes. Three sequence elements required for splicing—5′ and 3′ splice sites and a branchpoint—are especially well-characterized in Saccharomyces cerevisiae, but our understanding of additional intron features that impact splicing in this organism is incomplete, due largely to its small number of introns. To overcome this limitation
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Posttranscriptional modification to the core of tRNAs modulates translational misreading errors RNA (IF 4.5) Pub Date : 2024-01-01 Sima Saleh, Philip J. Farabaugh
Protein synthesis on the ribosome involves successive rapid recruitment of cognate aminoacyl-tRNAs and rejection of the much more numerous incorrect near- or non-cognates. The principal feature of translation elongation is that at every step, many incorrect aa-tRNAs unsuccessfully enter the A site for each cognate accepted. Normal levels of translational accuracy require that cognate tRNAs have relatively
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miR-7 is recruited to the high molecular weight RNA-induced silencing complex in CD8+ T cells upon activation and suppresses IL-2 signaling RNA (IF 4.5) Pub Date : 2024-01-01 Matilda Toivakka, Katrina Gordon, Sujai Kumar, José Roberto Bermudez-Barrientos, Cei Abreu-Goodger, Rose Zamoyska, Amy H. Buck
Increasing evidence suggests mammalian Argonaute (Ago) proteins partition into distinct complexes within cells, but there is still little biochemical or functional understanding of the miRNAs differentially associated with these complexes. In naïve T cells, Ago2 is found almost exclusively in low molecular weight (LMW) complexes which are associated with miRNAs but not their target mRNAs. Upon T-cell
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VODKA2: a fast and accurate method to detect non-standard viral genomes from large RNA-seq data sets RNA (IF 4.5) Pub Date : 2024-01-01 Emna Achouri, Sébastien A. Felt, Matthew Hackbart, Nicole S. Rivera-Espinal, Carolina B. López
During viral replication, viruses carrying an RNA genome produce non-standard viral genomes (nsVGs), including copy-back viral genomes (cbVGs) and deletion viral genomes (delVGs), that play a crucial role in regulating viral replication and pathogenesis. Because of their critical roles in determining the outcome of RNA virus infections, the study of nsVGs has flourished in recent years, exposing a
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Motifs in SARS-CoV-2 evolution RNA (IF 4.5) Pub Date : 2024-01-01 Christopher Barrett, Andrei C. Bura, Qijun He, Fenix W. Huang, Thomas J.X. Li, Christian M. Reidys
We present a novel framework enhancing the prediction of whether novel lineage poses the threat of eventually dominating the viral population. The framework is based purely on genomic sequence data, without requiring prior established biological analysis. Its building blocks are sets of coevolving sites in the alignment (motifs), identified via coevolutionary signals. The collection of such motifs
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RNA: Reviewers for Volume 29, 2023 RNA (IF 4.5) Pub Date : 2023-12-01
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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Corrigendum: Identification of Up47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium RNA (IF 4.5) Pub Date : 2023-12-01 Philippe Wolff, Antony Lechner, Louis Droogmans, Henri Grosjean, Eric Westhof
RNA 29: 551–556 (2023)
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A highly efficient human cell-free translation system RNA (IF 4.5) Pub Date : 2023-12-01 Nikolay A. Aleksashin, Stacey Tsai-Lan Chang, Jamie H.D. Cate
Cell-free protein synthesis (CFPS) systems enable easy in vitro expression of proteins with many scientific, industrial, and therapeutic applications. Here we present an optimized, highly efficient human cell-free translation system that bypasses many limitations of currently used in vitro systems. This CFPS system is based on extracts from human HEK293T cells engineered to endogenously express GADD34
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Rational design of eukaryotic riboswitches that up-regulate IRES-mediated translation initiation with high switching efficiency through a kinetic trapping mechanism in vitro RNA (IF 4.5) Pub Date : 2023-12-01 Hajime Takahashi, Masahiro Fujikawa, Atsushi Ogawa
In general, riboswitches functioning through a cotranscriptional kinetic trapping mechanism (kt-riboswitches) show higher switching efficiencies in response to practical concentrations of their ligand molecules than eq-riboswitches, which function by an equilibrium mechanism. However, the former have been much more difficult to design due to their more complex mechanism. We here successfully developed
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Adaptive sampling for nanopore direct RNA-sequencing RNA (IF 4.5) Pub Date : 2023-12-01 Isabel S. Naarmann-de Vries, Enio Gjerga, Catharina L.A. Gandor, Christoph Dieterich
Nanopore long-read sequencing enables real-time monitoring and controlling of individual nanopores. This allows us to enrich or deplete specific sequences in DNA sequencing in a process called “adaptive sampling.” So far, adaptive sampling (AS) was not applicable to the direct sequencing of RNA. Here, we show that AS is feasible and useful for direct RNA sequencing (DRS), which has its specific technical
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Quantification of elongation stalls and impact on gene expression in yeast RNA (IF 4.5) Pub Date : 2023-12-01 Wanfu Hou, Vince Harjono, Alex T. Harvey, Arvind Rasi Subramaniam, Brian M. Zid
Ribosomal pauses are a critical part of cotranslational events including protein folding and localization. However, extended ribosome pauses can lead to ribosome collisions, resulting in the activation of ribosome rescue pathways and turnover of protein and mRNA. While this relationship has been known, there has been little exploration of how ribosomal stalls impact translation duration at a quantitative
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Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development RNA (IF 4.5) Pub Date : 2023-12-01 Nozomi Ugajin, Koshi Imami, Hiraku Takada, Yasushi Ishihama, Shinobu Chiba, Yuichiro Mishima
The ribosome is a translational apparatus that comprises about 80 ribosomal proteins and four rRNAs. Recent studies reported that ribosome ubiquitination is crucial for translational regulation and ribosome-associated quality control (RQC). However, little is known about the dynamics of ribosome ubiquitination under complex biological processes of multicellular organisms. To explore ribosome ubiquitination
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The pseudotorsional space of RNA RNA (IF 4.5) Pub Date : 2023-12-01 Leandro Grille, Diego Gallego, Leonardo Darré, Gabriela da Rosa, Federica Battistini, Modesto Orozco, Pablo D. Dans
The characterization of the conformational landscape of the RNA backbone is rather complex due to the ability of RNA to assume a large variety of conformations. These backbone conformations can be depicted by pseudotorsional angles linking RNA backbone atoms, from which Ramachandran-like plots can be built. We explore here different definitions of these pseudotorsional angles, finding that the most
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Translational control by Trypanosoma brucei DRBD18 contributes to the maintenance of the procyclic state RNA (IF 4.5) Pub Date : 2023-12-01 Martin Ciganda, José Sotelo-Silveira, Ashutosh P. Dubey, Parul Pandey, Joseph T. Smith, Shichen Shen, Jun Qu, Pablo Smircich, Laurie K. Read
Trypanosoma brucei occupies distinct niches throughout its life cycle, within both the mammalian and tsetse fly hosts. The immunological and biochemical complexity and variability of each of these environments require a reshaping of the protein landscape of the parasite both to evade surveillance and face changing metabolic demands. In kinetoplastid protozoa, including T. brucei, posttranscriptional
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Cross-linking mass spectrometric analysis of the endogenous TREX complex from Saccharomyces cerevisiae RNA (IF 4.5) Pub Date : 2023-12-01 Carina Kern, Christin Radon, Wolfgang Wende, Alexander Leitner, Katja Sträßer
The conserved TREX complex has multiple functions in gene expression such as transcription elongation, 3′ end processing, mRNP assembly and nuclear mRNA export as well as the maintenance of genomic stability. In Saccharomyces cerevisiae, TREX is composed of the pentameric THO complex, the DEAD-box RNA helicase Sub2, the nuclear mRNA export adaptor Yra1, and the SR-like proteins Gbp2 and Hrb1. Here
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Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex RNA (IF 4.5) Pub Date : 2023-12-01 Dhaarsini Jaksch, Johanna Irnstorfer, Petra-Franziska Kalman, Javier Martinez
The mammalian tRNA ligase complex (tRNA-LC) catalyzes the splicing of intron-containing pre-tRNAs in the nucleus and the splicing of XBP1 mRNA during the unfolded protein response (UPR) in the cytoplasm. We recently reported that the tRNA-LC coevolved with PYROXD1, an essential oxidoreductase that protects the catalytic cysteine of RTCB, the catalytic subunit of the tRNA-LC, against aerobic oxidation
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Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data RNA (IF 4.5) Pub Date : 2023-12-01 Sam Bryce-Smith, Dominik Burri, Matthew R. Gazzara, Christina J. Herrmann, Weronika Danecka, Christina M. Fitzsimmons, Yuk Kei Wan, Farica Zhuang, Mervin M. Fansler, José M. Fernández, Meritxell Ferret, Asier Gonzalez-Uriarte, Samuel Haynes, Chelsea Herdman, Alexander Kanitz, Maria Katsantoni, Federico Marini, Euan McDonnel, Ben Nicolet, Chi-Lam Poon, Gregor Rot, Leonard Schärfen, Pin-Jou Wu, Yoseop
The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, limitations, and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there is an increasing need for benchmarks, and for the provision of infrastructure for continuous method evaluation. APAeval