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Chemical manipulation of m1A mediates its detection in human tRNA RNA (IF 4.5) Pub Date : 2024-05-01 Kinga Pajdzik, Ruitu Lyu, Xiaoyang Dou, Chang Ye, Li-Sheng Zhang, Qing Dai, Chuan He
N1-methyl adenosine (m1A) is a widespread RNA modification present in tRNA, rRNA, and mRNA. m1A modification sites in tRNAs are evolutionarily conserved and its formation on tRNA is catalyzed by methyltransferase TRMT61A and TRMT6 complex. m1A promotes translation initiation and elongation. Due to its positive charge under physiological conditions, m1A can notably modulate RNA structure. It also blocks
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ac4C: a fragile modification with stabilizing functions in RNA metabolism RNA (IF 4.5) Pub Date : 2024-05-01 Sarah Schiffers, Shalini Oberdoerffer
In recent years, concerted efforts to map and understand epitranscriptomic modifications in mRNA have unveiled new complexities in the regulation of gene expression. These studies cumulatively point to diverse functions in mRNA metabolism, spanning pre-mRNA processing, mRNA degradation, and translation. However, this emerging landscape is not without its intricacies and sources of discrepancies. Disparities
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2′-O-methylation (Nm) in RNA: progress, challenges, and future directions RNA (IF 4.5) Pub Date : 2024-05-01 Katherine I. Zhou, Chad V. Pecot, Christopher L. Holley
RNA 2′-O-methylation (Nm) is highly abundant in noncoding RNAs including ribosomal RNA (rRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA), and occurs in the 5′ cap of virtually all messenger RNAs (mRNAs) in higher eukaryotes. More recently, Nm has also been reported to occur at internal sites in mRNA. High-throughput methods have been developed for the transcriptome-wide detection of Nm. However
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The je ne sais quoi of 5-methylcytosine in messenger RNA RNA (IF 4.5) Pub Date : 2024-05-01 Marco Guarnacci, Thomas Preiss
The potential presence of 5-methylcytosine as a sparse internal modification of mRNA was first raised in 1975, and a first map of the modification was also part of the epitranscriptomics “big bang” in 2012. Since then, the evidence for its presence in mRNA has firmed up, and initial insights have been gained into the molecular function and broader biological relevance of 5-methylcytosine when present
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New directions for Ψ and m1A decoding in mRNA: deciphering the stoichiometry and function RNA (IF 4.5) Pub Date : 2024-05-01 Meiling Zhang, Xiaoting Zhang, Yichen Ma, Chengqi Yi
Over the past decade, advancements in epitranscriptomics have significantly enhanced our understanding of mRNA metabolism and its role in human development and diseases. This period has witnessed breakthroughs in sequencing technologies and the identification of key proteins involved in RNA modification processes. Alongside the well-studied m6A, Ψ and m1A have emerged as key epitranscriptomic markers
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Recent developments, opportunities, and challenges in the study of mRNA pseudouridylation RNA (IF 4.5) Pub Date : 2024-05-01 Wendy V. Gilbert
Pseudouridine is an abundant mRNA modification found in diverse organisms ranging from bacteria and viruses to multicellular plants and humans. New developments in pseudouridine profiling provide quantitative tools to map mRNA pseudouridylation sites. Sparse biochemical studies establish the potential for mRNA pseudouridylation to affect most stages of the mRNA life cycle from birth to death. This
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Adenosine deaminases that act on RNA, then and now RNA (IF 4.5) Pub Date : 2024-05-01 Brenda L. Bass
In this article, I recount my memories of key experiments that led to my entry into the RNA editing/modification field. I highlight initial observations made by the pioneers in the ADAR field, and how they fit into our current understanding of this family of enzymes. I discuss early mysteries that have now been solved, as well as those that still linger. Finally, I discuss important, outstanding questions
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Structural and functional effects of inosine modification in mRNA RNA (IF 4.5) Pub Date : 2024-05-01 Herra G. Mendoza, Peter A. Beal
Inosine (I), resulting from the deamination of adenosine (A), is a prominent modification in the human transcriptome. The enzymes responsible for the conversion of adenosine to inosine in human mRNAs are the ADARs (adenosine deaminases acting on RNA). Inosine modification introduces a layer of complexity to mRNA processing and function, as it can impact various aspects of RNA biology, including mRNA
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Multifaceted roles of RNA editing enzyme ADAR1 in innate immunity RNA (IF 4.5) Pub Date : 2024-05-01 Inga Jarmoskaite, Jin Billy Li
Innate immunity must be tightly regulated to enable sensitive pathogen detection while averting autoimmunity triggered by pathogen-like host molecules. A hallmark of viral infection, double-stranded RNAs (dsRNAs) are also abundantly encoded in mammalian genomes, necessitating surveillance mechanisms to distinguish “self” from “nonself.” ADAR1, an RNA editing enzyme, has emerged as an essential safeguard
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Principles, functions, and biological implications of m6A in plants RNA (IF 4.5) Pub Date : 2024-05-01 Peizhe Song, Zhihe Cai, Guifang Jia
Over the past decade, N6-methyladenosine (m6A) has emerged as a prevalent and dynamically regulated modification across the transcriptome; it has been reversibly installed, removed, and interpreted by specific binding proteins, and has played crucial roles in molecular and biological processes. Within this scope, we consolidate recent advancements of m6A research in plants regarding gene expression
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Challenges to mapping and defining m6A function in viral RNA RNA (IF 4.5) Pub Date : 2024-05-01 Stacy M. Horner, Matthew G. Thompson
Viral RNA molecules contain multiple layers of regulatory information. This includes features beyond the primary sequence, such as RNA structures and RNA modifications, including N6-methyladenosine (m6A). Many recent studies have identified the presence and location of m6A in viral RNA and have found diverse regulatory roles for this modification during viral infection. However, to date, viral m6A
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Understanding the redundant functions of the m6A-binding YTHDF proteins RNA (IF 4.5) Pub Date : 2024-05-01 Sara Zaccara, Samie R. Jaffrey
N6-methyladenosine (m6A) is the most prevalent modified nucleotide in mRNA, and it has important functions in mRNA regulation. However, our understanding of the specific functions of m6A along with its cytosolic readers, the YTHDF proteins, has changed substantially in recent years. The original view was that different m6A sites within an mRNA could have different functions depending on which YTHDF
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mRNA epitranscriptomics RNA (IF 4.5) Pub Date : 2024-05-01 Kate D. Meyer, Tao Pan
Epitranscriptomics refers to chemical changes in RNAs and includes numerous chemical types with varying stoichiometry and functions. RNA modifications are highly diverse in chemistry and respond in cell-type- and cell-state-dependent manners that enable and facilitate the execution of a wide array of biological functions. This includes roles in the regulation of transcription, translation, chromatin
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Note from the Editor RNA (IF 4.5) Pub Date : 2024-05-01 Tim Nilsen
RNA is pleased to present the third in a series of special issues, each devoted to a developing and exciting area of current RNA biology. The first two issues dealt with possible roles of RNA in biological condensates [edited by Tom Cech (January 2022; 28: 1–113)] and RNA therapeutics [edited by Adrian Krainer and Michelle Hastings (April 2023; 29: 393–515)].
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The Prp19C subunit Syf2 and the Prp19C-associated protein Cwc15 function in TREX occupancy and transcription elongation RNA (IF 4.5) Pub Date : 2024-04-16 Laura Henke-Schulz, Rashmi Minocha, Nils Holger Maier, Katja Sträβer
The Prp19 complex (Prp19C) also named NineTeen Complex (NTC) is conserved from yeast to human and functions in many different processes such as genome stability, splicing and transcription elongation. In the latter, Prp19C ensures TREX occupancy at transcribed genes. TREX in turn couples transcription to nuclear mRNA export by recruiting the mRNA exporter to transcribed genes and consequently to nascent
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Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex RNA (IF 4.5) Pub Date : 2024-04-16 Rebecca J. Haugen, Catherine Barnier, Nathan D. Elrod, Hua Luo, Madeline K. Jensen, Ping Ji, Craig A. Smibert, Howard D. Lipshitz, Eric J. Wagner, P. Lydia Freddolino, Aaron C. Goldstrohm
The sequence-specific RNA-binding protein Pumilio controls Drosophila development; however, the network of mRNAs that it regulates remains incompletely characterized. In this study, we utilize knockdown and knockout approaches coupled with RNA-Seq to measure the impact of Pumilio on the transcriptome of Drosophila cells in culture. We also use an improved RNA co-immunoprecipitation method to identify
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Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase (MDH2) RNA (IF 4.5) Pub Date : 2024-04-12 Michelle Noble, Aindrila Chatterjee, Thileepan Sekaran, Thomas Schwarzl, Matthias W Hentze
Several enzymes of intermediary metabolism have been identified to bind RNA in 2 cells, with potential consequences for the bound RNAs and/or the enzyme. In this 3 study, we investigate the RNA-binding activity of the mitochondrial enzyme malate 4 dehydrogenase 2 (MDH2), which functions in the tricarboxylic acid (TCA) cycle and 5 the malate-aspartate shuttle. We confirmed in cellulo RNA-binding of
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Contribution of an alternative 16S rRNA helix to biogenesis of the 30S subunit of the ribosome RNA (IF 4.5) Pub Date : 2024-04-03 Benjamin R. Warner, Kurt Fredrick
30S subunits become inactive upon exposure to low Mg2+ concentration, due to a reversible conformational change that entails nucleotides (nt) in the neck helix (h28) and 3’ tail of 16S rRNA. This active-to-inactive transition involves partial unwinding of h28 and re-pairing of nt 921-923 with nt 1532-1534, which requires flipping of the 3’ tail by ~180 degrees. Growing evidence suggests that immature
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Computational analysis of super-resolved in situ sequencing data reveals genes modified by immune-tumor contact events RNA (IF 4.5) Pub Date : 2024-04-04 Michal Danino-Levi, Tal Goldberg, Maya Keter, Nikol Akselrod, Noa Shprach-Buaron, Modi Safra, Gonen Singer, Shahar Alon
Cancer cells can manipulate immune cells and escape from the immune system response. Quantifying the molecular changes that occur when an immune cell is touching a tumor cell can increase our understanding of the underlying mechanisms. Recently, it became possible to perform such measurements in situ, for example using expansion sequencing, which enabled in situ sequencing of genes with super-resolution
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Inefficient recruitment of DDX39B impedes pre-spliceosome assembly on FOXP3 introns RNA (IF 4.5) Pub Date : 2024-04-04 Chloe K Nagasawa, Aaron O Bailey, William Russell, Mariano A. Garcia-Blanco
Forkhead box P3 (FOXP3) is the master fate-determining transcription factor in regulatory T (Treg) cells and is essential for their development, function and homeostasis. Mutations in FOXP3 cause immunodysregulation polyendocrinopathy enteropathy X-linked (IPEX) syndrome, and aberrant expression of FOXP3 has been implicated in other diseases such as multiple sclerosis and cancer. We previously demonstrated
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The novel pre-rRNA detection workflow “Riboprobing” allows simple identification of undescribed RNA species. RNA (IF 4.5) Pub Date : 2024-04-05 Magdalena Gerhalter, Lisa Kofler, Gertrude Zisser, Juliane Merl-Pham, Stefanie M. Hauck, Helmut Bergler
Ribosomes translate mRNA into proteins and are essential for every living organism. In eukaryotes both ribosomal subunits are rapidly assembled in a strict hierarchical order, starting in the nucleolus with transcription of a common precursor ribosomal RNA (pre-rRNA). This pre-rRNA encodes three of the four mature rRNAs which are formed by several, consecutive endonucleolytic and exonucleolytic processing
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NMR characterization and ligand binding site of the stem loop 2 motif (s2m) from the Delta variant of SARS-CoV-2 RNA (IF 4.5) Pub Date : 2024-04-02 Tobias Matzel, Maria Wirtz Martin, Alexander Herr, Anna Wacker, Christian Richter, Sridhar Sreeramulu, Harald Schwalbe
The stem loop 2 motif (s2m) in SARS-CoV-2 (SCoV-2) is located in the 3’-UTR. Although s2m has been reported to display characteristics of a mobile genomic element that might lead to an evolutionary advantage, its function has remained unknown. The secondary structure of the original SCoV-2 RNA sequence (Wuhan-Hu-1) was determined by NMR in late 2020, delineating the base pairing pattern and revealing
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Robo-Therm, a pipeline to RNA Thermometer discovery and validation RNA (IF 4.5) Pub Date : 2024-04-02 Davis M Sharts, Maria T. Almanza, Andrea Victoria Banks, Alyssa M Castellanos, Catherine G O. Hernandez, Monica L Lopez, Daniela Rodriguez, Alina Y Tong, Maximilian R Segeberg, Luiz F. M. Passalacqua, Michael M Abdelsayed
RNA thermometers are highly structured noncoding RNAs located in the 5′ untranslated regions (UTR) of genes that regulate expression by undergoing conformational changes in response to temperature. The discovery of RNA thermometers through bioinformatics is difficult because there is little sequence conservation among their structural elements. Thus, the abundance of these thermo-sensitive regulatory
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Molecular basis of human polyA polymerase recruitment by mPSF RNA (IF 4.5) Pub Date : 2024-03-27 Sofia Todesca, Felix Sandmeir, Achim Keidel, Elena Conti
3' end processing of most eukaryotic pre-mRNAs is a crucial co-transcriptional process that generally involves the cleavage and polyadenylation of the precursor transcripts. Within the human 3’ end processing machinery, the 4-subunit mammalian polyadenylation specificity factor (mPSF) recognizes the polyadenylation signal (PAS) in the pre-mRNA and recruits the polyA polymerase α (PAPOA) to it. To shed
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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