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The role of the 5’ sensing function of ribonuclease E in cyanobacteria RNA Biol. (IF 4.1) Pub Date : 2024-03-12 Ute A. Hoffmann, Elisabeth Lichtenberg, Said N. Rogh, Raphael Bilger, Viktoria Reimann, Florian Heyl, Rolf Backofen, Claudia Steglich, Wolfgang R. Hess, Annegret Wilde
RNA degradation is critical for synchronising gene expression with changing conditions in prokaryotic and eukaryotic organisms. In bacteria, the preference of the central ribonucleases RNase E, RNa...
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The high-density lipoprotein binding protein HDLBP is an unusual RNA-binding protein with multiple roles in cancer and disease RNA Biol. (IF 4.1) Pub Date : 2024-03-13 Jonathan Feicht, Ralf-Peter Jansen
The high-density lipoprotein binding protein (HDLBP) is the human member of an evolutionarily conserved family of RNA-binding proteins, the vigilin protein family. These proteins are characterized ...
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An elusive debate on the evidence for RNA editing in SARS-CoV-2 RNA Biol. (IF 4.1) Pub Date : 2024-03-01 Giorgio Mattiuz, Salvatore Di Giorgio, Silvestro G. Conticello
Published in RNA Biology (Vol. 21, No. 1, 2024)
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Urea supplementation improves mRNA in vitro transcription by decreasing both shorter and longer RNA byproducts RNA Biol. (IF 4.1) Pub Date : 2024-02-27 Combes Francis, Pettersson Frida J, Bui Thanh-Huong, Molska Alicja, Komissarov Artem, Parot Jérémie, Borgos Sven Even
The current letter to the editor describes the presence of RNA byproducts in small-scale in vitro transcription (IVT) reactions as evaluated by capillary gel electrophoresis, asymmetric flow field ...
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Single-cell analysis of the epitranscriptome: RNA modifications under the microscope RNA Biol. (IF 4.1) Pub Date : 2024-02-18 Eva Crespo-García, Alberto Bueno-Costa, Manel Esteller
The identification of mechanisms capable of modifying genetic information by the addition of covalent RNA modifications distinguishes a level of complexity in gene expression which challenges key l...
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Mature microRNA-binding protein QKI promotes microRNA-mediated gene silencing RNA Biol. (IF 4.1) Pub Date : 2024-02-19 Kyung-Won Min, Myung Hyun Jo, Minseok Song, Ji Won Lee, Min Ji Shim, Kyungmin Kim, Hyun Bong Park, Shinwon Ha, Hyejin Mun, Ahsan Polash, Markus Hafner, Jung-Hyun Cho, Dongsan Kim, Ji-Hoon Jeong, Seungbeom Ko, Sungchul Hohng, Sung-Ung Kang, Je-Hyun Yoon
Although Argonaute (AGO) proteins have been the focus of microRNA (miRNA) studies, we observed AGO-free mature miRNAs directly interacting with RNA-binding proteins, implying the sophisticated natu...
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RNA-dependent proteome solubility maintenance in Escherichia coli lysates analysed by quantitative mass spectrometry: Proteomic characterization in terms of isoelectric point, structural disorder, functional hub, and chaperone network RNA Biol. (IF 4.1) Pub Date : 2024-02-15 Chan Park, Bitnara Han, Yura Choi, Yoontae Jin, Kwang Pyo Kim, Seong Il Choi, Baik L. Seong
Protein aggregation, a consequence of misfolding and impaired proteostasis, can lead to cellular malfunctions such as various proteinopathies. The mechanisms protecting proteins from aggregation in...
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MRM-BERT: a novel deep neural network predictor of multiple RNA modifications by fusing BERT representation and sequence features RNA Biol. (IF 4.1) Pub Date : 2024-02-15 Linshu Wang, Yuan Zhou
RNA modifications play crucial roles in various biological processes and diseases. Accurate prediction of RNA modification sites is essential for understanding their functions. In this study, we pr...
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Small molecule inhibition of RNA binding proteins in haematologic cancer RNA Biol. (IF 4.1) Pub Date : 2024-02-08 Amit K. Jaiswal, Michelle L. Thaxton, Georgia M. Scherer, Jacob P. Sorrentino, Neil K. Garg, Dinesh S. Rao
In recent years, advances in biomedicine have revealed an important role for post-transcriptional mechanisms of gene expression regulation in pathologic conditions. In cancer in general and leukaem...
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Epitranscriptomic regulation in fasting hearts: implications for cardiac health RNA Biol. (IF 4.1) Pub Date : 2024-02-07 Daniel Benak, Kristyna Holzerova, Jaroslav Hrdlicka, Frantisek Kolar, Mark Olsen, Mati Karelson, Marketa Hlavackova
Cardiac tolerance to ischaemia can be increased by dietary interventions such as fasting, which is associated with significant changes in myocardial gene expression. Among the possible mechanisms o...
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MiRNAs differentially expressed in vegetative and reproductive organs of Marchantia polymorpha – insights into their expression pattern, gene structures and function RNA Biol. (IF 4.1) Pub Date : 2024-02-01 Bharti Aggarwal, Wojciech Maciej Karlowski, Przemyslaw Nuc, Artur Jarmolowski, Zofia Szweykowska-Kulinska, Halina Pietrykowska
MicroRNAs regulate gene expression affecting a variety of plant developmental processes. The evolutionary position of Marchantia polymorpha makes it a significant model to understand miRNA-mediated...
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Expression of RNautophagy/DNautophagy-related genes is regulated under control of an innate immune receptor RNA Biol. (IF 4.1) Pub Date : 2024-01-10 Yuuki Fujiwara, Kazuki Oroku, Yinping Zhou, Masayuki Takahashi, Taiichi Katayama, Keiji Wada, Nobuyuki Tsutsumi, Tetsuo Sato, Tomohiro Kabuta
Double-stranded RNA (dsRNA) is a molecular pattern uniquely produced in cells infected with various viruses as a product or byproduct of replication. Cells detect such molecules, which indicate non...
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Small RNA-big impact: exosomal miRNAs in mitochondrial dysfunction in various diseases RNA Biol. (IF 4.1) Pub Date : 2024-01-04 Xiaqing Li, Yi Han, Yu Meng, Lianghong Yin
Mitochondria are multitasking organelles involved in maintaining the cell homoeostasis. Beyond its well-established role in cellular bioenergetics, mitochondria also function as signal organelles t...
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Ordering events in a developing genetic code RNA Biol. (IF 4.1) Pub Date : 2024-01-03 Michael Yarus
Preexisting partial genetic codes can fuse to evolve towards the complete Standard Genetic Code (SGC). Such code fusion provides a path of ‘least selection’, readily generating precursor codes that...
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Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis RNA Biol. (IF 4.1) Pub Date : 2023-12-29 Thiruvenkadam Shanmugam, Palak Chaturvedi, Deniz Streit, Arindam Ghatak, Thorsten Bergelt, Stefan Simm, Wolfram Weckwerth, Enrico Schleiff
Arabidopsis contains hundreds of ribosomal DNA copies organized within the nucleolar organizing regions (NORs) in chromosomes 2 and 4. There are four major types of variants of rDNA, VAR1–4, based ...
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A comparative survey of the influence of small self-cleaving ribozymes on gene expression in human cell culture RNA Biol. (IF 4.1) Pub Date : 2023-12-25 Dennis Kläge, Elisabeth Müller, Jörg S. Hartig
Self-cleaving ribozymes are versatile tools for synthetic biologists when it comes to controlling gene expression. Up to date, 12 different classes are known, and over the past decades more and mor...
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LncRNA USP2-AS1 facilitates the osteogenic differentiation of bone marrow mesenchymal stem cells by targeting KDM3A/ETS1/USP2 to activate the Wnt/β-catenin signaling pathway RNA Biol. (IF 4.1) Pub Date : 2023-12-22 Wanxin Luo, Na Zhang, Ziping Wang, Hao Chen, Jie Sun, Chen Yao, Yafeng Zhang
Human bone marrow mesenchymal stem cells (HBMSCs) can promote new bone formation. Previous studies have proven the ability of long non-coding RNAs (lncRNAs) to modulate the osteogenic differentiati...
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CCAR-1 works together with the U2AF large subunit UAF-1 to regulate alternative splicing RNA Biol. (IF 4.1) Pub Date : 2023-12-21 Doreen I. Lugano, Lindsey N. Barrett, Dale Chaput, Margaret A. Park, Sandy D. Westerheide
The Cell Division Cycle and Apoptosis Regulator (CCAR) protein family members have recently emerged as regulators of alternative splicing and transcription, as well as having other key physiologica...
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Structure and function of the pseudouridine 5’-monophosphate glycosylase PUMY from Arabidopsis thaliana RNA Biol. (IF 4.1) Pub Date : 2023-12-20 Jeongyun Lee, Sang-Hoon Kim, Sangkee Rhee
Pseudouridine is a noncanonical C-nucleoside containing a C-C glycosidic linkage between uracil and ribose. In the two-step degradation of pseudouridine, pseudouridine 5’-monophosphate glycosylase ...
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Circular RNAs in non-alcoholic fatty liver disease: Functions and clinical significance RNA Biol. (IF 4.1) Pub Date : 2023-12-19 Qingmin Zeng, Chang-Hai Liu, Javier Ampuero, Dongbo Wu, Wei Jiang, Lingyun Zhou, Hong Li, Lang Bai, Manuel Romero-Gómez, Hong Tang
Nonalcoholic fatty liver disease (NAFLD), which affects approximately 25% of the global population, is an urgent health issue leading to various metabolic comorbidities. Circular RNAs (circRNAs), c...
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The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking RNA Biol. (IF 4.1) Pub Date : 2023-12-19 Daniel P. Neumann, Katherine A. Pillman, B. Kate Dredge, Andrew G. Bert, Caroline A. Phillips, Rachael Lumb, Yesha Ramani, Cameron P. Bracken, Brett G. Hollier, Luke A. Selth, Traude H. Beilharz, Gregory J. Goodall, Philip A. Gregory
Epithelial-mesenchymal transition (EMT) plays important roles in tumour progression and is orchestrated by dynamic changes in gene expression. While it is well established that post-transcriptional...
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Post-transcriptional regulation of BIRC5/survivin expression and induction of apoptosis in breast cancer cells by tristetraprolin RNA Biol. (IF 4.1) Pub Date : 2023-12-18 Suhad Al-Yahya, Maher Al-Saif, Maha Al-Ghamdi, Walid Moghrabi, Khalid S.A. Khabar, Norah Al-Souhibani
Inhibition of apoptosis is one of the hallmarks of cancer and is a target of various therapeutic interventions. BIRC5 is an inhibitor of apoptosis that is aberrantly expressed in cancer leading to ...
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Multiple Oligo assisted RNA Pulldown via Hybridization followed by Mass Spectrometry (MORPH-MS) for exploring the RNA-Protein interactions RNA Biol. (IF 4.1) Pub Date : 2023-12-17 Priyanka Pant, Regalla Kumarswamy
Understanding RNA-protein interactions is crucial for deciphering the cellular functions and molecular mechanisms of regulatory RNAs. Consequently, there is a constant need to develop innovative an...
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Structural and computational studies of HIV-1 RNA RNA Biol. (IF 4.1) Pub Date : 2023-12-15 Lev Levintov, Harish Vashisth
Viruses remain a global threat to animals, plants, and humans. The type 1 human immunodeficiency virus (HIV-1) is a member of the retrovirus family and carries an RNA genome, which is reverse trans...
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Therapeutic potential of natural antisense transcripts and various mechanisms involved for clinical applications and disease prevention RNA Biol. (IF 4.1) Pub Date : 2023-12-13 Ashiq Ali, Aisha Khatoon, Chenran Shao, Bilal Murtaza, Qaisar Tanveer, Zhongjing Su
Antisense transcription, a prevalent occurrence in mammalian genomes, gives rise to natural antisense transcripts (NATs) as RNA molecules. These NATs serve as agents of diverse transcriptional and ...
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Unraveling C-to-U RNA editing events from direct RNA sequencing RNA Biol. (IF 4.1) Pub Date : 2023-12-13 Adriano Fonzino, Caterina Manzari, Paola Spadavecchia, Uday Munagala, Serena Torrini, Silvestro Conticello, Graziano Pesole, Ernesto Picardi
In mammals, RNA editing events involve the conversion of adenosine (A) in inosine (I) by ADAR enzymes or the hydrolytic deamination of cytosine (C) in uracil (U) by the APOBEC family of enzymes, mo...
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mRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts RNA Biol. (IF 4.1) Pub Date : 2023-12-13 Alexander F. Palazzo, Yi Qiu, Yoon Mo Kang
The division of the cellular space into nucleoplasm and cytoplasm promotes quality control mechanisms that prevent misprocessed mRNAs and junk RNAs from gaining access to the translational machiner...
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The nexus of long noncoding RNAs, splicing factors, alternative splicing and their modulations RNA Biol. (IF 4.1) Pub Date : 2023-11-28 Pushkar Malakar, Sudhanshu Shukla, Meghna Mondal, Rajesh Kumar Kar, Jawed Akhtar Siddiqui
The process of alternative splicing (AS) is widely deregulated in a variety of cancers. Splicing is dependent upon splicing factors. Recently, several long noncoding RNAs (lncRNAs) have been shown ...
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Recent progress in miRNA biogenesis and decay RNA Biol. (IF 4.1) Pub Date : 2023-11-29 Xavier Bofill-De Ros, Ulf Andersson Vang Ørom
MicroRNAs are a class of small regulatory RNAs that mediate regulation of protein synthesis by recognizing sequence elements in mRNAs. MicroRNAs are processed through a series of steps starting fro...
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Post-transcriptional capping generates coenzyme A-linked RNA RNA Biol. (IF 4.1) Pub Date : 2023-11-30 Krishna Sapkota, Jordyn K. Lucas, Jarrett W. Faulkner, Matt F. Lichte, Yan-Lin Guo, Donald H. Burke, Faqing Huang
NAD can be inserted co-transcriptionally via non-canonical initiation to form NAD-RNA. However, that mechanism is unlikely for CoA-linked RNAs due to low intracellular concentration of the required...
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Discovering microproteins: making the most of ribosome profiling data RNA Biol. (IF 4.1) Pub Date : 2023-11-27 Sonia Chothani, Lena Ho, Sebastian Schafer, Owen Rackham
Building a reference set of protein-coding open reading frames (ORFs) has revolutionized biological process discovery and understanding. Traditionally, gene models have been confirmed using cDNA se...
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Determinants of DNMT2/TRDMT1 preference for substrates tRNA and DNA during the evolution RNA Biol. (IF 4.1) Pub Date : 2023-11-15 Huari Li, Daiyun Zhu, Yapeng Yang, Yunfei Ma, Yong Chen, Pingfang Xue, Juan Chen, Mian Qin, Dandan Xu, Chao Cai, Hongjing Cheng
RNA methyltransferase DNMT2/TRDMT1 is the most conserved member of the DNMT family from bacteria to plants and mammals. In previous studies, we found some determinants for tRNA recognition of DNMT2...
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Streptomyces rare codon UUA: from features associated with 2 adpA related locations to candidate phage regulatory translational bypassing RNA Biol. (IF 4.1) Pub Date : 2023-11-15 Ivan V. Antonov, Sinéad O’Loughlin, Alessandro N. Gorohovski, Patrick B.F. O’Connor, Pavel V. Baranov, John F. Atkins
In Streptomyces species, the cell cycle involves a switch from an early and vegetative state to a later phase where secondary products including antibiotics are synthesized, aerial hyphae form and ...
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Long non-coding RNA APDC plays important regulatory roles in metabolism of bone and adipose tissues RNA Biol. (IF 4.1) Pub Date : 2023-11-13 Yao Liu, Zoe Xiaofang Zhu, Elissa K. Zboinski, Wei Qiu, Junxiang Lian, Shibo Liu, Thomas E. Van Dyke, Hans E. Johansson, Qisheng Tu, En Luo, Jake Jinkun Chen
The long noncoding RNA (lncR) ANRIL in the human genome is an established genetic risk factor for atherosclerosis, periodontitis, diabetes, and cancer. However, the regulatory role of lncR-ANRIL in...
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Diverse roles of biomolecular condensation in eukaryotic translational regulation RNA Biol. (IF 4.1) Pub Date : 2023-10-31 Yuhan Zhang, Jun-Yan Kang, Mofang Liu, Ying Huang
Biomolecular condensates, forming membrane-less organelles, orchestrate the sub-cellular compartment to execute designated biological processes. An increasing body of evidence demonstrates the invo...
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Regulation and function of alternative polyadenylation in development and differentiation RNA Biol. (IF 4.1) Pub Date : 2023-10-31 Lorenzo Gallicchio, Gonzalo H. Olivares, Cameron W. Berry, Margaret T. Fuller
Alternative processing of nascent mRNAs is widespread in eukaryotic organisms and greatly impacts the output of gene expression. Specifically, alternative cleavage and polyadenylation (APA) is a co...
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Circular RNAs: biology and clinical significance of breast cancer RNA Biol. (IF 4.1) Pub Date : 2023-10-26 Zhanwei Wang, Hao Deng, Yao Jin, Meng Luo, Jia Huang, Jing Wang, Kun Zhang, Li Wang, Jiaojiao Zhou
Circular RNAs (circRNAs) are novel noncoding RNAs with covalently closed-loop structures that can regulate eukaryotic gene expression. Due to their stable structure, circRNAs are widely distributed...
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Regulatory circular RNAs in viral diseases: applications in diagnosis and therapy RNA Biol. (IF 4.1) Pub Date : 2023-10-26 Wei Wang, Lei Sun, Meng-Ting Huang, Yun Quan, Tao Jiang, Zhichao Miao, Qiong Zhang
Circular RNA (circRNA) forms closed loops via back-splicing in precursor mRNA, resisting exonuclease degradation. In higher eukaryotes, protein-coding genes create circRNAs through exon back-splici...
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An efficient, scarless, selection-free technology for phage engineering RNA Biol. (IF 4.1) Pub Date : 2023-10-16 Moran G. Goren, Tridib Mahata, Udi Qimron
Most recently developed phage engineering technologies are based on the CRISPR-Cas system. Here, we present a non-CRISPR-based method for genetically engineering the Escherichia coli phages T5, T7,...
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Maturation of small nucleolar RNAs: from production to function RNA Biol. (IF 4.1) Pub Date : 2023-10-05 Sarah F. Webster, Homa Ghalei
Small Nucleolar RNAs (snoRNAs) are an abundant group of non-coding RNAs with well-defined roles in ribosomal RNA processing, folding and chemical modification. Besides their classic roles in riboso...
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Synergistic correlation between host angiogenin and dengue virus replication RNA Biol. (IF 4.1) Pub Date : 2023-10-05 Deeksha Madhry, Shivani Malvankar, Sushant Phadnis, Rupesh K. Srivastava, Sankar Bhattacharyya, Bhupendra Verma
DENV infection poses a major health concern globally and the pathophysiology relies heavily on host-cellular machinery. Although virus replication relies heavily on the host, the mechanistic detail...
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Anticodon sequence determines the impact of mistranslating tRNAAla variants RNA Biol. (IF 4.1) Pub Date : 2023-09-30 Ecaterina Cozma, Megha Rao, Madison Dusick, Julie Genereaux, Ricard A. Rodriguez-Mias, Judit Villén, Christopher J. Brandl, Matthew D. Berg
Transfer RNAs (tRNAs) maintain translation fidelity through accurate charging by their cognate aminoacyl-tRNA synthetase and codon:anticodon base pairing with the mRNA at the ribosome. Mistranslati...
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Characterization of CoCas9 nuclease from Capnocytophaga ochracea RNA Biol. (IF 4.1) Pub Date : 2023-09-24 A. Vasileva, P. Selkova, A. Arseniev, M. Abramova, N. Shcheglova, O. Musharova, I. Mizgirev, T. Artamonova, M. Khodorkovskii, K. Severinov, I. Fedorova
Cas9 nucleases are widely used for genome editing and engineering. Cas9 enzymes encoded by CRISPR-Cas defence systems of various prokaryotic organisms possess different properties such as target si...
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A conserved HOTAIRM1-HOXA1 regulatory axis contributes early to neuronal differentiation RNA Biol. (IF 4.1) Pub Date : 2023-09-24 Dana Segal, Samy Coulombe, Jasper Sim, Josée Dostie
HOTAIRM1 is unlike most long non-coding RNAs in that its sequence is highly conserved across mammals. Such evolutionary conservation points to it having a role in key cellular processes. We previou...
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Endonucleolytic processing plays a critical role in the maturation of ribosomal RNA in Methanococcus maripaludis RNA Biol. (IF 4.1) Pub Date : 2023-09-20 Lei Qi, Huan Liu, Jian Gao, Kai Deng, Xiaoyan Wang, Xiuzhu Dong, Jie Li
Ribosomal RNA (rRNA) processing and maturation are fundamentally important for ribosome biogenesis, but the mechanisms in archaea, the third form of life, remains largely elusive. This study aimed ...
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Translational control of murine adiponectin expression by an upstream open reading frame element RNA Biol. (IF 4.1) Pub Date : 2023-09-13 Kommireddy Vasu, Iyappan Ramachandiran, Aayushi Chechi, Krishnendu Khan, Debjit Khan, Randall Kaufman, Paul L. Fox
ABSTRACT Adiponectin, an adipocyte-specific secretory protein encoded by the ADIPOQ gene has a causal role in insulin resistance. Anti-diabetic drugs increase plasma adiponectin by a poorly understood, post-transcriptional mechanism enhancing insulin sensitivity. Deletion analysis of a reporter bearing the mouse Adipoq mRNA 5’-leader identified an inhibitory cis-regulatory sequence. The 5’-leader harbours
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Lamotrigine compromises the fidelity of initiator tRNA recruitment to the ribosomal P-site by IF2 and the RbfA release from 30S ribosomes in Escherichia coli RNA Biol. (IF 4.1) Pub Date : 2023-09-07 Sudhir Singh, Kuldeep Lahry, Chandra Sekhar Mandava, Jitendra Singh, Riyaz Ahmad Shah, Suparna Sanyal, Umesh Varshney
ABSTRACT Lamotrigine (Ltg), an anticonvulsant drug, targets initiation factor 2 (IF2), compromises ribosome biogenesis and causes toxicity to Escherichia coli. However, our understanding of Ltg toxicity in E. coli remains unclear. While our in vitro assays reveal no effects of Ltg on the ribosome-dependent GTPase activity of IF2 or its role in initiation as measured by dipeptide formation in a fast
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DMD antisense oligonucleotide mediated exon skipping efficiency correlates with flanking intron retention time and target position within the exon RNA Biol. (IF 4.1) Pub Date : 2023-09-04 Remko Goossens, Nisha Verwey, Yavuz Ariyurek, Fred Schnell, Annemieke Aartsma-Rus
ABSTRACT Mutations in the DMD gene are causative for Duchenne muscular dystrophy (DMD). Antisense oligonucleotide (AON) mediated exon skipping to restore disrupted dystrophin reading frame is a therapeutic approach that allows production of a shorter but functional protein. As DMD causing mutations can affect most of the 79 exons encoding dystrophin, a wide variety of AONs are needed to treat the patient
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A full repertoire of Hemiptera genomes reveals a multi-step evolutionary trajectory of auto-RNA editing site in insect Adar gene RNA Biol. (IF 4.1) Pub Date : 2023-09-07 Ling Ma, Caiqing Zheng, Shiwen Xu, Ye Xu, Fan Song, Li Tian, Wanzhi Cai, Hu Li, Yuange Duan
ABSTRACT Adenosine-to-inosine (A-to-I) RNA editing, mediated by metazoan ADAR enzymes, is a prevalent post-transcriptional modification that diversifies the proteome and promotes adaptive evolution of organisms. The Drosophila Adar gene has an auto-recoding site (termed S>G site) that forms a negative-feedback loop and stabilizes the global editing activity. However, the evolutionary trajectory of
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Shortened CRISPR-Cas9 arrays enable multiplexed gene targeting in bacteria from a smaller DNA footprint RNA Biol. (IF 4.1) Pub Date : 2023-08-31 Sandra Gawlitt, Chunyu Liao, Tatjana Achmedov, Chase L. Beisel
ABSTRACT CRISPR technologies comprising a Cas nuclease and a guide RNA (gRNA) can utilize multiple gRNAs to enact multi-site editing or regulation in the same cell. Nature devised a highly compact means of encoding gRNAs in the form of CRISPR arrays composed of conserved repeats separated by targeting spacers. However, the capacity to acquire new spacers keeps the arrays longer than necessary for CRISPR
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Comprehensive identification of diverse ribosomal RNA modifications by targeted nanopore direct RNA sequencing and JACUSA2 RNA Biol. (IF 4.1) Pub Date : 2023-08-27 Isabel S. Naarmann-de Vries, Christiane Zorbas, Amina Lemsara, Michael Piechotta, Felix G. M. Ernst, Ludivine Wacheul, Denis L. J. Lafontaine, Christoph Dieterich
ABSTRACT Ribosomal RNAs are decorated by numerous post-transcriptional modifications whose exact roles in ribosome biogenesis, function, and human pathophysiology remain largely unknown. Here, we report a targeted direct rRNA sequencing approach involving a substrate selection step and demonstrate its suitability to identify differential modification sites in combination with the JACUSA2 software.
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Characterization of microRNAs in the cyst nematode Heterodera glycines identifies possible candidates involved in cross-kingdom interactions with its host Glycine max RNA Biol. (IF 4.1) Pub Date : 2023-08-20 Dave T. Ste-Croix, Richard R. Bélanger, Benjamin Mimee
ABSTRACT The soybean cyst nematode (SCN – Heterodera glycines) is one of the most damaging pests to the cultivated soybean worldwide. Using a wide array of stylet-secreted effector proteins, this nematode can restructure its host cells into a complex and highly active feeding structure called the syncytium. Tight regulation of these proteins is thought to be essential to the successful formation of
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Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex RNA Biol. (IF 4.1) Pub Date : 2023-08-21 Mor Bordeynik-Cohen, Michal Sperber, Lena Ebbers, Naama Messika-Gold, Constanze Krohs, Tal Koffler-Brill, Yael Noy, Ran Elkon, Hans Gerd Nothwang, Karen B. Avraham
ABSTRACT The peripheral and central auditory subsystems together form a complex sensory network that allows an organism to hear. The genetic programs of the two subsystems must therefore be tightly coordinated during development. Yet, their interactions and common expression pathways have never been systematically explored. MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression
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Research progress of circRNA in malignant tumour metabolic reprogramming RNA Biol. (IF 4.1) Pub Date : 2023-08-20 Yikun Geng, Min Wang, Zhouying Wu, Jianchao Jia, Tingyu Yang, Lan Yu
ABSTRACT Cancer is a multi-factor systemic malignant disease, which has seriously threatened human health and created a heavy burden on the world economy. Metabolic reprogramming, one of the important signs of malignant tumours, provides necessary nutrition for tumorigenesis and cancer development; thus, it has recently become a research hot spot, even though the metabolic mechanism is quite intricate
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Sensing intracellular signatures with synthetic mRNAs RNA Biol. (IF 4.1) Pub Date : 2023-08-15 Hiroki Ono, Hirohide Saito
ABSTRACT The bottom-up assembly of biological components in synthetic biology has contributed to a better understanding of natural phenomena and the development of new technologies for practical applications. Over the past few decades, basic RNA research has unveiled the regulatory roles of RNAs underlying gene regulatory networks; while advances in RNA biology, in turn, have highlighted the potential
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RNA modification-mediated translational control in immune cells RNA Biol. (IF 4.1) Pub Date : 2023-08-16 Yujuan Zhang, Weiguo Hu, Hua-Bing Li
ABSTRACT RNA modifications play a vital role in multiple pathways of mRNA metabolism, and translational regulation is essential for immune cells to promptly respond to stimuli and adapt to the microenvironment. N6-methyladenosine (m6A) methylation, which is the most abundant mRNA modification in eukaryotes, primarily functions in the regulation of RNA splicing and degradation. However, the role of
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Cup is essential for oskar mRNA translational repression during early Drosophila oogenesis RNA Biol. (IF 4.1) Pub Date : 2023-08-08 Livia V. Bayer, Samantha Milano, Stephen K. Formel, Harpreet Kaur, Rishi Ravichandran, Juan A. Cambeiro, Lizaveta Slinko, Irina E. Catrina, Diana P. Bratu
ABSTRACT Study of the timing and location for mRNA translation across model systems has begun to shed light on molecular events fundamental to such processes as intercellular communication, morphogenesis, and body pattern formation. In D. melanogaster, the posterior mRNA determinant, oskar, is transcribed maternally but translated only when properly localized at the oocyte’s posterior cortex. Two effector
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Inefficient splicing of long non-coding RNAs is associated with higher transcript complexity in human and mouse RNA Biol. (IF 4.1) Pub Date : 2023-08-06 Koushiki Basu, Anubha Dey, Manjari Kiran
ABSTRACT Recent reports show that long non-coding RNAs (lncRNAs) have inefficient splicing and fewer alternative splice variants than mRNAs. Here, we have explored the efficiency of lncRNAs and mRNAs in producing various splice variants, given the number of exons in humans and mice. Intriguingly, lncRNAs produce more splice variants per exon, referred to as Transcript Complexity, than mRNAs. Most lncRNA
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Pre-mRNA splicing-associated diseases and therapies RNA Biol. (IF 4.1) Pub Date : 2023-08-01 Sierra L. Love, Joseph D. Emerson, Kazunori Koide, Aaron A. Hoskins
ABSTRACT Precursor mRNA (pre-mRNA) splicing is an essential step in human gene expression and is carried out by a large macromolecular machine called the spliceosome. Given the spliceosome's role in shaping the cellular transcriptome, it is not surprising that mutations in the splicing machinery can result in a range of human diseases and disorders (spliceosomopathies). This review serves as an introduction