RNA Biology, Volume 20, Issue 1 (2023)

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RNA Biology, Volume 20, Issue 1 (2023)

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Research Paper

Article
Dynamic and static circulating cancer microRNA biomarkers – a validation study
Masood Abu-Halima, Andreas Keller, Lea Simone Becker, Ulrike Fischer, Annika Engel, Nicole Ludwig, Fabian Kern, Trine B. Rounge, Hilde Langseth, Eckart Meese & Verena Keller
Pages: 1-9
Published online: 13 Dec 2022
AbstractforDynamic and static circulating cancer microRNA biomarkers – a validation study | Full Text | References | PDF (1 MB) | EPUB | Supplemental
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Open Access
Article
A variant of guanidine-IV riboswitches exhibits evidence of a distinct ligand specificity
Felina Lenkeit, Iris Eckert, Malte Sinn, Franziskus Hauth, Jörg S. Hartig & Zasha Weinberg
Pages: 10-19
Published online: 22 Dec 2022
AbstractforA variant of guanidine-IV riboswitches exhibits evidence of a distinct ligand specificity | Full Text | References | PDF (1 MB) | EPUB | Supplemental
  • 1309 Views
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Open Access
Article
A beneficial fungal root endophyte triggers systemic RNA silencing and DNA methylation of a host reporter gene
Athanasios Dalakouras, Afrodite Katsaouni, Marianna Avramidou, Elena Dadami, Olga Tsiouri, Sotirios Vasileiadis, Athanasios Makris, Maria Eleni Georgopoulou & Kalliope K. Papadopoulou
Pages: 20-30
Published online: 27 Dec 2022
AbstractforA beneficial fungal root endophyte triggers systemic RNA silencing and DNA methylation of a host reporter gene | Full Text | References | PDF (8.2 MB) | EPUB | Supplemental
  • 2357 Views
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Open Access
Article
Identification of circular RNAs hosted by the RPGR ORF15 genomic locus
Tatyana Appelbaum, Gustavo D. Aguirre & William A. Beltran
Pages: 31-47
Published online: 02 Jan 2023
AbstractforIdentification of circular RNAs hosted by the RPGR ORF15 genomic locus | Full Text | References | PDF (6 MB) | EPUB | Supplemental
  • 1741 Views
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Open Access
Article
On distinguishing between canonical tRNA genes and tRNA gene fragments in prokaryotes
Peter T.S. van der Gulik, Martijn Egas, Ken Kraaijeveld, Nina Dombrowski, Astrid T. Groot, Anja Spang, Wouter D. Hoff & Jenna Gallie
Pages: 48-58
Published online: 02 Feb 2023
AbstractforOn distinguishing between canonical tRNA genes and tRNA gene fragments in prokaryotes | Full Text | References | PDF (5.7 MB) | EPUB | Supplemental
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Open Access
Article
Hfq protein and GcvB small RNA tailoring of oppA target mRNA to levels allowing translation activation by MicF small RNA in Escherichia coli
Marie-Claude Carrier, David Lalaouna & Eric Massé
Pages: 59-76
Published online: 01 Mar 2023
AbstractforHfq protein and GcvB small RNA tailoring of oppA target mRNA to levels allowing translation activation by MicF small RNA in Escherichia coli | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
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Open Access

Brief Communication

Brief Report
Escherichia coli transcriptome assembly from a compendium of RNA-seq data sets
Brian Tjaden
Pages: 77-84
Published online: 15 Mar 2023
AbstractforEscherichia coli transcriptome assembly from a compendium of RNA-seq data sets | Full Text | References | PDF (1.3 MB) | EPUB | Supplemental
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Open Access

Technical Paper

Report
A translational repression reporter assay for the analysis of RNA-binding protein consensus sites
Jessica Nowacki, Mateo Malenica, Stefan Schmeing, Damian Schiller, Benjamin Buchmuller, Gulshan Amrahova & Peter ‘t Hart
Pages: 85-94
Published online: 22 Mar 2023
AbstractforA translational repression reporter assay for the analysis of RNA-binding protein consensus sites | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 1489 Views
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Open Access

Research Paper

Article
Transcription termination complex, Rtt103-Rai1-Rat1, regulates sub-telomeric transcripts in Saccharomyces cerevisiae
Kathirvel Ramalingam & Krishnaveni Mishra
Pages: 95-108
Published online: 27 Mar 2023
AbstractforTranscription termination complex, Rtt103-Rai1-Rat1, regulates sub-telomeric transcripts in Saccharomyces cerevisiae | Full Text | References | PDF (7.5 MB) | EPUB | Supplemental
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Open Access

Review

Review
Cross-kingdom small RNA communication between plants and fungal phytopathogens-recent updates and prospects for future agriculture
Bijayalaxmi Mahanty, Rukmini Mishra & Raj Kumar Joshi
Pages: 109-119
Published online: 29 Mar 2023
AbstractforCross-kingdom small RNA communication between plants and fungal phytopathogens-recent updates and prospects for future agriculture | Full Text | References | PDF (1.1 MB) | EPUB
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Research Paper

Article
Ribonuclease E strongly impacts bacterial adaptation to different growth conditions
Janek Börner, Tobias Friedrich, Marek Bartkuhn & Gabriele Klug
Pages: 120-135
Published online: 29 Mar 2023
AbstractforRibonuclease E strongly impacts bacterial adaptation to different growth conditions | Full Text | References | PDF (8.3 MB) | EPUB | Supplemental
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Review

Review
Small regulatory RNAs: from bench to bedside – a keystone symposia meeting report
Soo Mi Lee, Michael T. Winters, Ivan Martinez & Frank J. Slack
Pages: 136-139
Published online: 04 Apr 2023
AbstractforSmall regulatory RNAs: from bench to bedside – a keystone symposia meeting report | Full Text | References | PDF (241 KB) | EPUB
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Open Access

Research paper

Article
L1CAM immunocapture generates a unique extracellular vesicle population with a reproducible miRNA fingerprint
Rachael Anne Dunlop, Sandra Anne Banack & Paul Alan Cox
Pages: 140-148
Published online: 11 Apr 2023
AbstractforL1CAM immunocapture generates a unique extracellular vesicle population with a reproducible miRNA fingerprint | Full Text | References | PDF (474.3 KB) | EPUB | Supplemental
  • 2363 Views
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Open Access
Article
Proteins Rpr2 and Pop3 increase the activity and thermal stability of yeast RNase P
Anna Perederina, Igor Berezin & Andrey S. Krasilnikov
Pages: 149-153
Published online: 19 Apr 2023
AbstractforProteins Rpr2 and Pop3 increase the activity and thermal stability of yeast RNase P | Full Text | References | PDF (4.7 MB) | EPUB | Supplemental
  • 802 Views
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Review

Review
Nucleic acid strand displacement – from DNA nanotechnology to translational regulation
Friedrich C. Simmel
Pages: 154-163
Published online: 24 Apr 2023
AbstractforNucleic acid strand displacement – from DNA nanotechnology to translational regulation | Full Text | References | PDF (1.5 MB) | EPUB
  • 3033 Views
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Research Paper

Article
MiR-2b-2-5p regulates lipid metabolism and reproduction by targeting CREB in Bactrocera dorsalis
Shengfeng Zhang, Junfei Xie, Rengang Luo, Hongyu Zhang & Weiwei Zheng
Pages: 164-176
Published online: 24 Apr 2023
AbstractforMiR-2b-2-5p regulates lipid metabolism and reproduction by targeting CREB in Bactrocera dorsalis | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
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Open Access

Review

Review
The Importance of Being RNA-est: considering RNA-mediated ribosome plasticity
Christian Trahan & Marlene Oeffinger
Pages: 177-185
Published online: 26 Apr 2023
AbstractforThe Importance of Being RNA-est: considering RNA-mediated ribosome plasticity | Full Text | References | PDF (930.5 KB) | EPUB
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Open Access

Research Paper

Article
Prior metabolite extraction fully preserves RNAseq quality and enables integrative multi-‘omics analysis of the liver metabolic response to viral infection
Zachary B Madaj, Michael S. Dahabieh, Vijayvardhan Kamalumpundi, Brejnev Muhire, J. Pettinga (Dean) , Rebecca A. Siwicki, Abigail E. Ellis, Christine Isaguirre, Martha L. Escobar Galvis, Lisa DeCamp, Russell G. Jones, Scott A. Givan, Marie Adams & Ryan D. Sheldon
Pages: 186-197
Published online: 24 Apr 2023
AbstractforPrior metabolite extraction fully preserves RNAseq quality and enables integrative multi-‘omics analysis of the liver metabolic response to viral infection | Full Text | References | PDF (9.3 MB) | EPUB | Supplemental
  • 2331 Views
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Open Access

Review

Review
Synthetic biology tools to promote the folding and function of RNA aptamers in mammalian cells
Qian Hou & Samie R. Jaffrey
Pages: 198-206
Published online: 02 May 2023
AbstractforSynthetic biology tools to promote the folding and function of RNA aptamers in mammalian cells | Full Text | References | PDF (457.2 KB) | EPUB
  • 3019 Views
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Open Access
Review Article
The potential regulatory role of RNA methylation in ovarian cancer
Shijie Zhao, Mengxue Zhang, Xiaolan Zhu, Jie Xing, Jiaming Zhou & Xinming Yin
Pages: 207-218
Published online: 16 May 2023
AbstractforThe potential regulatory role of RNA methylation in ovarian cancer | Full Text | References | PDF (5.6 MB) | EPUB
  • 2044 Views
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Open Access

Commentary

Article Commentary
The continuing discovery on the evidence for RNA editing in SARS-CoV-2
Xiaoxin Pu, Qinwei Xu, Jinxiang Wang & Baoyi Liu
Pages: 219-222
Published online: 18 May 2023
AbstractforThe continuing discovery on the evidence for RNA editing in SARS-CoV-2 | Full Text | References | PDF (1.1 MB) | EPUB
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Open Access

Review

Review Article
The impact of RNA binding proteins and the associated long non-coding RNAs in the TCA cycle on cancer pathogenesis
Tao Shen, Haiyang Wang, Bin Tang, Guoping Zhu & Xiangting Wang
Pages: 223-234
Published online: 23 May 2023
AbstractforThe impact of RNA binding proteins and the associated long non-coding RNAs in the TCA cycle on cancer pathogenesis | Full Text | References | PDF (801.8 KB) | EPUB
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Open Access

Research Paper

Article
Impact of phage predation on P. aeruginosa adhered to human airway epithelium: major transcriptomic changes in metabolism and virulence-associated genes
Ana C. Brandão, Leena Putzeys, Diana P. Pires, Marleen Voet, Jan Paeshuyse, Joana Azeredo & Rob Lavigne
Pages: 235-247
Published online: 24 May 2023
AbstractforImpact of phage predation on P. aeruginosa adhered to human airway epithelium: major transcriptomic changes in metabolism and virulence-associated genes | Full Text | References | PDF (6.9 MB) | EPUB | Supplemental
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Open Access
Article
PacBio full-length transcriptome analysis provides new insights into transcription of chloroplast genomes
Jinsong Shi, Shuangyong Yan, Wenjing Li, Xiurong Yang, Zhongqiu Cui, Junling Li, Guangsheng Li, Yuejiao Li, Yanping Hu & Shan Gao
Pages: 248-256
Published online: 25 May 2023
AbstractforPacBio full-length transcriptome analysis provides new insights into transcription of chloroplast genomes | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 811 Views
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Open Access
Article
Human nucleolar protein 7 (NOL7) is required for early pre-rRNA accumulation and pre-18S rRNA processing
Mason A. McCool, Carson J. Bryant, Hannah Huang, Lisa M. Ogawa, Katherine I. Farley-Barnes, Samuel B. Sondalle, Laura Abriola, Yulia V. Surovtseva & Susan J. Baserga
Pages: 257-271
Published online: 29 May 2023
AbstractforHuman nucleolar protein 7 (NOL7) is required for early pre-rRNA accumulation and pre-18S rRNA processing | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 1114 Views
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Open Access

Research Article

Article
Biochemistry-informed design selects potent siRNAs against SARS-CoV-2
Élisabeth Houbron, Sophie Mockly, Sophia Rafasse, Nathalie Gros, Delphine Muriaux & Hervé Seitz
Pages: 272-280
Published online: 04 Jun 2023
AbstractforBiochemistry-informed design selects potent siRNAs against SARS-CoV-2 | Full Text | References | PDF (9.3 MB) | EPUB | Supplemental
  • 807 Views
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Open Access

Research Paper

Article
Hybrid-seq deciphers the complex transcriptional profile of the human BRCA1 DNA repair associated gene
Panagiotis G. Adamopoulos, Konstantina Athanasopoulou, Michaela A. Boti, Georgios Dimitroulis, Glykeria N. Daneva, Panagiotis Tsiakanikas & Andreas Scorilas
Pages: 281-295
Published online: 04 Jun 2023
AbstractforHybrid-seq deciphers the complex transcriptional profile of the human BRCA1 DNA repair associated gene | Full Text | References | PDF (5.1 MB) | EPUB | Supplemental
  • 1216 Views
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Open Access
Article
PlmCas12e (CasX2) cleavage of CCR5: impact of guide RNA spacer length and PAM sequence on cleavage activity
David A. Armstrong, Taylor R. Hudson, Christine A. Hodge, Thomas H. Hampton, Alexandra L. Howell & Matthew S. Hayden
Pages: 296-305
Published online: 07 Jun 2023
AbstractforPlmCas12e (CasX2) cleavage of CCR5: impact of guide RNA spacer length and PAM sequence on cleavage activity | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
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Open Access

Preface

A special issue dedicated to the memory of Jonathan R. Warner (1936-2019), a pioneer of ribosome biology
Marlene Oeffinger
Page: 306
Published online: 07 Jun 2023
CitationforA special issue dedicated to the memory of Jonathan R. Warner (1936-2019), a pioneer of ribosome biology | Full Text | PDF (155 KB) | EPUB
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Editorial

Editorial
Special focus on the ribosome life cycle
Marlene Oeffinger
Pages: 307-310
Published online: 13 Jun 2023
First Page PreviewforSpecial focus on the ribosome life cycle | Full Text | References | PDF (210.1 KB) | EPUB
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Research Paper

Article
The paralogues MAGOH and MAGOHB are oncogenic factors in high-grade gliomas and safeguard the splicing of cell division and cell cycle genes
Rodrigo A. S. Barreiro, Gabriela D. A. Guardia, Fabiana M. Meliso, Xiufen Lei, Wei-Qing Li, Andre Savio, Martin Fellermeyer, Helena B. Conceição, Rafael L. V. Mercuri, Tesha Landry, Mei Qiao, Lorea Blazquez, Jernej Ule, Luiz O.F. Penalva & Pedro A. F. Galante
Pages: 311-322
Published online: 09 Jun 2023
AbstractforThe paralogues MAGOH and MAGOHB are oncogenic factors in high-grade gliomas and safeguard the splicing of cell division and cell cycle genes | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 1147 Views
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Open Access
Article
Three alternative splicing variants of Loquacious play different roles in miRNA- and siRNA-mediated RNAi pathways in Locusta migratoria
Yanli Wang, Huiyong Li, Xiaojian Liu, Lu Gao, Yunhe Fan, Kun Yan Zhu & Jianzhen Zhang
Pages: 323-333
Published online: 13 Jun 2023
AbstractforThree alternative splicing variants of Loquacious play different roles in miRNA- and siRNA-mediated RNAi pathways in Locusta migratoria | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 891 Views
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Open Access

Review

Review Article
Implications of LncRNAs and CircRNAs in psoriasis: a review
Rongcan Shi, Rui Ma, Xingyu Jiang, Xinyi Tang, Yu Gong, Zengyang Yu & Yuling Shi
Pages: 334-347
Published online: 13 Jun 2023
AbstractforImplications of LncRNAs and CircRNAs in psoriasis: a review | Full Text | References | PDF (1.6 MB) | EPUB
  • 1260 Views
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Review Article
Abasic RNA: its formation and potential role in cellular stress response
Tanya Prashar, Fernand De La Selle & Katalin A. Hudak
Pages: 348-358
Published online: 15 Jun 2023
AbstractforAbasic RNA: its formation and potential role in cellular stress response | Full Text | References | PDF (4.3 MB) | EPUB
  • 1477 Views
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Research Paper

Article
Serine-arginine splicing factor 2 promotes oesophageal cancer progression by regulating alternative splicing of interferon regulatory factor 3
Ziqing Wei, Yuyao Wang, Wenyuan Ma, Wenqing Xing, Peng Lu, Zhijie Shang, Feng Li, Huiyu Li & Yuxuan Wang
Pages: 359-367
Published online: 19 Jun 2023
AbstractforSerine-arginine splicing factor 2 promotes oesophageal cancer progression by regulating alternative splicing of interferon regulatory factor 3 | Full Text | References | PDF (4.2 MB) | EPUB
  • 708 Views
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Open Access
Article
Novel compounds that synergize with aminoglycoside G418 or eRF3 degraders for translational readthrough of nonsense mutant TP53 and PTEN
Angelos Heldin, Matko Cancer, Mireia Palomar-Siles, Susanne Öhlin, Meiqiongzi Zhang, Alexander Sun-Zhang, Anna Mariani, Jianping Liu, Vladimir J.N. Bykov & Klas G. Wiman
Pages: 368-383
Published online: 20 Jun 2023
AbstractforNovel compounds that synergize with aminoglycoside G418 or eRF3 degraders for translational readthrough of nonsense mutant TP53 and PTEN | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 1113 Views
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Open Access

Review

Review Article
RNA-targeted small-molecule drug discoveries: a machine-learning perspective
Huan Xiao, Xin Yang, Yihao Zhang, Zongkang Zhang, Ge Zhang & Bao-Ting Zhang
Pages: 384-397
Published online: 19 Jun 2023
AbstractforRNA-targeted small-molecule drug discoveries: a machine-learning perspective | Full Text | References | PDF (1.8 MB) | EPUB
  • 2402 Views
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Open Access

Research Paper

Article
Characteristics of Human and Microbiome RNA Profiles in Saliva
Fangjia Tong, Gongyu Tang & Xiaowei Wang
Pages: 398-408
Published online: 03 Jul 2023
AbstractforCharacteristics of Human and Microbiome RNA Profiles in Saliva | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 918 Views
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Open Access
Article
Investigating the correlation between Xrn1-resistant RNAs and frameshifter pseudoknots
Ivar W. Dilweg, Megan G. Oskam, Sophie Overbeek & René C.L. Olsthoorn
Pages: 409-418
Published online: 03 Jul 2023
AbstractforInvestigating the correlation between Xrn1-resistant RNAs and frameshifter pseudoknots | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 866 Views
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Technical Paper

Report
Using sno-lncRNAs as potential markers for Prader-Willi syndrome diagnosis
Jiu-Ru Sun, Liang-Zhong Yang, Yang-Li Dai, Huang Wu, Siqi Li, Yi-Feng Xu, Youkui Huang, Hao Wu, Zheng Shen, Chaochun Zou & Ling-Ling Chen
Pages: 419-430
Published online: 05 Jul 2023
AbstractforUsing sno-lncRNAs as potential markers for Prader-Willi syndrome diagnosis | Full Text | References | PDF (5.6 MB) | EPUB | Supplemental
  • 1239 Views
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Research Paper

Article
Characterizing RNA-binding ligands on structures, chemical information, binding affinity and drug-likeness
Cong Fan, Xin Wang, Tianze Ling, Yuedong Yang & Huiying Zhao
Pages: 431-443
Published online: 06 Jul 2023
AbstractforCharacterizing RNA-binding ligands on structures, chemical information, binding affinity and drug-likeness | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 903 Views
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Open Access
Article
SARS-CoV-2 Nsp1 mediated mRNA degradation requires mRNA interaction with the ribosome
Soraya I. Shehata & Roy Parker
Pages: 444-456
Published online: 06 Jul 2023
AbstractforSARS-CoV-2 Nsp1 mediated mRNA degradation requires mRNA interaction with the ribosome | Full Text | References | PDF (7.6 MB) | EPUB | Supplemental
  • 1961 Views
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Open Access

Review

Review Article
Tapping the potential of synthetic riboswitches: reviewing the versatility of the tetracycline aptamer
Daniel Kelvin & Beatrix Suess
Pages: 457-468
Published online: 17 Jul 2023
AbstractforTapping the potential of synthetic riboswitches: reviewing the versatility of the tetracycline aptamer | Full Text | References | PDF (1.3 MB) | EPUB
  • 1585 Views
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Research Paper

Article
Uridylation of the histone mRNA stem-loop weakens binding interactions with SLBP while maintaining interactions with 3’hExo
Morgan Shine, Sarah E. Harris, Kendy A. Pellegrene, Adam H. Kensinger, Mihaela Rita Mihailescu, Jeffrey D. Evanseck & Patrick E. Lackey
Pages: 469-481
Published online: 30 Jul 2023
AbstractforUridylation of the histone mRNA stem-loop weakens binding interactions with SLBP while maintaining interactions with 3’hExo | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 729 Views
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Open Access
Article
Ageing-associated small RNA cargo of extracellular vesicles
Fabian Kern, Thomas Kuhn, Nicole Ludwig, Martin Simon, Laura Gröger, Natalie Fabis, Ernesto Aparicio-Puerta, Abdulrahman Salhab, Tobias Fehlmann, Oliver Hahn, Annika Engel, Viktoria Wagner, Marcus Koch, Katarzyna Winek, Hermona Soreq, Irina Nazarenko, Gregor Fuhrmann, Tony Wyss-Coray, Eckart Meese, Verena Keller, Matthias W. Laschke & Andreas Keller
Pages: 482-494
Published online: 27 Jul 2023
AbstractforAgeing-associated small RNA cargo of extracellular vesicles | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 1917 Views
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Open Access
Article
Why are G-quadruplexes good at preventing protein aggregation?
Theodore J. Litberg, Rajesh Kumar Reddy Sannapureddi, Zijue Huang, Ahyun Son, Bharathwaj Sathyamoorthy & Scott Horowitz
Pages: 495-509
Published online: 26 Jul 2023
AbstractforWhy are G-quadruplexes good at preventing protein aggregation? | Full Text | References | PDF (4.7 MB) | EPUB | Supplemental
  • 1113 Views
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Review Article
RNA origami: design, simulation and application
Erik Poppleton, Niklas Urbanek, Taniya Chakraborty, Alessandra Griffo, Luca Monari & Kerstin Göpfrich
Pages: 510-524
Published online: 27 Jul 2023
AbstractforRNA origami: design, simulation and application | Full Text | References | PDF (3.1 MB) | EPUB
  • 3653 Views
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Review

Review Article
Pre-mRNA splicing-associated diseases and therapies
Sierra L. Love, Joseph D. Emerson, Kazunori Koide & Aaron A. Hoskins
Pages: 525-538
Published online: 01 Aug 2023
AbstractforPre-mRNA splicing-associated diseases and therapies | Full Text | References | PDF (1.8 MB) | EPUB
  • 2669 Views
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Brief Communication

Rapid Communication
SNHG15 aids SARS-CoV-2 entry via RABL2A
Samuel Pushparaj, Chaitanya Gandikota, Kishore Vaddadi, Yurong Liang & Lin Liu
Pages: 539-547
Published online: 01 Aug 2023
AbstractforSNHG15 aids SARS-CoV-2 entry via RABL2A | Full Text | References | PDF (5.7 MB) | EPUB
  • 660 Views
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Review

Review Article
Structural diversity and biological role of the 5’ untranslated regions of picornavirus
Tingyu Peng, Fayu Yang, Fan Yang, Weijun Cao, Haixue Zheng & Zixiang Zhu
Pages: 548-562
Published online: 03 Aug 2023
AbstractforStructural diversity and biological role of the 5’ untranslated regions of picornavirus | Full Text | References | PDF (1 MB) | EPUB
  • 1268 Views
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Brief Communication

Rapid Communication
Inefficient splicing of long non-coding RNAs is associated with higher transcript complexity in human and mouse
Koushiki Basu, Anubha Dey & Manjari Kiran
Pages: 563-572
Published online: 06 Aug 2023
AbstractforInefficient splicing of long non-coding RNAs is associated with higher transcript complexity in human and mouse | Full Text | References | PDF (5.5 MB) | EPUB | Supplemental
  • 885 Views
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Research Paper

Article
Cup is essential for oskar mRNA translational repression during early Drosophila oogenesis
Livia V. Bayer, Samantha Milano, Stephen K. Formel, Harpreet Kaur, Rishi Ravichandran, Juan A. Cambeiro, Lizaveta Slinko, Irina E. Catrina & Diana P. Bratu
Pages: 573-587
Published online: 08 Aug 2023
AbstractforCup is essential for oskar mRNA translational repression during early Drosophila oogenesis | Full Text | References | PDF (8.4 MB) | EPUB | Supplemental
  • 800 Views
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Review

Review Article
Sensing intracellular signatures with synthetic mRNAs
Hiroki Ono & Hirohide Saito
Pages: 588-602
Published online: 15 Aug 2023
AbstractforSensing intracellular signatures with synthetic mRNAs | Full Text | References | PDF (1.1 MB) | EPUB
  • 1510 Views
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Review Article
RNA modification-mediated translational control in immune cells
Yujuan Zhang, Weiguo Hu & Hua-Bing Li
Pages: 603-613
Published online: 16 Aug 2023
AbstractforRNA modification-mediated translational control in immune cells | Full Text | References | PDF (1.6 MB) | EPUB
  • 1221 Views
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Research Paper

Article
Characterization of microRNAs in the cyst nematode Heterodera glycines identifies possible candidates involved in cross-kingdom interactions with its host Glycine max
Dave T. Ste-Croix, Richard R. Bélanger & Benjamin Mimee
Pages: 614-628
Published online: 20 Aug 2023
AbstractforCharacterization of microRNAs in the cyst nematode Heterodera glycines identifies possible candidates involved in cross-kingdom interactions with its host Glycine max | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 853 Views
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Article
Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex
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
Pages: 629-640
Published online: 21 Aug 2023
AbstractforShared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
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Review

Review Article
Research progress of circRNA in malignant tumour metabolic reprogramming
Yikun Geng, Min Wang, Zhouying Wu, Jianchao Jia, Tingyu Yang & Lan Yu
Pages: 641-651
Published online: 20 Aug 2023
AbstractforResearch progress of circRNA in malignant tumour metabolic reprogramming | Full Text | References | PDF (2.6 MB) | EPUB
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Technical Paper

Report
Comprehensive identification of diverse ribosomal RNA modifications by targeted nanopore direct RNA sequencing and JACUSA2
Isabel S. Naarmann-de Vries, Christiane Zorbas, Amina Lemsara, Michael Piechotta, Felix G. M. Ernst, Ludivine Wacheul, Denis L. J. Lafontaine & Christoph Dieterich
Pages: 652-665
Published online: 27 Aug 2023
AbstractforComprehensive identification of diverse ribosomal RNA modifications by targeted nanopore direct RNA sequencing and JACUSA2 | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
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Research Paper

Article
Shortened CRISPR-Cas9 arrays enable multiplexed gene targeting in bacteria from a smaller DNA footprint
Sandra Gawlitt, Chunyu Liao, Tatjana Achmedov & Chase L. Beisel
Pages: 666-680
Published online: 31 Aug 2023
AbstractforShortened CRISPR-Cas9 arrays enable multiplexed gene targeting in bacteria from a smaller DNA footprint | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
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Article
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
Sudhir Singh, Kuldeep Lahry, Chandra Sekhar Mandava, Jitendra Singh, Riyaz Ahmad Shah, Suparna Sanyal & Umesh Varshney
Pages: 681-692
Published online: 07 Sep 2023
AbstractforLamotrigine compromises the fidelity of initiator tRNA recruitment to the ribosomal P-site by IF2 and the RbfA release from 30S ribosomes in Escherichia coli | Full Text | References | PDF (5.7 MB) | EPUB | Supplemental
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Research paper

Article
DMD antisense oligonucleotide mediated exon skipping efficiency correlates with flanking intron retention time and target position within the exon
Remko Goossens, Nisha Verwey, Yavuz Ariyurek, Fred Schnell & Annemieke Aartsma-Rus
Pages: 693-702
Published online: 04 Sep 2023
AbstractforDMD antisense oligonucleotide mediated exon skipping efficiency correlates with flanking intron retention time and target position within the exon | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
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Brief Communication

Rapid Communication
A full repertoire of Hemiptera genomes reveals a multi-step evolutionary trajectory of auto-RNA editing site in insect Adar gene
Ling Ma, Caiqing Zheng, Shiwen Xu, Ye Xu, Fan Song, Li Tian, Wanzhi Cai, Hu Li & Yuange Duan
Pages: 703-714
Published online: 07 Sep 2023
AbstractforA full repertoire of Hemiptera genomes reveals a multi-step evolutionary trajectory of auto-RNA editing site in insect Adar gene | Full Text | References | PDF (16.2 MB) | EPUB | Supplemental
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Review

Review Article
Maturation of small nucleolar RNAs: from production to function
Sarah F. Webster & Homa Ghalei
Pages: 715-736
Published online: 05 Oct 2023
AbstractforMaturation of small nucleolar RNAs: from production to function | Full Text | References | PDF (2.6 MB) | EPUB
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Research paper

Article
Translational control of murine adiponectin expression by an upstream open reading frame element
Kommireddy Vasu, Iyappan Ramachandiran, Aayushi Chechi, Krishnendu Khan, Debjit Khan, Randal J Kaufman & Paul L. Fox
Pages: 737-749
Published online: 13 Sep 2023
AbstractforTranslational control of murine adiponectin expression by an upstream open reading frame element | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 872 Views
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Article
Characterization of CoCas9 nuclease from Capnocytophaga ochracea
A. Vasileva, P. Selkova, A. Arseniev, M. Abramova, N. Shcheglova, O. Musharova, I. Mizgirev, T. Artamonova, M. Khodorkovskii, K. Severinov & I. Fedorova
Pages: 750-759
Published online: 24 Sep 2023
AbstractforCharacterization of CoCas9 nuclease from Capnocytophaga ochracea | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
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Article
Endonucleolytic processing plays a critical role in the maturation of ribosomal RNA in Methanococcus maripaludis
Lei Qi, Huan Liu, Jian Gao, Kai Deng, Xiaoyan Wang, Xiuzhu Dong & Jie Li
Pages: 760-773
Published online: 20 Sep 2023
AbstractforEndonucleolytic processing plays a critical role in the maturation of ribosomal RNA in Methanococcus maripaludis | Full Text | References | PDF (5.3 MB) | EPUB | Supplemental
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Article
Anticodon sequence determines the impact of mistranslating tRNAAla variants
Ecaterina Cozma, Megha Rao, Madison Dusick, Julie Genereaux, Ricard A. Rodriguez-Mias, Judit Villén, Christopher J. Brandl & Matthew D. Berg
Pages: 791-804
Published online: 30 Sep 2023
AbstractforAnticodon sequence determines the impact of mistranslating tRNAAla variants | Full Text | References | PDF (15.2 MB) | EPUB | Supplemental
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Article
Synergistic correlation between host angiogenin and dengue virus replication
Deeksha Madhry, Shivani Malvankar, Sushant Phadnis, Rupesh K. Srivastava, Sankar Bhattacharyya & Bhupendra Verma
Pages: 805-816
Published online: 05 Oct 2023
AbstractforSynergistic correlation between host angiogenin and dengue virus replication | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 758 Views
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Review

Review Article
Dynamic RNA synthetic biology: new principles, practices and potential
Yueyi Li, Anibal Arce, Tyler Lucci, Rebecca A. Rasmussen & Julius B. Lucks
Pages: 817-829
Published online: 03 Dec 2023
AbstractforDynamic RNA synthetic biology: new principles, practices and potential | Full Text | References | PDF (7.4 MB) | EPUB
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Research Paper

Article
An efficient, scarless, selection-free technology for phage engineering
Moran G. Goren, Tridib Mahata & Udi Qimron
Pages: 830-835
Published online: 16 Oct 2023
AbstractforAn efficient, scarless, selection-free technology for phage engineering | Full Text | References | PDF (1.1 MB) | EPUB | Supplemental
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Research paper

Article
Long non-coding RNA APDC plays important regulatory roles in metabolism of bone and adipose tissues
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
Pages: 836-846
Published online: 13 Nov 2023
AbstractforLong non-coding RNA APDC plays important regulatory roles in metabolism of bone and adipose tissues | Full Text | References | PDF (6.9 MB) | EPUB | Supplemental
  • 804 Views
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Review

Review Article
Regulatory circular RNAs in viral diseases: applications in diagnosis and therapy
Wei Wang, Lei Sun, Meng-Ting Huang, Yun Quan, Tao Jiang, Zhichao Miao & Qiong Zhang
Pages: 847-858
Published online: 26 Oct 2023
AbstractforRegulatory circular RNAs in viral diseases: applications in diagnosis and therapy | Full Text | References | PDF (2 MB) | EPUB
  • 1341 Views
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Review Article
Circular RNAs: biology and clinical significance of breast cancer
Zhanwei Wang, Hao Deng, Yao Jin, Meng Luo, Jia Huang, Jing Wang, Kun Zhang, Li Wang & Jiaojiao Zhou
Pages: 859-874
Published online: 26 Oct 2023
AbstractforCircular RNAs: biology and clinical significance of breast cancer | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
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Research paper

Article
Determinants of DNMT2/TRDMT1 preference for substrates tRNA and DNA during the evolution
Huari Li, Daiyun Zhu, Yapeng Yang, Yunfei Ma, Yong Chen, Pingfang Xue, Juan Chen, Mian Qin, Dandan Xu, Chao Cai & Hongjing Cheng
Pages: 875-892
Published online: 15 Nov 2023
AbstractforDeterminants of DNMT2/TRDMT1 preference for substrates tRNA and DNA during the evolution | Full Text | References | PDF (17.1 MB) | EPUB | Supplemental
  • 466 Views
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Review

Review Article
Diverse roles of biomolecular condensation in eukaryotic translational regulation
Yuhan Zhang, Jun-Yan Kang, Mofang Liu & Ying Huang
Pages: 893-907
Published online: 31 Oct 2023
AbstractforDiverse roles of biomolecular condensation in eukaryotic translational regulation | Full Text | References | PDF (1.3 MB) | EPUB
  • 985 Views
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Review Article
Regulation and function of alternative polyadenylation in development and differentiation
Lorenzo Gallicchio, Gonzalo H. Olivares, Cameron W. Berry & Margaret T. Fuller
Pages: 908-925
Published online: 31 Oct 2023
AbstractforRegulation and function of alternative polyadenylation in development and differentiation | Full Text | References | PDF (14.9 MB) | EPUB
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Research paper

Article
Streptomyces rare codon UUA: from features associated with 2 adpA related locations to candidate phage regulatory translational bypassing
Ivan V. Antonov, Sinéad O’Loughlin, Alessandro N. Gorohovski, Patrick B.F. O’Connor, Pavel V. Baranov & John F. Atkins
Pages: 926-942
Published online: 15 Nov 2023
AbstractforStreptomyces rare codon UUA: from features associated with 2 adpA related locations to candidate phage regulatory translational bypassing | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 746 Views
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Review

Review Article
Discovering microproteins: making the most of ribosome profiling data
Sonia Chothani, Lena Ho, Sebastian Schafer & Owen Rackham
Pages: 943-954
Published online: 27 Nov 2023
AbstractforDiscovering microproteins: making the most of ribosome profiling data | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 1736 Views
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Research paper

Article
A conserved HOTAIRM1-HOXA1 regulatory axis contributes early to neuronal differentiation
Dana Segal, Samy Coulombe, Jasper Sim & Josée Dostie
Pages: 1523-1539
Published online: 24 Sep 2023
AbstractforA conserved HOTAIRM1-HOXA1 regulatory axis contributes early to neuronal differentiation | Full Text | References | PDF (4.3 MB) | EPUB | Supplemental
  • 656 Views
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