RNA Biology, Volume 18, Issue 12 (2021)

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RNA Biology, Volume 18, Issue 12 (2021)

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Review

Insights into circular RNAs: their biogenesis, detection, and emerging role in cardiovascular disease
Zoe Ward, John Pearson, Sebastian Schmeier, Vicky Cameron & Anna Pilbrow
Pages: 2055-2072
Published online: 28 Mar 2021
AbstractforInsights into circular RNAs: their biogenesis, detection, and emerging role in cardiovascular disease | Full Text | References | PDF (2.4 MB) | EPUB
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Localization of RNAs in the nucleus: cis- and trans- regulation
Chong Tong & Yafei Yin
Pages: 2073-2086
Published online: 08 Mar 2021
AbstractforLocalization of RNAs in the nucleus: cis- and trans- regulation | Full Text | References | PDF (746.8 KB) | EPUB
  • 2670 Views
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Recent advances in the regulation of plant miRNA biogenesis
Mu Li & Bin Yu
Pages: 2087-2096
Published online: 17 Mar 2021
AbstractforRecent advances in the regulation of plant miRNA biogenesis | Full Text | References | PDF (1 MB) | EPUB
  • 6829 Views
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Interrogating lncRNA functions via CRISPR/Cas systems
Meira S. Zibitt, Corrine Corrina R. Hartford & Ashish Lal
Pages: 2097-2106
Published online: 26 Mar 2021
AbstractforInterrogating lncRNA functions via CRISPR/Cas systems | Full Text | References | PDF (1.8 MB) | EPUB
  • 3936 Views
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The distinct roles of zinc finger CCHC-type (ZCCHC) superfamily proteins in the regulation of RNA metabolism
Yishu Wang, Yu Yu, Yidan Pang, Haojun Yu, Wenqi Zhang, Xian Zhao & Jianxiu Yu
Pages: 2107-2126
Published online: 04 May 2021
AbstractforThe distinct roles of zinc finger CCHC-type (ZCCHC) superfamily proteins in the regulation of RNA metabolism | Full Text | References | PDF (3.5 MB) | EPUB
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RNA methylation in chloroplasts or mitochondria in plants
Stefano Manduzio & Hunseung Kang
Pages: 2127-2135
Published online: 05 Apr 2021
AbstractforRNA methylation in chloroplasts or mitochondria in plants | Full Text | References | PDF (640.4 KB) | EPUB
  • 2612 Views
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Functions and mechanisms of circular RNAs in regulating stem cell differentiation
Zhengjun Lin, Xianzhe Tang, Jia Wan, Xianghong Zhang, Chunfeng Liu & Tang Liu
Pages: 2136-2149
Published online: 26 Apr 2021
AbstractforFunctions and mechanisms of circular RNAs in regulating stem cell differentiation | Full Text | References | PDF (1.1 MB) | EPUB
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TTP-mediated regulation of mRNA stability in immune cells contributes to adaptive immunity, immune tolerance and clinical applications
Yiwei Zhang, Jian Zhou, Zhiyuan Wei, Hui Dong, Di Yang, Yuanyu Deng, Jiahui Li, Saiyu Shi, Yi Sun, Huimin Lu, Jizhao Yuan, Bing Ni, Yuzhang Wu, Yi Tian & Chao Han
Pages: 2150-2156
Published online: 27 Apr 2021
AbstractforTTP-mediated regulation of mRNA stability in immune cells contributes to adaptive immunity, immune tolerance and clinical applications | Full Text | References | PDF (652.6 KB) | EPUB
  • 1266 Views
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Novel insights into the roles of tRNA-derived small RNAs
Qiyu Pan, Tingting Han & Guoping Li
Pages: 2157-2167
Published online: 17 May 2021
AbstractforNovel insights into the roles of tRNA-derived small RNAs | Full Text | References | PDF (4.2 MB) | EPUB
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Mitochondrial noncoding RNAs: new wine in an old bottle
Huixin Liang, Jiayu Liu, Shicheng Su & Qiyi Zhao
Pages: 2168-2182
Published online: 10 Jun 2021
AbstractforMitochondrial noncoding RNAs: new wine in an old bottle | Full Text | References | PDF (1.8 MB) | EPUB
  • 3584 Views
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RNA modifications act as regulators of cell death
Lei Xu, Chong Zhang, Hang Yin, Shuai Gong, Nai Wu, Zeqiang Ren & Yi Zhang
Pages: 2183-2193
Published online: 27 Jul 2021
AbstractforRNA modifications act as regulators of cell death | Full Text | References | PDF (1.9 MB) | EPUB
  • 4494 Views
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Human cytomegalovirus (HCMV)-encoded microRNAs: potential biomarkers and clinical applications
Raquel Fernández-Moreno, Julián Torre-Cisneros & Sara Cantisán
Pages: 2194-2202
Published online: 26 May 2021
AbstractforHuman cytomegalovirus (HCMV)-encoded microRNAs: potential biomarkers and clinical applications | Full Text | References | PDF (1.2 MB) | EPUB
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Technical Paper

In vivo discovery of RNA proximal proteins via proximity-dependent biotinylation
Xianzhi Lin, Marcos A. S. Fonseca, Joshua J. Breunig, Rosario I. Corona & Kate Lawrenson
Pages: 2203-2217
Published online: 19 May 2021
AbstractforIn vivo discovery of RNA proximal proteins via proximity-dependent biotinylation | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
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A DNA intercalating dye-based RT-qPCR alternative to diagnose SARS-CoV-2
Federico Fuchs Wightman, Micaela A. Godoy Herz, Juan C. Muñoz, José N. Stigliano, Laureano Bragado, Nicolas Nieto Moreno, Marcos Palavecino, Lucas Servi, Gonzalo Cabrerizo, José Clemente, Martín Avaro, Andrea Pontoriero, Estefanía Benedetti, Elsa Baumeister, Fabian Rudolf, Federico Remes Lenicov, Cybele Garcia, Valeria Buggiano, Alberto R. Kornblihtt, Anabella Srebrow, Manuel de la Mata, Manuel J. Muñoz, Ignacio E. Schor & Ezequiel Petrillo
Pages: 2218-2225
Published online: 26 May 2021
AbstractforA DNA intercalating dye-based RT-qPCR alternative to diagnose SARS-CoV-2 | Full Text | References | PDF (5.3 MB) | EPUB | Supplemental
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Bisulphite miRNA-seq reveals widespread CpG and non-CpG 5-(hydroxy)methyl-Cytosine in human microRNAs
Claudia Carissimi, Ilaria Laudadio, Elisa Lorefice, Gianluca Azzalin, Veronica De Paolis & Valerio Fulci
Pages: 2226-2235
Published online: 07 Jun 2021
AbstractforBisulphite miRNA-seq reveals widespread CpG and non-CpG 5-(hydroxy)methyl-Cytosine in human microRNAs | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
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Research Paper

Article
Accurate identification of RNA D modification using multiple features
Lijun Dou, Wenyang Zhou, Lichao Zhang, Lei Xu & Ke Han
Pages: 2236-2246
Published online: 17 Mar 2021
AbstractforAccurate identification of RNA D modification using multiple features | Full Text | References | PDF (744.1 KB) | EPUB | Supplemental
  • 935 Views
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Article
MicroRNA-140-3p alleviates intervertebral disc degeneration via KLF5/N-cadherin/MDM2/Slug axis
Zhenyu Wang, Shaokun Zhang, Yuguang Zhao, Zhigang Qu, Xinming Zhuang, Qingxu Song, Jiali Leng & Yi Liu
Pages: 2247-2260
Published online: 27 Apr 2021
AbstractforMicroRNA-140-3p alleviates intervertebral disc degeneration via KLF5/N-cadherin/MDM2/Slug axis | Full Text | References | PDF (1.1 MB) | EPUB | Supplemental
  • 1377 Views
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Article
Transcriptional regulation of telomeric repeat-containing RNA by acridine derivatives
Shuangshuang Kang, Jiaojiao Cao, Meiling Zhang, Xiaoya Li, Qian-Liang Guo, Huang Zeng, Zuzhuang Wei, Xue Gong, Jing Wang, Bobo Liu, Bing Shu, Xiaoli Xu, Zhi-Shu Huang & Ding Li
Pages: 2261-2277
Published online: 22 Mar 2021
AbstractforTranscriptional regulation of telomeric repeat-containing RNA by acridine derivatives | Full Text | References | PDF (4.3 MB) | EPUB | Supplemental
  • 1867 Views
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Article
Dihydrouridine synthesis in tRNAs is under reductive evolution in Mollicutes
Bruno Faivre, Murielle Lombard, Soufyan Fakroun, Chau-Duy-Tam Vo, Catherine Goyenvalle, Vincent Guérineau, Ludovic Pecqueur, Marc Fontecave, Valérie De Crécy-Lagard, Damien Brégeon & Djemel Hamdane
Pages: 2278-2289
Published online: 22 Mar 2021
AbstractforDihydrouridine synthesis in tRNAs is under reductive evolution in Mollicutes | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 1165 Views
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Article
lncRNADetector: a bioinformatics pipeline for long non-coding RNA identification and MAPslnc: a repository of medicinal and aromatic plant lncRNAs
Bhaskar Shukla, Sanchita Gupta, Gaurava Srivastava, Ashok Sharma, Ashutosh K. Shukla & Ajit K. Shasany
Pages: 2290-2295
Published online: 18 Mar 2021
AbstractforlncRNADetector: a bioinformatics pipeline for long non-coding RNA identification and MAPslnc: a repository of medicinal and aromatic plant lncRNAs | Full Text | References | PDF (992.2 KB) | EPUB | Supplemental
  • 3264 Views
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Article
Identification of conserved slow codons that are important for protein expression and function
Michal Perach, Zohar Zafrir, Tamir Tuller & Oded Lewinson
Pages: 2296-2307
Published online: 05 Apr 2021
AbstractforIdentification of conserved slow codons that are important for protein expression and function | Full Text | References | PDF (4.3 MB) | EPUB | Supplemental
  • 1634 Views
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Article
miRSM: an R package to infer and analyse miRNA sponge modules in heterogeneous data
Junpeng Zhang, Lin Liu, Taosheng Xu, Wu Zhang, Chunwen Zhao, Sijing Li, Jiuyong Li, Nini Rao & Thuc Duy Le
Pages: 2308-2320
Published online: 06 Apr 2021
AbstractformiRSM: an R package to infer and analyse miRNA sponge modules in heterogeneous data | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 1111 Views
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Article
All genera of Flaviviridae host a conserved Xrn1-resistant RNA motif
Ivar W. Dilweg, Anya Savina, Susanne Köthe, Alexander P. Gultyaev, Peter J. Bredenbeek & René C.L. Olsthoorn
Pages: 2321-2329
Published online: 16 Apr 2021
AbstractforAll genera of Flaviviridae host a conserved Xrn1-resistant RNA motif | Full Text | References | PDF (3 MB) | EPUB
  • 1753 Views
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Article
Amber codon is genetically unstable in generation of premature termination codon (PTC)-harbouring Foot-and-mouth disease virus (FMDV) via genetic code expansion
Rongzeng Hao, Kun Ma, Yi Ru, Dan Li, Gaoyuan Song, Bingzhou Lu, Huanan Liu, Yajun Li, Jiaoyan Zhang, Chunping Wu, Guicai Zhang, Haitao Hu, Jianxun Luo & Haixue Zheng
Pages: 2330-2341
Published online: 14 Apr 2021
AbstractforAmber codon is genetically unstable in generation of premature termination codon (PTC)-harbouring Foot-and-mouth disease virus (FMDV) via genetic code expansion | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 2002 Views
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Article
RGG-motif containing mRNA export factor Gbp2 acts as a translation repressor
Gopalakrishna Poornima, Gaurav Srivastava, Brinta Roy, Ishwarya Achappa Kuttanda, Iladeiti Kurbah & Purusharth I. Rajyaguru
Pages: 2342-2353
Published online: 29 Apr 2021
AbstractforRGG-motif containing mRNA export factor Gbp2 acts as a translation repressor | Full Text | References | PDF (4.3 MB) | EPUB | Supplemental
  • 2354 Views
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Article
M6ADD: a comprehensive database of m6A modifications in diseases
Dianshuang Zhou, Hongli Wang, Fanqi Bi, Jie Xing, Yue Gu, Cong Wang, Menyan Zhang, Yan Huang, Jiaqi Zeng, Qiong Wu & Yan Zhang
Pages: 2354-2362
Published online: 27 Apr 2021
AbstractforM6ADD: a comprehensive database of m6A modifications in diseases | Full Text | References | PDF (5 MB) | EPUB
  • 2866 Views
  • 5 CrossRef citations
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Article
Optimization of a fluorescent-mRNA based real-time assay for precise kinetic measurements of ribosomal translocation
Changil Kim, Mikael Holm, Chandra Sekhar Mandava & Suparna Sanyal
Pages: 2363-2375
Published online: 03 May 2021
AbstractforOptimization of a fluorescent-mRNA based real-time assay for precise kinetic measurements of ribosomal translocation | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 1358 Views
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Article
Optimal RNA binding by Egalitarian, a Dynein cargo adaptor, is critical for maintaining oocyte fate in Drosophila
Chandler H. Goldman, Hannah Neiswender, Frederick Baker, Rajalakshmi Veeranan-Karmegam, Saurav Misra & Graydon B. Gonsalvez
Pages: 2376-2389
Published online: 27 Apr 2021
AbstractforOptimal RNA binding by Egalitarian, a Dynein cargo adaptor, is critical for maintaining oocyte fate in Drosophila | Full Text | References | PDF (19.4 MB) | EPUB | Supplemental
  • 913 Views
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Article
RNA nanotechnology to build a dodecahedral genome of single-stranded RNA virus
Hui Li, Kaiming Zhang, Daniel W. Binzel, Lyudmila S. Shlyakhtenko, Yuri L. Lyubchenko, Wah Chiu & Peixuan Guo
Pages: 2390-2400
Published online: 29 Apr 2021
AbstractforRNA nanotechnology to build a dodecahedral genome of single-stranded RNA virus | Full Text | References | PDF (3.3 MB) | EPUB
  • 1511 Views
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Article
Global identification of RsmA/N binding sites in Pseudomonas aeruginosa by in vivo UV CLIP-seq
Kotaro Chihara, Lars Barquist, Kenichi Takasugi, Naohiro Noda & Satoshi Tsuneda
Pages: 2401-2416
Published online: 27 Apr 2021
AbstractforGlobal identification of RsmA/N binding sites in Pseudomonas aeruginosa by in vivo UV CLIP-seq | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 1556 Views
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Article
Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes
Kenneth I. Brewer, Etienne B. Greenlee, Gadareth Higgs, Diane Yu, Gayan Mirihana Arachchilage, Xi Chen, Nicholas King, Neil White & Ronald R. Breaker
Pages: 2417-2432
Published online: 10 May 2021
AbstractforComprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes | Full Text | References | PDF (5.6 MB) | EPUB | Supplemental
  • 3922 Views
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Article
The translation initiation factor EIF4E5 from Leishmania: crystal structure and interacting partners
Gustavo Barbosa de Lima, Thaíse Yasmine Vasconcelos de Lima Cavalcanti, Adriana Neuman Albuquerque Lins Moura de Brito, Ludmilla Arruda de Assis, Rafaela Paiva Andrade-Vieira, Eden Ribeiro Freire, Tatiana Reichert da Silva Assunção, Christian Robson de Souza Reis, Nilson Ivo Tonin Zanchin, Beatriz Gomes Guimarães & Osvaldo Pompílio de-Melo-Neto
Pages: 2433-2449
Published online: 04 May 2021
AbstractforThe translation initiation factor EIF4E5 from Leishmania: crystal structure and interacting partners | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 1295 Views
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Article
A conserved motif in human BTG1 and BTG2 proteins mediates interaction with the poly(A) binding protein PABPC1 to stimulate mRNA deadenylation
Hamza Amine, Nina Ripin, Sahil Sharma, Georg Stoecklin, Frédéric H Allain, Bertrand Séraphin & Fabienne Mauxion
Pages: 2450-2465
Published online: 01 Jun 2021
AbstractforA conserved motif in human BTG1 and BTG2 proteins mediates interaction with the poly(A) binding protein PABPC1 to stimulate mRNA deadenylation | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 2734 Views
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Article
Structural model of the M7G46 Methyltransferase TrmB in complex with tRNA
Katharina F. Blersch, Jan-Philipp Burchert, Sophie-Charlotte August, Luisa Welp, Piotr Neumann, Sarah Köster, Henning Urlaub & Ralf Ficner
Pages: 2466-2479
Published online: 19 May 2021
AbstractforStructural model of the M7G46 Methyltransferase TrmB in complex with tRNA | Full Text | References | PDF (10 MB) | EPUB | Supplemental
  • 1470 Views
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Article
The RNA structurome in the asexual blood stages of malaria pathogen plasmodium falciparum
Diana Renteria Alvarez, Alejandra Ospina, Tiffany Barwell, Bo Zheng, Abhishek Dey, Chong Li, Shrabani Basu, Xinghua Shi, Sabah Kadri & Kausik Chakrabarti
Pages: 2480-2497
Published online: 23 Jun 2021
AbstractforThe RNA structurome in the asexual blood stages of malaria pathogen plasmodium falciparum | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 2243 Views
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Article
M6A-BiNP: predicting N6-methyladenosine sites based on bidirectional position-specific propensities of polynucleotides and pointwise joint mutual information
Mingzhao Wang, Juanying Xie & Shengquan Xu
Pages: 2498-2512
Published online: 23 Jun 2021
AbstractforM6A-BiNP: predicting N6-methyladenosine sites based on bidirectional position-specific propensities of polynucleotides and pointwise joint mutual information | Full Text | References | PDF (4.8 MB) | EPUB | Supplemental
  • 1667 Views
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Article
MIR210HG regulates glycolysis, cell proliferation, and metastasis of pancreatic cancer cells through miR-125b-5p/HK2/PKM2 axis
Tianzhu Yu, Guoping Li, Chenggang Wang, Gaoquan Gong, Liangwen Wang, Changyu Li, Yi Chen & Xiaolin Wang
Pages: 2513-2530
Published online: 10 Jun 2021
AbstractforMIR210HG regulates glycolysis, cell proliferation, and metastasis of pancreatic cancer cells through miR-125b-5p/HK2/PKM2 axis | Full Text | References | PDF (4.8 MB) | EPUB | Supplemental
  • 1983 Views
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Article
New substrates and determinants for tRNA recognition of RNA methyltransferase DNMT2/TRDMT1
Huari Li, Daiyun Zhu, Jian Wu, Yunfei Ma, Chao Cai, Yong Chen, Mian Qin & Hanchuan Dai
Pages: 2531-2545
Published online: 10 Jun 2021
AbstractforNew substrates and determinants for tRNA recognition of RNA methyltransferase DNMT2/TRDMT1 | Full Text | References | PDF (9.5 MB) | EPUB | Supplemental
  • 1494 Views
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Article
In lysate RNA digestion provides insights into the angiogenin’s specificity towards transfer RNAs
Yasutoshi Akiyama, Yoshihisa Tomioka, Takaaki Abe, Paul Anderson & Pavel Ivanov
Pages: 2546-2555
Published online: 04 Jun 2021
AbstractforIn lysate RNA digestion provides insights into the angiogenin’s specificity towards transfer RNAs | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 1282 Views
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Article
An integrated DNA and RNA variant detector identifies a highly conserved three base exon in the MAP4K5 kinase locus
Małgorzata Kurkowiak, Giuseppa Grasso, Jakub Faktor, Lisa Scheiblecker, Małgorzata Winniczuk, Marcos Yebenes Mayordomo, J. Robert O’Neill, Bodil Oster, Borek Vojtesek, Ali Al-Saadi, Natalia Marek-Trzonkowska & Ted R. Hupp
Pages: 2556-2575
Published online: 30 Jun 2021
AbstractforAn integrated DNA and RNA variant detector identifies a highly conserved three base exon in the MAP4K5 kinase locus | Full Text | References | PDF (7.1 MB) | EPUB | Supplemental
  • 2087 Views
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Article
Synergistic roles for human U1 snRNA stem-loops in pre-mRNA splicing
William Martelly, Bernice Fellows, Paul Kang, Ajay Vashisht, James A. Wohlschlegel & Shalini Sharma
Pages: 2576-2593
Published online: 09 Jun 2021
AbstractforSynergistic roles for human U1 snRNA stem-loops in pre-mRNA splicing | Full Text | References | PDF (8 MB) | EPUB | Supplemental
  • 1950 Views
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Article
Alternative polyadenylated mRNAs behave as asynchronous rhythmic transcription in Arabidopsis
Juncheng Lin, Zhibo Yu, Congting Ye, Liwei Hong, Yiru Chu, Yingjia Shen & Qingshun Q. Li
Pages: 2594-2604
Published online: 07 Jun 2021
AbstractforAlternative polyadenylated mRNAs behave as asynchronous rhythmic transcription in Arabidopsis | Full Text | References | PDF (2.9 MB) | EPUB
  • 1067 Views
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Article
Comprehensive characterization of mRNAs associated with yeast cytosolic aminoacyl-tRNA synthetases
Shahar Garin, Ofri Levi, Megan E. Forrest, Anthony Antonellis & Yoav S. Arava
Pages: 2605-2616
Published online: 10 Jun 2021
AbstractforComprehensive characterization of mRNAs associated with yeast cytosolic aminoacyl-tRNA synthetases | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 1674 Views
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Article
A small ribosome-associated ncRNA globally inhibits translation by restricting ribosome dynamics
Julia Reuther, Lukas Schneider, Ioan Iacovache, Andreas Pircher, Walid H. Gharib, Benoît Zuber & Norbert Polacek
Pages: 2617-2632
Published online: 13 Jun 2021
AbstractforA small ribosome-associated ncRNA globally inhibits translation by restricting ribosome dynamics | Full Text | References | PDF (11 MB) | EPUB | Supplemental
  • 1809 Views
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Retraction

Retraction
Statement of Retraction: Salidroside alleviates high-glucose-induced injury in retinal pigment epithelial cell line ARPE-19 by down-regulation of miR-138
Page: 2633
Published online: 30 Apr 2021
CitationforStatement of Retraction: Salidroside alleviates high-glucose-induced injury in retinal pigment epithelial cell line ARPE-19 by down-regulation of miR-138 | Full Text | PDF (112.7 KB) | EPUB
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