RNA Biology, Volume 18, Issue 11 (2021)

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RNA Biology, Volume 18, Issue 11 (2021)

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Review

Review
The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation
Jin-Der Wen, Syue-Ting Kuo & Hsin-Hung David Chou
Pages: 1489-1500
Published online: 21 Dec 2020
AbstractforThe diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation | Full Text | References | PDF (1.9 MB) | EPUB
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Review
The uniqueness of AlaRS and its human disease connections
Han Zhang, Xiang-Lei Yang & Litao Sun
Pages: 1501-1511
Published online: 23 Dec 2020
AbstractforThe uniqueness of AlaRS and its human disease connections | Full Text | References | PDF (2.9 MB) | EPUB
  • 2525 Views
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Review
U1 snRNP telescripting: molecular mechanisms and beyond
Yi Ran, Yanhui Deng & Chengguo Yao
Pages: 1512-1523
Published online: 15 Jan 2021
AbstractforU1 snRNP telescripting: molecular mechanisms and beyond | Full Text | References | PDF (1.6 MB) | EPUB
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Review
The effects of RNA editing in cancer tissue at different stages in carcinogenesis
Małgorzata Kurkowiak, Łukasz Arcimowicz, Elżbieta Chruściel, Zuzanna Urban-Wójciuk, Ines Papak, Liam Keegan, Mary O’Connell, Jacek Kowalski, Ted Hupp & Natalia Marek-Trzonkowska
Pages: 1524-1539
Published online: 17 Feb 2021
AbstractforThe effects of RNA editing in cancer tissue at different stages in carcinogenesis | Full Text | References | PDF (863.7 KB) | EPUB
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Review
Small RNA-directed DNA elimination: the molecular mechanism and its potential for genome editing
Carolien Bastiaanssen & Chirlmin Joo
Pages: 1540-1545
Published online: 08 Feb 2021
AbstractforSmall RNA-directed DNA elimination: the molecular mechanism and its potential for genome editing | Full Text | References | PDF (1 MB) | EPUB
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Brief Communication

Rapid Communication
Long non-coding RNA NEAT1_1 ameliorates TDP-43 toxicity in in vivo models of TDP-43 proteinopathy
Koji Matsukawa, Michail S. Kukharsky, Sei-Kyoung Park, Sangeun Park, Naruaki Watanabe, Takeshi Iwatsubo, Tadafumi Hashimoto, Susan W. Liebman & Tatyana A. Shelkovnikova
Pages: 1546-1554
Published online: 11 Jan 2021
AbstractforLong non-coding RNA NEAT1_1 ameliorates TDP-43 toxicity in in vivo models of TDP-43 proteinopathy | Full Text | References | PDF (5.9 MB) | EPUB | Supplemental
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Rapid Communication
Ribosome profiling analysis of human skeletal muscle identifies reduced translation of mitochondrial proteins with age
Ravi Tharakan, Ceereena Ubaida-Mohien, Yulan Piao, Myriam Gorospe & Luigi Ferrucci
Pages: 1555-1559
Published online: 21 Jan 2021
AbstractforRibosome profiling analysis of human skeletal muscle identifies reduced translation of mitochondrial proteins with age | Full Text | References | PDF (621.1 KB) | EPUB | Supplemental
  • 2548 Views
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Rapid Communication
crRNA complementarity shifts endogenous CRISPR-Cas systems between transcriptional repression and DNA defense
Hannah K. Ratner & David S. Weiss
Pages: 1560-1573
Published online: 18 Mar 2021
AbstractforcrRNA complementarity shifts endogenous CRISPR-Cas systems between transcriptional repression and DNA defense | Full Text | References | PDF (1.2 MB) | EPUB | Supplemental
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Technical Paper

3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists
Wenbin Guo, Nikoleta A Tzioutziou, Gordon Stephen, Iain Milne, Cristiane PG Calixto, Robbie Waugh, John W. S. Brown & Runxuan Zhang
Pages: 1574-1587
Published online: 19 Dec 2020
Abstractfor3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists | Full Text | References | PDF (13.1 MB) | EPUB | Supplemental
  • 10149 Views
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5´XP sRNA-seq: efficient identification of transcripts with and without 5´ phosphorylation reveals evolutionary conserved small RNA
Unn Kugelberg, Daniel Nätt, Signe Skog, Claudia Kutter & Anita Öst
Pages: 1588-1599
Published online: 31 Dec 2020
Abstractfor5´XP sRNA-seq: efficient identification of transcripts with and without 5´ phosphorylation reveals evolutionary conserved small RNA | Full Text | References | PDF (10.1 MB) | EPUB | Supplemental
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Target-capture full-length double-strand cDNA sequencing for alternative splicing analysis
Hiroki Ura, Sumihito Togi & Yo Niida
Pages: 1600-1607
Published online: 20 Jan 2021
AbstractforTarget-capture full-length double-strand cDNA sequencing for alternative splicing analysis | Full Text | References | PDF (2.5 MB) | EPUB
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CBRPP: a new RNA-centric method to study RNA–protein interactions
Yunfei Li, Shengde Liu, Lili Cao, Yujie Luo, Hongqiang Du, Siji Li, Zeming Zhang, Xuefei Guo, Wenmin Tian, Catherine Cl Wong & Fuping You
Pages: 1608-1621
Published online: 17 Feb 2021
AbstractforCBRPP: a new RNA-centric method to study RNA–protein interactions | Full Text | References | PDF (8.1 MB) | EPUB | Supplemental
  • 3872 Views
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PhasiRNAnalyzer: an integrated analyser for plant phased siRNAs
Yuhan Fei, Jiejie Feng, Rui Wang, Baoyi Zhang, Hongsheng Zhang & Ji Huang
Pages: 1622-1629
Published online: 04 Feb 2021
AbstractforPhasiRNAnalyzer: an integrated analyser for plant phased siRNAs | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 1437 Views
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Research Paper

Article
Towards the mechanism(s) of YB-3 synthesis regulation by YB-1
D.N. Lyabin, E.A. Smolin, K.S. Budkina, I.A. Eliseeva & L.P. Ovchinnikov
Pages: 1630-1641
Published online: 27 Dec 2020
AbstractforTowards the mechanism(s) of YB-3 synthesis regulation by YB-1 | Full Text | References | PDF (1.2 MB) | EPUB | Supplemental
  • 986 Views
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Article
Distinct roles of nucleosome sliding and histone modifications in controlling the fidelity of transcription initiation
Huiming Zhang, Zhaolian Lu, Yu Zhan, Judith Rodriguez, Chen Lu, Yong Xue & Zhenguo Lin
Pages: 1642-1652
Published online: 28 Jan 2021
AbstractforDistinct roles of nucleosome sliding and histone modifications in controlling the fidelity of transcription initiation | Full Text | References | PDF (6.6 MB) | EPUB | Supplemental
  • 1033 Views
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Article
Dissecting protein domain variability in the core RNA interference machinery of five insect orders
Fabricio Barbosa Monteiro Arraes, Diogo Martins-de-Sa, Daniel D. Noriega Vasquez, Bruno Paes Melo, Muhammad Faheem, Leonardo Lima Pepino de Macedo, Carolina Vianna Morgante, Joao Alexandre R. G Barbosa, Roberto Coiti Togawa, Valdeir Junio Vaz Moreira, Etienne G. J. Danchin & Maria Fatima Grossi-de-Sa
Pages: 1653-1681
Published online: 31 Dec 2020
AbstractforDissecting protein domain variability in the core RNA interference machinery of five insect orders | Full Text | References | PDF (13.3 MB) | EPUB | Supplemental
  • 1859 Views
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Article
Hormonal regulation of microRNA expression dynamics in the gut of the yellow fever mosquito Aedes aegypti
Xiufeng Zhang & Alexander S. Raikhel
Pages: 1682-1691
Published online: 23 Dec 2020
AbstractforHormonal regulation of microRNA expression dynamics in the gut of the yellow fever mosquito Aedes aegypti | Full Text | References | PDF (534.2 KB) | EPUB | Supplemental
  • 978 Views
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Article
Polynucleotide phosphorylase and RNA helicase CshA cooperate in Bacillus subtilis mRNA decay
Shakti Ingle, Shivani Chhabra, Denise Laspina, Elizabeth Salvo, Bo Liu & David H. Bechhofer
Pages: 1692-1701
Published online: 31 Dec 2020
AbstractforPolynucleotide phosphorylase and RNA helicase CshA cooperate in Bacillus subtilis mRNA decay | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 982 Views
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Article
Discovery and functional understanding of MiRNAs in molluscs: a genome-wide profiling approach
Songqian Huang, Kazutoshi Yoshitake, Md Asaduzzaman, Shigeharu Kinoshita, Shugo Watabe & Shuichi Asakawa
Pages: 1702-1715
Published online: 07 Jan 2021
AbstractforDiscovery and functional understanding of MiRNAs in molluscs: a genome-wide profiling approach | Full Text | References | PDF (11.3 MB) | EPUB | Supplemental
  • 1174 Views
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Article
Bulges control pri-miRNA processing in a position and strand-dependent manner
Shaohua Li, Thi Nhu-Y Le, Trung Duc Nguyen, Tam Anh Trinh & Tuan Anh Nguyen
Pages: 1716-1726
Published online: 31 Dec 2020
AbstractforBulges control pri-miRNA processing in a position and strand-dependent manner | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 2700 Views
  • 10 CrossRef citations
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Article
Characterization of synthetic riboswitch in cell-free protein expression systems
Yaroslav Chushak, Svetlana Harbaugh, Kathryn Zimlich, Bryan Alfred, Jorge Chávez & Nancy Kelley-Loughnane
Pages: 1727-1738
Published online: 11 Jan 2021
AbstractforCharacterization of synthetic riboswitch in cell-free protein expression systems | Full Text | References | PDF (6.1 MB) | EPUB | Supplemental
  • 1810 Views
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Article
Exon-level estimates improve the detection of differentially expressed genes in RNA-seq studies
Arfa Mehmood, Asta Laiho & Laura L. Elo
Pages: 1739-1746
Published online: 30 Jan 2021
AbstractforExon-level estimates improve the detection of differentially expressed genes in RNA-seq studies | Full Text | References | PDF (1 MB) | EPUB
  • 2815 Views
  • 1 CrossRef citations
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Article
Off-target effects of RNAi correlate with the mismatch rate between dsRNA and non-target mRNA
Jiasheng Chen, Yingchuan Peng, Hainan Zhang, Kangxu Wang, Chunqing Zhao, Guanheng Zhu, Subba Reddy Palli & Zhaojun Han
Pages: 1747-1759
Published online: 04 Jan 2021
AbstractforOff-target effects of RNAi correlate with the mismatch rate between dsRNA and non-target mRNA | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 4479 Views
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Article
Mapping rRNA 2’-O-methylations and identification of C/D snoRNAs in Arabidopsis thaliana plants
J. Azevedo-Favory, C. Gaspin, L. Ayadi, C. Montacié, V. Marchand, E. Jobet, M. Rompais, C. Carapito, Y. Motorin & J. Sáez-Vásquez
Pages: 1760-1777
Published online: 17 Feb 2021
AbstractforMapping rRNA 2’-O-methylations and identification of C/D snoRNAs in Arabidopsis thaliana plants | Full Text | References | PDF (5.1 MB) | EPUB | Supplemental
  • 2777 Views
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Article
Differential transcription profiling of the phage LUZ19 infection process in different growth media
Ana Brandão, Diana P. Pires, Lucas Coppens, Marleen Voet, Rob Lavigne & Joana Azeredo
Pages: 1778-1790
Published online: 15 Jan 2021
AbstractforDifferential transcription profiling of the phage LUZ19 infection process in different growth media | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 2278 Views
  • 8 CrossRef citations
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Article
Hypoxia activated long non-coding RNA HABON regulates the growth and proliferation of hepatocarcinoma cells by binding to and antagonizing HIF-1 alpha
Cheng-Ning Ma, Lu-Lu Wo, Di-Fei Wang, Ci-Xiang Zhou, Jing-Chi Li, Xin Zhang, Xiu-Feng Gong, Chen-Long Wang, Ming He & Qian Zhao
Pages: 1791-1806
Published online: 21 Jan 2021
AbstractforHypoxia activated long non-coding RNA HABON regulates the growth and proliferation of hepatocarcinoma cells by binding to and antagonizing HIF-1 alpha | Full Text | References | PDF (8.5 MB) | EPUB | Supplemental
  • 2489 Views
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Article
Identification and initial characterization of POLIII-driven transcripts by msRNA-sequencing
Peter Zorn, Danny Misiak, Michael Gekle & Marcel Köhn
Pages: 1807-1817
Published online: 18 Jan 2021
AbstractforIdentification and initial characterization of POLIII-driven transcripts by msRNA-sequencing | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 1255 Views
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Article
Exploring the expression and functionality of the rsm sRNAs in Pseudomonas syringae pv. tomato DC3000
María-Dolores Ferreiro, Lara Vanessa Behrmann, Ana Corral, Joaquina Nogales & María-Trinidad Gallegos
Pages: 1818-1833
Published online: 23 Feb 2021
AbstractforExploring the expression and functionality of the rsm sRNAs in Pseudomonas syringae pv. tomato DC3000 | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 1150 Views
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Article
A chromatin-associated splicing isoform of OIP5-AS1 acts in cis to regulate the OIP5 oncogene
Elżbieta Wanowska, Magdalena Kubiak, Izabela Makałowska & Michał Wojciech Szcześniak
Pages: 1834-1845
Published online: 20 Jan 2021
AbstractforA chromatin-associated splicing isoform of OIP5-AS1 acts in cis to regulate the OIP5 oncogene | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 2256 Views
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Article
Intron-assisted, viroid-based production of insecticidal circular double-stranded RNA in Escherichia coli
Beltrán Ortolá, Teresa Cordero, Xu Hu & José-Antonio Daròs
Pages: 1846-1857
Published online: 20 Jan 2021
AbstractforIntron-assisted, viroid-based production of insecticidal circular double-stranded RNA in Escherichia coli | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 2996 Views
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Article
Biochemical analysis of cleavage and ligation activities of the pistol ribozyme from Paenibacillus polymyxa
Yuliia Lihanova & Christina E. Weinberg
Pages: 1858-1866
Published online: 23 Feb 2021
AbstractforBiochemical analysis of cleavage and ligation activities of the pistol ribozyme from Paenibacillus polymyxa | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 1136 Views
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Article
Post-transcriptional regulation of redox homeostasis by the small RNA SHOxi in haloarchaea
Diego Rivera Gelsinger, Rahul Reddy, Kathleen Whittington, Sara Debic & Jocelyne DiRuggiero
Pages: 1867-1881
Published online: 31 Jan 2021
AbstractforPost-transcriptional regulation of redox homeostasis by the small RNA SHOxi in haloarchaea | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 2045 Views
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Article
HSM6AP: a high-precision predictor for the Homo sapiens N6-methyladenosine (m^6 A) based on multiple weights and feature stitching
Jing Li, Shida He, Fei Guo & Quan Zou
Pages: 1882-1892
Published online: 12 Feb 2021
AbstractforHSM6AP: a high-precision predictor for the Homo sapiens N6-methyladenosine (m^6 A) based on multiple weights and feature stitching | Full Text | References | PDF (1 MB) | EPUB | Supplemental
  • 1153 Views
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Article
ncRNA BC1 influences translation in the oocyte
D. Aleshkina, R. Iyyappan, Ch. J. Lin, T. Masek, M. Pospisek & A. Susor
Pages: 1893-1904
Published online: 08 Feb 2021
AbstractforncRNA BC1 influences translation in the oocyte | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 1342 Views
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Article
Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation
Nicky Jonkhout, Sonia Cruciani, Helaine Graziele Santos Vieira, Julia Tran, Huanle Liu, Ganqiang Liu, Russell Pickford, Dominik Kaczorowski, Gloria R. Franco, Franz Vauti, Noelia Camacho, Seyedeh Sedigheh Abedini, Hossein Najmabadi, Lluís Ribas de Pouplana, Daniel Christ, Nicole Schonrock, John S. Mattick & Eva Maria Novoa
Pages: 1905-1919
Published online: 15 Feb 2021
AbstractforSubcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 2580 Views
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Article
Deciphering nucleotide modification-induced structure and stability changes
Travis Hurst & Shi-Jie Chen
Pages: 1920-1930
Published online: 15 Feb 2021
AbstractforDeciphering nucleotide modification-induced structure and stability changes | Full Text | References | PDF (1.4 MB) | EPUB | Supplemental
  • 1120 Views
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Article
Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogen Clostridioides difficile
Pierre Boudry, Emma Piattelli, Emilie Drouineau, Johann Peltier, Anaïs Boutserin, Maxence Lejars, Eliane Hajnsdorf, Marc Monot, Bruno Dupuy, Isabelle Martin-Verstraete, Daniel Gautheret, Claire Toffano-Nioche & Olga Soutourina
Pages: 1931-1952
Published online: 25 Feb 2021
AbstractforIdentification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogen Clostridioides difficile | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 2593 Views
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Article
The role and mechanism of miR-557 in inhibiting the differentiation and maturation of megakaryocytes in immune thrombocytopenia
Yan Wang, Yujie Guo, Xiaolei Zhang, Hui Zhao, Bingbing Zhang, Yi Wu & Jingyu Zhang
Pages: 1953-1968
Published online: 15 Feb 2021
AbstractforThe role and mechanism of miR-557 in inhibiting the differentiation and maturation of megakaryocytes in immune thrombocytopenia | Full Text | References | PDF (5 MB) | EPUB | Supplemental
  • 1198 Views
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Article
PCID2, a subunit of the Drosophila TREX-2 nuclear export complex, is essential for both mRNA nuclear export and its subsequent cytoplasmic trafficking
A. A. Glukhova, M. M. Kurshakova, E. N. Nabirochkina, S. G. Georgieva & D. V. Kopytova
Pages: 1969-1980
Published online: 19 Feb 2021
AbstractforPCID2, a subunit of the Drosophila TREX-2 nuclear export complex, is essential for both mRNA nuclear export and its subsequent cytoplasmic trafficking | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 1001 Views
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Article
NEDD4 triggers FOXA1 ubiquitination and promotes colon cancer progression under microRNA-340-5p suppression and ATF1 upregulation
Meng Yue, Zhennan Yun, Shiquan Li, Guoqiang Yan & Zhenhua Kang
Pages: 1981-1995
Published online: 11 Feb 2021
AbstractforNEDD4 triggers FOXA1 ubiquitination and promotes colon cancer progression under microRNA-340-5p suppression and ATF1 upregulation | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 1428 Views
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Article
Structural studies of RNase M5 reveal two-metal-ion supported two-step dsRNA cleavage for 5S rRNA maturation
Stephanie Oerum, Marjorie Catala, Maxime Bourguet, Laetitia Gilet, Pierre Barraud, Sarah Cianférani, Ciarán Condon & Carine Tisné
Pages: 1996-2006
Published online: 23 Feb 2021
AbstractforStructural studies of RNase M5 reveal two-metal-ion supported two-step dsRNA cleavage for 5S rRNA maturation | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 780 Views
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Article
Thermal adaptation of structural dynamics and regulatory function of adenine riboswitch
Lin Wu, Zhijun Liu & Yu Liu
Pages: 2007-2015
Published online: 25 Feb 2021
AbstractforThermal adaptation of structural dynamics and regulatory function of adenine riboswitch | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 951 Views
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Article
Direct RNA–RNA interaction between Neat1 and RNA targets, as a mechanism for RNAs paraspeckle retention
Audrey Jacq, Denis Becquet, Séverine Guillen, Bénédicte Boyer, Maria-Montserrat Bello-Goutierrez, Jean-Louis Franc & Anne-Marie François-Bellan
Pages: 2016-2027
Published online: 15 Mar 2021
AbstractforDirect RNA–RNA interaction between Neat1 and RNA targets, as a mechanism for RNAs paraspeckle retention | Full Text | References | PDF (1.1 MB) | EPUB | Supplemental
  • 1649 Views
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Article
Universal functions of the σ finger in alternative σ factors during transcription initiation by bacterial RNA polymerase
Anastasiya Oguienko, Ivan Petushkov, Danil Pupov, Daria Esyunina & Andrey Kulbachinskiy
Pages: 2028-2037
Published online: 25 Feb 2021
AbstractforUniversal functions of the σ finger in alternative σ factors during transcription initiation by bacterial RNA polymerase | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 1243 Views
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Commentary

Article Commentary
Exosomes provide unappreciated carrier effects that assist transfers of their miRNAs to targeted cells; I. They are ‘The Elephant in the Room’
Philip W. Askenase
Pages: 2038-2053
Published online: 04 May 2021
AbstractforExosomes provide unappreciated carrier effects that assist transfers of their miRNAs to targeted cells; I. They are ‘The Elephant in the Room’ | Full Text | References | PDF (4.5 MB) | EPUB
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