RNA Biology, Volume 21, Issue 1 (2024)

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RNA Biology, Volume 21, Issue 1 (2024)

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Research Paper

Article
Post-transcriptional regulation of BIRC5/survivin expression and induction of apoptosis in breast cancer cells by tristetraprolin
Suhad Al-Yahya, Maher Al-Saif, Maha Al-Ghamdi, Walid Moghrabi, Khalid S.A. Khabar & Norah Al-Souhibani
Pages: 1-15
Published online: 18 Dec 2023
AbstractforPost-transcriptional regulation of BIRC5/survivin expression and induction of apoptosis in breast cancer cells by tristetraprolin | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
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Research paper

Article
Unraveling C-to-U RNA editing events from direct RNA sequencing
Adriano Fonzino, Caterina Manzari, Paola Spadavecchia, Uday Munagala, Serena Torrini, Silvestro Conticello, Graziano Pesole & Ernesto Picardi
Pages: 1-14
Published online: 13 Dec 2023
AbstractforUnraveling C-to-U RNA editing events from direct RNA sequencing | Full Text | References | PDF (4.8 MB) | EPUB | Supplemental
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Review

Review Article
Therapeutic potential of natural antisense transcripts and various mechanisms involved for clinical applications and disease prevention
Ashiq Ali, Aisha Khatoon, Chenran Shao, Bilal Murtaza, Qaisar Tanveer & Zhongjing Su
Pages: 1-18
Published online: 13 Dec 2023
AbstractforTherapeutic potential of natural antisense transcripts and various mechanisms involved for clinical applications and disease prevention | Full Text | References | PDF (2.2 MB) | EPUB
  • 2003 Views
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Review Article
mRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts
Alexander F. Palazzo, Yi Qiu & Yoon Mo Kang
Pages: 1-12
Published online: 13 Dec 2023
AbstractformRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts | Full Text | References | PDF (2.4 MB) | EPUB
  • 2015 Views
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Research Paper

Article
Structure and function of the pseudouridine 5’-monophosphate glycosylase PUMY from Arabidopsis thaliana
Jeongyun Lee, Sang-Hoon Kim & Sangkee Rhee
Pages: 1-10
Published online: 20 Dec 2023
AbstractforStructure and function of the pseudouridine 5’-monophosphate glycosylase PUMY from Arabidopsis thaliana | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
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Review

Review Article
Structural and computational studies of HIV-1 RNA
Lev Levintov & Harish Vashisth
Pages: 1-32
Published online: 15 Dec 2023
AbstractforStructural and computational studies of HIV-1 RNA | Full Text | References | PDF (13.5 MB) | EPUB
  • 2052 Views
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Research paper

Article
The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking
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
Pages: 1-11
Published online: 19 Dec 2023
AbstractforThe landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 940 Views
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Research Paper

Article
A comparative survey of the influence of small self-cleaving ribozymes on gene expression in human cell culture
Dennis Kläge, Elisabeth Müller & Jörg S. Hartig
Pages: 1-11
Published online: 25 Dec 2023
AbstractforA comparative survey of the influence of small self-cleaving ribozymes on gene expression in human cell culture | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 1034 Views
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Article
Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis
Thiruvenkadam Shanmugam, Palak Chaturvedi, Deniz Streit, Arindam Ghatak, Thorsten Bergelt, Stefan Simm, Wolfram Weckwerth & Enrico Schleiff
Pages: 1-15
Published online: 29 Dec 2023
AbstractforLow dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 778 Views
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Review

Review Article
Small RNA-big impact: exosomal miRNAs in mitochondrial dysfunction in various diseases
Xiaqing Li, Yi Han, Yu Meng & Lianghong Yin
Pages: 1-20
Published online: 04 Jan 2024
AbstractforSmall RNA-big impact: exosomal miRNAs in mitochondrial dysfunction in various diseases | Full Text | References | PDF (2 MB) | EPUB
  • 1110 Views
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Research Paper

Article
Ordering events in a developing genetic code
Michael Yarus
Pages: 1-8
Published online: 03 Jan 2024
AbstractforOrdering events in a developing genetic code | Full Text | References | PDF (1.1 MB) | EPUB
  • 371 Views
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Review

Review Article
The nexus of long noncoding RNAs, splicing factors, alternative splicing and their modulations
Pushkar Malakar, Sudhanshu Shukla, Meghna Mondal, Rajesh Kumar Kar & Jawed Akhtar Siddiqui
Pages: 1-20
Published online: 28 Nov 2023
AbstractforThe nexus of long noncoding RNAs, splicing factors, alternative splicing and their modulations | Full Text | References | PDF (2.5 MB) | EPUB
  • 1816 Views
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Research Paper

Article
MiRNAs differentially expressed in vegetative and reproductive organs of Marchantia polymorpha – insights into their expression pattern, gene structures and function
Bharti Aggarwal, Wojciech Maciej Karlowski, Przemyslaw Nuc, Artur Jarmolowski, Zofia Szweykowska-Kulinska & Halina Pietrykowska
Pages: 1-12
Published online: 01 Feb 2024
AbstractforMiRNAs differentially expressed in vegetative and reproductive organs of Marchantia polymorpha – insights into their expression pattern, gene structures and function | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 423 Views
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Review

Review Article
Small molecule inhibition of RNA binding proteins in haematologic cancer
Amit K. Jaiswal, Michelle L. Thaxton, Georgia M. Scherer, Jacob P. Sorrentino, Neil K. Garg & Dinesh S. Rao
Pages: 1-14
Published online: 08 Feb 2024
AbstractforSmall molecule inhibition of RNA binding proteins in haematologic cancer | Full Text | References | PDF (7.7 MB) | EPUB | Supplemental
  • 1394 Views
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Research Paper

Article
Epitranscriptomic regulation in fasting hearts: implications for cardiac health
Daniel Benak, Kristyna Holzerova, Jaroslav Hrdlicka, Frantisek Kolar, Mark Olsen, Mati Karelson & Marketa Hlavackova
Pages: 1-14
Published online: 07 Feb 2024
AbstractforEpitranscriptomic regulation in fasting hearts: implications for cardiac health | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 609 Views
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Review

Review Article
Single-cell analysis of the epitranscriptome: RNA modifications under the microscope
Eva Crespo-García, Alberto Bueno-Costa & Manel Esteller
Pages: 1-8
Published online: 18 Feb 2024
AbstractforSingle-cell analysis of the epitranscriptome: RNA modifications under the microscope | Full Text | References | PDF (1.3 MB) | EPUB
  • 1082 Views
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Review Article
The high-density lipoprotein binding protein HDLBP is an unusual RNA-binding protein with multiple roles in cancer and disease
Jonathan Feicht & Ralf-Peter Jansen
Pages: 1-10
Published online: 13 Mar 2024
AbstractforThe high-density lipoprotein binding protein HDLBP is an unusual RNA-binding protein with multiple roles in cancer and disease | Full Text | References | PDF (2.1 MB) | EPUB
  • 535 Views
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Research Paper

Article
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
Chan Park, Bitnara Han, Yura Choi, Yoontae Jin, Kwang Pyo Kim, Seong Il Choi & Baik L. Seong
Pages: 1-18
Published online: 15 Feb 2024
AbstractforRNA-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 | Full Text | References | PDF (4.9 MB) | EPUB | Supplemental
  • 630 Views
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Open Access
Article
MRM-BERT: a novel deep neural network predictor of multiple RNA modifications by fusing BERT representation and sequence features
Linshu Wang & Yuan Zhou
Pages: 1-10
Published online: 15 Feb 2024
AbstractforMRM-BERT: a novel deep neural network predictor of multiple RNA modifications by fusing BERT representation and sequence features | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 623 Views
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Article
Mature microRNA-binding protein QKI promotes microRNA-mediated gene silencing
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
Pages: 1-15
Published online: 19 Feb 2024
AbstractforMature microRNA-binding protein QKI promotes microRNA-mediated gene silencing | Full Text | References | PDF (4.7 MB) | EPUB | Supplemental
  • 769 Views
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Open Access
Article
Urea supplementation improves mRNA in vitro transcription by decreasing both shorter and longer RNA byproducts
Combes Francis, Pettersson Frida J, Bui Thanh-Huong, Molska Alicja, Komissarov Artem, Parot Jérémie & Borgos Sven Even
Pages: 1-6
Published online: 27 Feb 2024
AbstractforUrea supplementation improves mRNA in vitro transcription by decreasing both shorter and longer RNA byproducts | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 2576 Views
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Letter to the Editor

Letter to the Editor
An elusive debate on the evidence for RNA editing in SARS-CoV-2
Giorgio Mattiuz, Salvatore Di Giorgio & Silvestro G. Conticello
Pages: 1-2
Published online: 01 Mar 2024
CitationforAn elusive debate on the evidence for RNA editing in SARS-CoV-2 | Full Text | References | PDF (168.1 KB) | EPUB
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Review

Review Article
Recent progress in miRNA biogenesis and decay
Xavier Bofill-De Ros & Ulf Andersson Vang Ørom
Pages: 1-8
Published online: 29 Nov 2023
AbstractforRecent progress in miRNA biogenesis and decay | Full Text | References | PDF (744.2 KB) | EPUB
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Research Paper

Article
The role of the 5’ sensing function of ribonuclease E in cyanobacteria
Ute A. Hoffmann, Elisabeth Lichtenberg, Said N. Rogh, Raphael Bilger, Viktoria Reimann, Florian Heyl, Rolf Backofen, Claudia Steglich, Wolfgang R. Hess & Annegret Wilde
Pages: 1-18
Published online: 12 Mar 2024
AbstractforThe role of the 5’ sensing function of ribonuclease E in cyanobacteria | Full Text | References | PDF (4.6 MB) | EPUB | Supplemental
  • 411 Views
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Review

Review Article
RNA nanostructures for targeted drug delivery and imaging
Laura Teodori, Marjan Omer & Jørgen Kjems
Pages: 1-19
Published online: 31 Mar 2024
AbstractforRNA nanostructures for targeted drug delivery and imaging | Full Text | References | PDF (2.6 MB) | EPUB
  • 784 Views
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Open Access

Research Paper

Article
BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification
Anderson P. Avila Santos, Breno L. S. de Almeida, Robson P. Bonidia, Peter F. Stadler, Polonca Stefanic, Ines Mandic-Mulec, Ulisses Rocha, Danilo S. Sanches & André C.P.L.F. de Carvalho
Pages: 1-12
Published online: 25 Mar 2024
AbstractforBioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification | Full Text | References | PDF (1.3 MB) | EPUB
  • 786 Views
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Open Access
Article
Tissue-specific silencing of integrated transgenes achieved through endogenous RNA interference in Caenorhabditis elegans
Siyu Chen, Weihong Liu, Lei Xiong, Zhiju Tao & Di Zhao
Pages: 1-10
Published online: 26 Mar 2024
AbstractforTissue-specific silencing of integrated transgenes achieved through endogenous RNA interference in Caenorhabditis elegans | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 567 Views
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Review

Review Article
mRNA vaccine designs for optimal adjuvanticity and delivery
Yuki Mochida & Satoshi Uchida
Pages: 1-27
Published online: 26 Mar 2024
AbstractformRNA vaccine designs for optimal adjuvanticity and delivery | Full Text | References | PDF (3.6 MB) | EPUB
  • 1924 Views
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Review Article
Role of RNA binding proteins of the Drosophila behavior and human splicing (DBHS) family in health and cancer
Toshihiko Takeiwa, Kazuhiro Ikeda, Kuniko Horie & Satoshi Inoue
Pages: 1-17
Published online: 29 Mar 2024
AbstractforRole of RNA binding proteins of the Drosophila behavior and human splicing (DBHS) family in health and cancer | Full Text | References | PDF (1.9 MB) | EPUB
  • 714 Views
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Research Paper

Article
Global and single-nucleotide resolution detection of 7-methylguanosine in RNA
Silvia D’Ambrosi, Raquel García-Vílchez, Darek Kedra, Patrice Vitali, Nuria Macias-Cámara, Laura Bárcena, Monika Gonzalez-Lopez, Ana M. Aransay, Sabine Dietmann, Antonio Hurtado & Sandra Blanco
Pages: 1-18
Published online: 02 Apr 2024
AbstractforGlobal and single-nucleotide resolution detection of 7-methylguanosine in RNA | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 492 Views
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Editorial

Editorial
Synthetic RNA biology
Beatrix Suess
Pages: 1-2
Published online: 14 Apr 2024
CitationforSynthetic RNA biology | Full Text | References | PDF (193.9 KB) | EPUB
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Review

Review Article
The regulatory roles of small nucleolar RNAs within their host locus
Étienne Fafard-Couture, Stéphane Labialle & Michelle S Scott
Pages: 1-11
Published online: 16 Apr 2024
AbstractforThe regulatory roles of small nucleolar RNAs within their host locus | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 484 Views
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Research Paper

Article
Mistranslating the genetic code with leucine in yeast and mammalian cells
Josephine Davey-Young, Farah Hasan, Rasangi Tennakoon, Peter Rozik, Henry Moore, Peter Hall, Ecaterina Cozma, Julie Genereaux, Kyle S. Hoffman, Patricia P. Chan, Todd M. Lowe, Christopher J. Brandl & Patrick O’Donoghue
Pages: 1-23
Published online: 17 Apr 2024
AbstractforMistranslating the genetic code with leucine in yeast and mammalian cells | Full Text | References | PDF (6 MB) | EPUB | Supplemental
  • 540 Views
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Research paper

Article
Post-transcriptional capping generates coenzyme A-linked RNA
Krishna Sapkota, Jordyn K. Lucas, Jarrett W. Faulkner, Matt F. Lichte, Yan-Lin Guo, Donald H. Burke & Faqing Huang
Pages: 1-12
Published online: 30 Nov 2023
AbstractforPost-transcriptional capping generates coenzyme A-linked RNA | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 1055 Views
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Research Paper

Article
Transcriptional landscape of small non-coding RNAs reveals diversity of categories and functions in molluscs
Songqian Huang, Kazutoshi Yoshitake, Shigeharu Kinoshita & Shuichi Asakawa
Pages: 1-13
Published online: 01 May 2024
AbstractforTranscriptional landscape of small non-coding RNAs reveals diversity of categories and functions in molluscs | Full Text | References | PDF (5.8 MB) | EPUB | Supplemental
  • 198 Views
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Article
Truncating the spliceosomal ‘rope protein’ Prp45 results in Htz1 dependent phenotypes
Kateřina Abrhámová, Martina Groušlová, Anna Valentová, Xinxin Hao, Beidong Liu, Martin Převorovský, Ondřej Gahura, František Půta, Per Sunnerhagen & Petr Folk
Pages: 1-17
Published online: 06 May 2024
AbstractforTruncating the spliceosomal ‘rope protein’ Prp45 results in Htz1 dependent phenotypes | Full Text | References | PDF (6.4 MB) | EPUB | Supplemental
  • 209 Views
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Open Access
Article
Nm-Nano: a machine learning framework for transcriptome-wide single-molecule mapping of 2´-O-methylation (Nm) sites in nanopore direct RNA sequencing datasets
Doaa Hassan, Aditya Ariyur, Swapna Vidhur Daulatabad, Quoseena Mir & Sarath Chandra Janga
Pages: 1-15
Published online: 17 May 2024
AbstractforNm-Nano: a machine learning framework for transcriptome-wide single-molecule mapping of 2´-O-methylation (Nm) sites in nanopore direct RNA sequencing datasets | Full Text | References | PDF (8.5 MB) | EPUB | Supplemental
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Review

Review Article
Programmable RNA targeting with CRISPR-Cas13
Peiguo Shi & Xuebing Wu
Pages: 1-9
Published online: 19 May 2024
AbstractforProgrammable RNA targeting with CRISPR-Cas13 | Full Text | References | PDF (2.5 MB) | EPUB
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Research Paper

Article
Multiple Oligo assisted RNA Pulldown via Hybridization followed by Mass Spectrometry (MORPH-MS) for exploring the RNA-Protein interactions
Priyanka Pant & Regalla Kumarswamy
Pages: 1-9
Published online: 17 Dec 2023
AbstractforMultiple Oligo assisted RNA Pulldown via Hybridization followed by Mass Spectrometry (MORPH-MS) for exploring the RNA-Protein interactions | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
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Review

Review Article
Circular RNAs in non-alcoholic fatty liver disease: Functions and clinical significance
Qingmin Zeng, Chang-Hai Liu, Javier Ampuero, Dongbo Wu, Wei Jiang, Lingyun Zhou, Hong Li, Lang Bai, Manuel Romero-Gómez & Hong Tang
Pages: 1-15
Published online: 19 Dec 2023
AbstractforCircular RNAs in non-alcoholic fatty liver disease: Functions and clinical significance | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 1237 Views
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Research Paper

Article
Expression of RNautophagy/DNautophagy-related genes is regulated under control of an innate immune receptor
Yuuki Fujiwara, Kazuki Oroku, Yinping Zhou, Masayuki Takahashi, Taiichi Katayama, Keiji Wada, Nobuyuki Tsutsumi, Tetsuo Sato & Tomohiro Kabuta
Pages: 1-9
Published online: 10 Jan 2024
AbstractforExpression of RNautophagy/DNautophagy-related genes is regulated under control of an innate immune receptor | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 728 Views
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Article
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
Wanxin Luo, Na Zhang, Ziping Wang, Hao Chen, Jie Sun, Chen Yao & Yafeng Zhang
Pages: 1-13
Published online: 22 Dec 2023
AbstractforLncRNA 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 | Full Text | References | PDF (16.2 MB) | EPUB | Supplemental
  • 697 Views
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Research paper

Article
CCAR-1 works together with the U2AF large subunit UAF-1 to regulate alternative splicing
Doreen I. Lugano, Lindsey N. Barrett, Dale Chaput, Margaret A. Park & Sandy D. Westerheide
Pages: 1-11
Published online: 21 Dec 2023
AbstractforCCAR-1 works together with the U2AF large subunit UAF-1 to regulate alternative splicing | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 650 Views
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Programmable RNA targeting with CRISPR-Cas13
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Nm-Nano: a machine learning framework for transcriptome-wide single-molecule mapping of 2´-O-methylation (Nm) sites in nanopore direct RNA sequencing datasets
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Truncating the spliceosomal ‘rope protein’ Prp45 results in Htz1 dependent phenotypes
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Transcriptional landscape of small non-coding RNAs reveals diversity of categories and functions in molluscs
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