Article
Biochemistry & Molecular Biology
Alfredo Berzal-Herranz, Beatriz Berzal-Herranz, Sara Esther Ramos-Lorente, Cristina Romero-Lopez
Summary: This study provides evidence that West Nile virus promotes a cap-independent translation initiation mechanism in mammalian and insect cells, and suggests that its 3' UTR is involved in fine-tuned translation regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Catia Andreassi, Raphaelle Luisier, Hamish Crerar, Marousa Darsinou, Sasja Blokzijl-Franke, Tchern Lenn, Nicholas M. Luscombe, Giovanni Cuda, Marco Gaspari, Adolfo Saiardi, Antonella Riccio
Summary: The 3' untranslated regions (3' UTRs) of mRNA play essential roles in mRNA metabolism, with incorrect processing potentially leading to developmental defects and neurological disorders. Deep sequencing revealed cleavage of 3' UTRs in transcripts in sympathetic neuron axons, generating translatable isoforms crucial for axon integrity. This study provides insights into mRNA metabolism that regulates local protein synthesis and generates a new class of 3' UTR-derived RNAs.
Article
Microbiology
Maryam Hajikarimlou, Mohsen Hooshyar, Noor Sunba, Nazila Nazemof, Mohamed Taha Moutaoufik, Sadhena Phanse, Kamaledin B. B. Said, Mohan Babu, Martin Holcik, Bahram Samanfar, Myron Smith, Ashkan Golshani
Summary: Mitochondria possess their own DNA (mtDNA) and are capable of carrying out their transcription and translation. The presence of the 3'-UTR from OXA1 gene is correlated with mitochondrial translation in yeast.
Article
Biochemistry & Molecular Biology
Wan-Jung C. Lai, Mingyi Zhu, Margarita Belinite, Gregory Ballard, David H. Mathews, Dmitri N. Ermolenko
Summary: Adding unstructured sequences to the 3'UTR of mRNA decreases translation, resulting in a weakened ability of the poly(A) tail.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Cell Biology
Luba Farberov, Ariel Ionescu, Yazeed Zoabi, Guy Shapira, Amjd Ibraheem, Yosi Azan, Eran Perlson, Noam Shomron
Summary: Rapid responses to changes within subcellular compartments of highly polarized cells, such as neuron axons, depend on the regulation of miRNAs. Through live cell imaging and RNA sequencing analysis, it was found that miRNAs can differentially control transcripts at the subcellular level. The binding site number of miRNAs at the 3'UTR of the mRNA, rather than the miRNA seed match length, regulates the axonal transcriptome.
Article
Multidisciplinary Sciences
Jastin Edrian Cocuangco Revilleza, Megumi Sato, Kaoru Irie, Yasuyuki Suda, Tomoaki Mizuno, Kenji Irie
Summary: The stability of RNA has an important role in gene expression, and the Ccr4-Not complex is involved in mRNA degradation. This study investigated the regulation of CLB1-6 genes by Ccr4, and found that Ccr4 affects the mRNA levels of CLB1-6 and consequently influences the protein levels of Clb1, Clb4, and Clb6. Further analysis identified destabilizing sequences in both the coding sequence and 3' untranslated region (3' UTR) of CLB6 mRNA, and it was determined that Ccr4 is involved in the destabilization process.
Review
Cell Biology
Jia Jia Chan, Hossein Tabatabaeian, Yvonne Tay
Summary: The majority of human mRNAs generate alternative 3' UTRs through various processes, including RNA editing, m6A methylation, and alternative polyadenylation (APA), with 3' UTR splicing as an emerging mechanism. Regulation of these processes at the genome and transcriptome levels contribute to 3' UTR heterogeneity. Genomic variants in 3' UTR regions and aberrant 3' UTR processing are associated with cancer and their deregulation may contribute to cancer pathogenesis. In-depth characterization of these events will enhance our understanding of their significance and aid in therapeutic development.
TRENDS IN CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ekaterina S. Komarova, Anna N. Slesarchuk, Maria P. Rubtsova, Ilya A. Osterman, Alexey E. Tupikin, Dmitry Pyshnyi, Olga A. Dontsova, Marsel R. Kabilov, Petr Sergiev
Summary: Flow-seq is a method that combines fluorescently activated cell sorting and next-generation sequencing to deduce a large amount of data about translation efficiency from a single experiment. It has been demonstrated that a variable length 5'-UTR library can be created and analyzed with Flow-seq, and the influence of RNA secondary structure and Shine-Dalgarno sequences on translation efficiency is smaller for natural 5'-UTRs compared to randomized libraries.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Katie M. Yergert, Caleb A. Doll, Rebecca O'Rouke, Jacob H. Hines, Bruce Appel
Summary: The text discusses the formation and growth process of myelin sheaths, as well as the impact of local mechanisms and mRNA localization on the maturation of myelin sheaths. The study found that consensus sequences in the 3'UTR can determine the enrichment of mRNA in myelin sheaths.
Article
Multidisciplinary Sciences
Christina Akirtava, Gemma E. May, C. Joel McManus
Summary: The study found that the putative IRESes previously reported in Hox gene hTLs are rarely included in transcript leaders and instead function independently as transcriptional promoters. Additionally, the proposed RNA structure of the putative Hoxa9 IRES is not conserved. The majority of hTLs with putative IRES activity overlap with transcriptional promoters, enhancers, and 3' splice sites, arguing against widespread IRES-like activities from hTLs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Cristina Romero-Lopez, Margarita Roda-Herreros, Beatriz Berzal-Herranz, Sara Esther Ramos-Lorente, Alfredo Berzal-Herranz
Summary: RNA viruses rely on RNA-RNA interactions involving genomic structural elements for viral replication and translation. In this study, intra- and intermolecular RNA-RNA interactions in the 3' UTR of the West Nile virus genome are observed, with intermolecular interactions forming molecular dimers. Functional analysis suggests a relationship between 3' UTR dimerization and viral translation efficiency. These findings imply the existence of a network of RNA-RNA interactions involving 3' UTR structural elements that regulate viral translation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Chemistry, Medicinal
Mahsa Rasekhian, Farzin Roohvand, Solomon Habtemariam, Marzieh Marzbany, Monireh Kazemimanesh
Summary: The central dogma of molecular biology explains the flow of genetic information from DNA to proteins, with a focus on the interactions between mRNA, RNA-binding proteins (RBP) and miRs determining mRNA fate and stability. The 3'UTR plays a critical role in viral RNA replication, impacting mRNA stability and translation in RNA viruses, particularly those with positive-sense genomes.
MINI-REVIEWS IN MEDICINAL CHEMISTRY
(2021)
Article
Microbiology
Shih-Chia Yeh, Mayra Diosa-Toro, Wei-Lian Tan, Florian Rachenne, Arthur Hain, Celestia Pei Xuan Yeo, Ines Bribes, Benjamin Wong Wei Xiang, Gayathiri Sathiamoorthy Kannan, Menchie Casayuran Manuel, Dorothee Misse, Yu Keung Mok, Julien Pompon
Summary: This study successfully identified 14 RBPs in Aedes aegypti cells that interact with DENV 2 3'UTR, providing new insights into the pro- and anti-viral functions of these RBPs in mosquitoes. The findings have important implications for the design of novel therapeutic interventions against Dengue viruses and for studying the role of RBPs in virus-vector interactions.
Article
Multidisciplinary Sciences
Setu M. Vora, Pietro Fontana, Tianyang Mao, Valerie Leger, Ying Zhang, Tian-Min Fu, Judy Lieberman, Lee Gehrke, Ming Shi, Longfei Wang, Akiko Iwasaki, Hao Wu
Summary: A study has found that SARS-CoV-2 utilizes its nonstructural protein 1 (Nsp1) to suppress host protein synthesis, but targeting the SL1 region of the SARS-CoV-2 5' untranslated region (5' UTR) can evade Nsp1-mediated translational suppression and hinder viral replication. The findings provide a conservative therapeutic target for COVID-19.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Qiang Zhang, Bin Tian
Summary: The 3' untranslated region (3'UTR) of mRNA is crucial for post-transcriptional regulation of gene expression. Eukaryotic protein-coding genes express multiple 3'UTR isoforms due to alternative cleavage and polyadenylation (APA). Cell proliferation, differentiation, and stress conditions lead to changes in the 3'UTR isoform expression profile. This review focuses on the regulation of 3'UTR isoforms in cell metabolic reprogramming, specifically exploring cell growth and autophagy responses mediated by the mTOR pathway.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2023)
Article
Multidisciplinary Sciences
Satoshi Hashimoto, Takato Sugiyama, Reina Yamazaki, Risa Nobuta, Toshifumi Inada
SCIENTIFIC REPORTS
(2020)
Article
Biochemistry & Molecular Biology
Yasuko Matsuki, Taishi Saito, Yu Nakano, Satoshi Hashimoto, Yoshitaka Matsuo, Toshifumi Inada
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2020)
Article
Cell Biology
Peixun Han, Yuichi Shichino, Tilman Schneider-Poetsch, Mari Mito, Satoshi Hashimoto, Tsuyoshi Udagawa, Kenji Kohno, Minoru Yoshida, Yuichiro Mishima, Toshifumi Inada, Shintaro Iwasaki
Article
Biochemistry & Molecular Biology
Risa Nobuta, Kodai Machida, Misaki Sato, Satoshi Hashimoto, Yasuhito Toriumi, Shizuka Nakajima, Daiki Suto, Hiroaki Imataka, Toshifumi Inada
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Mahabub Alam, Hiroki Shima, Yoshitaka Matsuo, Nguyen Chi Long, Mitsuyo Matsumoto, Yusho Ishii, Nichika Sato, Takato Sugiyama, Risa Nobuta, Satoshi Hashimoto, Liang Liu, Mika K. Kaneko, Yukinari Kato, Toshifumi Inada, Kazuhiko Igarashi
Summary: The study reveals the regulatory role of methionine adenosyltransferase (MAT) and S-adenosylmethionine (SAM) in protein synthesis. MAT2A, present in cancer cells, is positively correlated with cell proliferation. The experiment shows that under normal culture conditions, MAT2A limits protein synthesis. Additionally, MAT2 interacts with proteins involved in rRNA processing and ribosome biogenesis, and its inhibition results in reduced processing of 18S rRNA. The study also demonstrates the dynamic methylation of translation factors in response to MAT2A activity.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Momoko Narita, Timo Denk, Yoshitaka Matsuo, Takato Sugiyama, Chisato Kikuguchi, Sota Ito, Nichika Sato, Toru Suzuki, Satoshi Hashimoto, Iva Machova, Petr Tesina, Roland Beckmann, Toshifumi Inada
Summary: The authors discovered that collided ribosomes play a crucial role in quality control mechanisms. By ubiquitination, the collided ribosomes are marked and the quality control complex is recruited for subunit dissociation. The ubiquitination activity and K63-linked polyubiquitination of uS10 are critical for ribosome dissociation.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Shota Tomomatsu, Atsuya Watanabe, Petr Tesina, Satoshi Hashimoto, Ken Ikeuchi, Sihan Li, Yoshitaka Matsuo, Roland Beckmann, Toshifumi Inada
Summary: Ribosome collisions trigger the ribosome-associated quality control (RQC) and lead to the degradation of mRNA called no-go decay (NGD) through endonucleolytic cleavage. In yeast, NGD can occur in two modes, either coupled to RQC (NGD(RQC+)) or uncoupled from RQC (NGD(RQC-)), depending on the mechanism of substrate recognition by Cue2 endonuclease. The study found that the ubiquitin binding activity of Cue2 is necessary for NGD(RQC-) but not for NGD(RQC+), and it involves the first two N-terminal Cue domains of Cue2. Additionally, Trp122 of Cue2 plays a crucial role in NGD(RQC+), while Mbf1 prevents ribosomal frameshifting induced by rare codon staller.
NUCLEIC ACIDS RESEARCH
(2023)
