Article
Virology
Deya Wang, Chen Yang, Yanmei Deng, Xue Cao, Wei Xu, Zishuo Han, Qingliang Li, Yang Yang, Xuefeng Yuan
Summary: This study identified a conserved RNA secondary structure in the 5'-UTR of Cherry virus A (CVA), which is found to regulate translation. The four types of CVA 5'-UTR showed weak translation enhancement activity and mutations in the 5'-UTR suppressed translation.
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
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
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
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
Cell Biology
Jia Jia Chan, Bin Zhang, Xiao Hong Chew, Adil Salhi, Zhi Hao Kwok, Chun You Lim, Ng Desi, Nagavidya Subramaniam, Angela Siemens, Tyas Kinanti, Shane Ong, Avencia Sanchez-Mejias, Phuong Thao Ly, Omer An, Raghav Sundar, Xiaonan Fan, Shi Wang, Bei En Siew, Kuok Chung Lee, Choon Seng Chong, Bettina Lieske, Wai-Kit Cheong, Yufen Goh, Wee Nih Fam, Melissa G. Ooi, Bryan T. H. Koh, Shridhar Ganpathi Iyer, Wen Huan Ling, Jianbin Chen, Boon-Koon Yoong, Rawisak Chanwat, Glenn Kunnath Bonney, Brian K. P. Goh, Weiwei Zhai, Melissa J. Fullwood, Wilson Wang, Ker-Kan Tan, Wee Joo Chng, Yock Young Dan, Jason J. Pitt, Xavier Roca, Ernesto Guccione, Leah A. Vardy, Leilei Chen, Xin Gao, Pierce K. H. Chow, Henry Yang, Yvonne Tay
Summary: This study systematically reveals the role of 3' UTR splicing in cancer, finding its widespread presence in various types of cancer and its correlation with poor prognosis. Inhibiting 3' UTR splicing can effectively reduce oncogene expression and impede tumor progression, providing new directions for RNA-based anti-cancer therapeutics.
NATURE CELL BIOLOGY
(2022)
Review
Cell Biology
Hanxiao Sun, Kai Li, Cong Liu, Chengqi Yi
Summary: Nucleobase modifications are widespread in eukaryotic mRNA and play crucial roles in post-transcriptional gene regulation. The most extensively studied modification is N-6-methyladenosine (m(6)A), but other modifications are also being investigated. This Review focuses on the emerging mechanisms and functions of these non-m(6)A modifications.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
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
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
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
Plant Sciences
Tao Huang, Wei-Jie He, Cheng Li, Jing-Bo Zhang, Yu-Cai Liao, Bo Song, Peng Yang
Summary: This study discovers the important role of N6-methyladenosine (m6A) in translation regulation in hexaploid wheat. The methylation extent of m6A is negatively correlated with mRNA expression levels, and m6A at different locations has different impacts on mRNA translation. m6a methylated genes are more conserved and enriched in genes with close expression levels. m6A-containing mRNAs are enriched in processes and pathways of translation and RNA transport.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Joseph V. Geisberg, Zarmik Moqtaderi, Kevin Struhl
Summary: Alternative polyadenylation generates multiple 3' mRNA isoforms with different stability, structure, and function. This study investigates how environmental conditions affect isoform turnover and structure in yeast cells. It is found that isoform stability generally increases with slower cell growth, and individual isoforms have similar structures across different conditions. Most mRNA stabilizing and destabilizing elements function only in one growth condition, and condition-specific stability elements might contribute to adaptation to different growth environments.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
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
Genetics & Heredity
Chidiebere U. Awah, Yana Glemaud, Fayola Levine, Kiseok Yang, Afrin Ansary, Fu Dong, Leonard Ash, Junfei Zhang, Olorunseun O. Ogunwobi
Summary: Resistance to targeted therapy is a challenge in breast, lung, and colorectal cancers, leading to a large number of deaths annually. We found that ERBB2+ cancer cells have mRNA-stabilizing sequences on their 3'UTR. By manipulating these sequences, we successfully degraded ERBB2 transcripts and reduced protein levels in various cancer cell types, providing a new approach to control oncogenic signals where current therapies fail.
FRONTIERS IN GENETICS
(2023)
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
Neurosciences
June Bryan de la Pena, Paulino Barragan-Iglesias, Tzu-Fang Lou, Nikesh Kunder, Sarah Loerch, Tarjani Shukla, Lokesh Basavarajappa, Jane Song, Dominique N. James, Salim Megat, Jamie K. Moy, Andi Wanghzou, Pradipta R. Ray, Kenneth Hoyt, Oswald Steward, Theodore J. Price, Jason Shepherd, Zachary T. Campbell
Summary: Studies have shown that activity-dependent protein Arc plays an important role in translational regulation in sensory neurons, potentially regulating neurogenic inflammation in the skin through intercellular signaling.
JOURNAL OF NEUROSCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Chen Qiu, Robert N. Wine, Zachary T. Campbell, Traci M. Tanaka Hall
Summary: In C. elegans, PUF proteins are involved in promoting germline stem cell self-renewal, with their functions relying on partnerships with proteins, particularly LST-1, to modulate mRNA regulation by FBF2. LST-1 contains two interaction sites with FBF-2, LST-1 A and B, which have distinct effects on FBF-2's RNA-binding affinity. The specific binding interactions between FBF-2 and LST-1 A and B, particularly in the N- and C-terminal regions, determine the impact on mRNA regulation, highlighting the functional diversity of FBF binding sites in LST-1.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Patrick R. Smith, Sarah Loerch, Nikesh Kunder, Alexander D. Stanowick, Tzu-Fang Lou, Zachary T. Campbell
Summary: The eEF2 kinase plays a crucial role in regulating ribosome availability and processing body abundance by inhibiting translation, impacting the state of ribosomes and playing a key role in sensory neurons.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Bradley P. Klemm, Andrew P. Sikkema, Allen L. Hsu, James C. Horng, Traci M. Tanaka Hall, Mario J. Borgnia, Roel M. Schaaper
Summary: This study reveals the allosteric activation of a dGTPase by dATP, providing new insights into the regulatory function of dNTPases.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Patrick R. Smith, Sapna C. Pandit, Sarah Loerch, Zachary T. Campbell
Summary: In addition to their central functions in translation, ribosomes can adopt inactive structures that are fully assembled yet devoid of mRNA. The abundance of idle ribosomes is influenced by a broad range of biological conditions, and these vacant ribosomes may provide a means to exclude ribosomes from translation while also protecting them from degradation. Regulating the balance between idle and active ribosomes may provide a way to fine-tune translation.
TRENDS IN BIOCHEMICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Rebecca Chase, June Bryan de la Pena, Patrick R. Smith, Jennifer Lawson, Tzu-Fang Lou, Alexander D. Stanowick, Bryan J. Black, Zachary T. Campbell
Summary: Nociceptors are sensory neurons that play a crucial role in pain sensation. A recent study explored the potential of using sensory neurons derived from human induced pluripotent stem cells (hiPSCs) as a model for nociceptor research. The study compared the gene expression profiles of hiPSC-derived sensory neurons with mouse dorsal root ganglion (DRG) tissues and found similarities in key pain-related transcripts. Additionally, the study identified a translation factor called eIF5A as a potential target for inflammation-associated pain. Inhibition of eIF5A activity showed promising results in preventing pain hypersensitivity in vivo and reducing hiPSC activity in vitro.
Article
Neurosciences
Nikesh Kunder, June Bryan de la Pena, Tzu-Fang Lou, Rebecca Chase, Prarthana Suresh, Jennifer Lawson, Tarjani Shukla, Bryan Black, Zachary T. Campbell
Summary: In this study, the researchers found that HuR protein plays an important role in translation and local control of mRNA stability. It also reveals a new biological function for a broadly conserved post-transcriptional regulatory factor.
JOURNAL OF NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Karina Jouravleva, Dmitrij Golovenko, Gabriel Demo, Robert C. Dutcher, Traci M. Tanaka Hall, Phillip D. Zamore, Andrei A. Korostelev
Summary: The study of the structures of Drosophila Dicer-1 reveals the collaborative mechanism of Dicer-1 and Loqs-PB in different stages, including before and after pre-miRNA binding, as well as after cleavage and product release. The findings suggest that the Dicer-1???Loqs-PB complex plays a crucial role in specific binding and cleavage of pre-miRNA, facilitating product release.
Editorial Material
Biochemistry & Molecular Biology
Meg Critcher, Lara A. Gruijs da Silva, Dorothee Dormann, Zachary T. Campbell, Thi Khanh Le, Palma Rocchi, Michele Sorgenfrei
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Article
Neurosciences
June Bryan de la Pena, Rebecca Chase, Nikesh Kunder, Patrick R. Smith, Tzu-Fang Lou, Alexander Stanowick, Prarthana Suresh, Tarjani Shukla, Samuel E. Butcher, Theodore J. Price, Zachary T. Campbell
Summary: The stability of RNA is carefully controlled, and the suspension of nonsense-mediated decay (NMD) promotes pain by stimulating the integrated stress response (ISR).
JOURNAL OF NEUROSCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Meghan S. Warden, Eugene F. DeRose, Joel Tamayo, Geoffrey A. Mueller, Elizabeth R. Gavis, Traci M. Tanaka Hall
Summary: The Drosophila melanogaster protein Glorund (Glo) represses nos translation by recognizing both G-tract and UA-rich motifs using its quasi-RNA recognition motifs (qRRMs). The study shows that any two qRRMs are sufficient for nos translation repression. This research reveals how multiple RNA recognition modules within a protein can diversify the regulation of recognized RNAs.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Chen Qiu, Zihan Zhang, Robert N. Wine, Zachary T. Campbell, Jun Zhang, Traci M. Tanaka Hall
Summary: This study reveals that the intrinsically disordered region (IDR) at the C-terminus of FBF-2 protein autoinhibits its RNA-binding affinity. The interaction between LST-1 and the C-terminal region of FBF-2 releases the autoinhibition and increases the RNA-binding affinity. This regulatory mechanism explains the interdependence of FBF-2 and LST-1 in germline stem cell self-renewal.
NATURE COMMUNICATIONS
(2023)
Article
Medicine, Research & Experimental
Eric Wistrom, Rebecca Chase, Patrick R. Smith, Zachary T. Campbell
Summary: This article presents methods for identifying and validating pain-related genes, provides a list of genes associated with pain behavior, and analyzes their expression patterns. It also discusses the potential of forward genetic screening approaches to improve the identification of pain genes.
WIRES MECHANISMS OF DISEASE
(2022)
Review
Chemistry, Physical
Laura K. Rivera-Tarazona, Zachary T. Campbell, Taylor H. Ware
Summary: Stimuli-responsive materials undergo controllable changes in response to external cues, and Engineered Living Materials (ELMs) combining living cells and synthetic materials have shown promising responses to biochemical and physical stimuli. Advances in genetic engineering and processing-property relationships of ELMs have enabled their applications in environmental sensors, biomedical sensors, drug delivery vehicles, and soft robots.