Article
Oncology
Xiao Han, Mengke Wang, Yong-Liang Zhao, Ying Yang, Yun-Gui Yang
Summary: RNA methylations play critical roles in regulating various biological processes and their dysregulation is closely related to human malignancies. The advancements in high-throughput sequencing technology have facilitated research on how methylation of coding and non-coding RNAs regulates cancer progression. This review discusses the regulatory role of representative RNA modifications in cancers and their potential clinical value in diagnostic and therapeutic implications.
SEMINARS IN CANCER BIOLOGY
(2021)
Review
Pharmacology & Pharmacy
Chen Li, Pengfei Xu, Yurong Huang, Yuting Wang, Yajie Wu, Hui Li, Yanhui Peng, Xiao Wang, Guoying Li, Juan He, Chenggui Miao
Summary: Depression is a complex disorder caused by various factors. RNA methylations play a key role in many biological mechanisms and are closely linked to depression. Recent research has deepened our understanding of the pathogenesis of depression and provided new targets for its prevention and treatment.
BIOCHEMICAL PHARMACOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Damien Bregeon, Ludovic Pecqueur, Sabrine Toubdji, Claudia Sudol, Murielle Lombard, Marc Fontecave, Valerie de Crecy-Lagard, Yuri Motorin, Mark Helm, Djemel Hamdane
Summary: Recent studies have revealed that RNA molecules undergo post-transcriptional modifications, including dihydrouridine modifications that were originally believed to be specific to tRNA. These modifications have been found not only in tRNA but also in mRNA, and they play important roles in meiotic chromosome segregation, protein translation rates, and cell proliferation. Dihydrouridine modifications are introduced by dihydrouridine synthases.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Xi Zhao, Xianglin Ji, Jin Qu, Kai Xie, Zixun Wang, Peilin Fang, Yuan Wang, Youyang Wan, Yang Yang, Wenjun Zhang, Peng Shi
Summary: RNA epigenetics is a new layer of mechanism to regulate gene expression. This study presents a molecule proximity-based technique for simultaneous analysis of multiple types of mRNA methylation with specific gene information in living cells. The technique utilizes a chip with vertically aligned diamond nanoneedles to access the intracellular domain and isolate the mRNAs while keeping the cells alive. The isolated RNAs are then encoded, amplified, and visualized to derive a quantitative measurement of the associated gene-specific m6A or m1A modifications. The study reveals the involvement of m6A and m1A in mRNA in cellular stress response and the rare occurrence of m6A and m1A dual methylation in a specific transcript.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Xiao-Meng Tang, Tian -Tian Ye, Xue-Jiao You, Xiao-Ming Yin, Jiang -Hui Ding, Wen-Xuan Shao, Meng -Yuan Chen, Bi-Feng Yuan, Yu-Qi Feng
Summary: In this study, a method for purifying plant ribosomal RNA (rRNA) was proposed and modifications in plant 18S rRNA and 25S rRNA were characterized using LC-ESI-MS/MS. The study revealed the presence of new modifications in plant rRNAs, including 2 modifications in 18S rRNA and 4 modifications in 25S rRNA. Exposure to cadmium induced significant changes in rRNA modifications, highlighting the importance of rRNA modifications in response to environmental stress. The discovery of new modifications expands our understanding of plant rRNA modifications and enhances the investigation of the functional roles of plant ribosomes in gene expression regulation.
CHINESE CHEMICAL LETTERS
(2023)
Review
Biochemistry & Molecular Biology
Hyein Jo, Kyeonghee Shim, Dooil Jeoung
Summary: RNA methylations play critical roles in various RNA processes and regulators of RNA methylations show differential expression between tumor tissues/cancer cells and normal tissues/adjacent cells. Targeting m6A regulators can be a strategy for developing anticancer drugs and these drugs are currently being tested in clinical trials. m6A regulators also have the potential to enhance the effects of current chemotherapy drugs. This review summarizes the roles of m6A regulators in cancer initiation and progression, autophagy, and anticancer drug resistance, as well as their potential as diagnostic markers and therapeutic targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Editorial Material
Cell Biology
Marta Montes, Maite Huarte
Summary: A new study reveals that increased reactive oxygen species in cancer cause widespread, sequence-specific modifications of guanines in microRNA seed regions, altering their target genes and impacting tumorigenesis.
NATURE CELL BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Chenglong Cheng, Yajie Wu, Xin Wang, Qiuyun Xue, Yurong Huang, Faxue Liao, Xiao Wang, Qiangjun Duan, Chenggui Miao
Summary: RNA methylation, especially m6A methylation, plays a crucial role in the occurrence and development of hepatic fibrosis (HF). The pathophysiological regulation of HF by RNA methylation is achieved through the interaction of methyltransferases, demethylases, and reading proteins, which may provide a new therapeutic and diagnostic target.
CELL AND BIOSCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Olivier Finet, Carlo Yague-Sanz, Lara Katharina Kruger, Phong Tran, Valerie Migeot, Max Louski, Alicia Nevers, Mathieu Rougemaille, Jingjing Sun, Felix G. M. Ernst, Ludivine Wacheul, Maxime Wery, Antonin Morillon, Peter Dedon, Denis L. J. Lafontaine, Damien Hermand
Summary: This study reveals the importance of RNA modifications in gene expression control, and develops a new integrated pipeline to detect modifications in a transcriptome-wide manner. The researchers identify a novel RNA modification and demonstrate its biological function in mRNA of fission yeast. They also find that the modification is evolutionarily conserved in human cells.
Review
Biochemistry & Molecular Biology
Olivier Finet, Carlo Yague-Sanz, Florian Marchand, Damien Hermand
Summary: The universal dihydrouridine (D) mark, generated by the Dus family of enzymes, has unique structural characteristics and potential biological significance. Recent studies have shown that D is not only present in tRNAs but also in mRNAs, highlighting its critical physiological relevance.
Article
Virology
Alice Decombe, Priscila El Kazzi, Etienne Decroly
Summary: Viral RNAs (vRNAs) can be modified by methylation, which affects the biological functions of RNA related to sequence, structure, and protein interactions. 2'-O-methylation was initially found to target the cap structure of mRNA, and recently, it was also reported in vRNA. The consequences of these methylations are still unclear, as they have been associated with both pro-viral and anti-viral effects. This article focuses on the mechanisms and potential roles of vRNA 2'-O-methylation in viral replication.
CURRENT OPINION IN VIROLOGY
(2023)
Review
Biochemistry & Molecular Biology
Yan Zhang, Liang Lu, Xiaoyu Li
Summary: This article reviews the existing knowledge of RNA modification detection technologies and discusses the challenges for current detection tools, providing valuable information for a comprehensive understanding of the epitranscriptome.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2022)
Review
Pharmacology & Pharmacy
Wanwan Zhou, Changhui Wang, Jun Chang, Yurong Huang, Qiuyun Xue, Chenggui Miao, Peng Wu
Summary: Cardiovascular diseases are the leading cause of morbidity and mortality worldwide, necessitating new diagnostic biomarkers and therapeutic measures. RNA methylations play crucial roles in the pathogenesis of CVDs, contributing to the elucidation of pathological mechanisms and discovery of new therapeutic targets.
FRONTIERS IN PHARMACOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Marta Jedynak-Slyvka, Agata Jabczynska, Roman J. Szczesny
Summary: Mitochondria, known as the powerhouses of cells, play crucial roles in energy production, apoptosis, calcium homeostasis, and regulation of the immune response. Abnormalities in mitochondria can lead to severe diseases, making it important to study their functions and physiological consequences. Despite progress in understanding RNA processing in mitochondria, there are still many unknowns and controversies in the field.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Anthony Yulin Chen, Michael C. Owens, Kathy Fange Liu
Summary: Gene expression regulation is critical, particularly in the nervous system, and can be achieved through enzyme-mediated RNA modifications known as epitranscriptomic regulation. RNA modifications, which are chemically diverse covalent modifications of RNA nucleotides, provide a robust and rapid mechanism for gene expression regulation. Recent evidence suggests potential crosstalk and coordination of modifications across RNA species, revealing a new direction in epitranscriptomic research.
MOLECULAR PSYCHIATRY
(2023)
Review
Biochemical Research Methods
Mette Thorsing, Patricia Teixeira dos Santos, Birgitte Haahr Kallipolitis
CURRENT OPINION IN BIOTECHNOLOGY
(2018)
Article
Microbiology
Patricia T. dos Santos, Pilar Menendez-Gil, Dharmesh Sabharwal, Jens-Henrik Christensen, Maja Z. Brunhede, Eva M. S. Lillebaek, Birgitte H. Kallipolitis
FRONTIERS IN MICROBIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Marina Alexeeva, Marivi N. Moen, Kristin Grosvik, Almaz N. Tesfahun, Xiang Ming Xu, Izaskun Muruzabal-Lecumberri, Kristine M. Olsen, Anette Rasmussen, Peter Ruoff, Finn Kirpekar, Arne Klungland, Svein Bjelland
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Joseph A. Ross, Mette Thorsing, Eva Maria Sternkopf Lillebaek, Patricia Teixeira Dos Santos, Birgitte H. Kallipolitis
Article
Biochemistry & Molecular Biology
Catarina M. Marinho, Patricia T. Dos Santos, Birgitte H. Kallipolitis, Jorgen Johansson, Dmitriy Ignatov, Duarte N. Guerreiro, Pascal Piveteau, Conor P. O'Byrne
Article
Biochemistry & Molecular Biology
Christel Enroth, Line Dahl Poulsen, Soren Iversen, Finn Kirpekar, Anders Albrechtsen, Jeppe Vinther
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Rita Pinto, Cathrine B. Vagbo, Magnus E. Jakobsson, Yeji Kim, Marijke P. Baltissen, Marie-Francoise O'Donohue, Ulises H. Guzman, Jedrzej M. Malecki, Jie Wu, Finn Kirpekar, Jesper Olsen, Pierre-Emmanuel Gleizes, Michiel Vermeulen, Sebastian A. Leidel, Geir Slupphaug, Pal O. Falnes
NUCLEIC ACIDS RESEARCH
(2020)
Article
Microbiology
Lang Sun, Pernille Kronholm Rasmussen, Yinlei Bai, Xiulan Chen, Tanxi Cai, Jifeng Wang, Xiaojing Guo, Zhensheng Xie, Xiang Ding, Lili Niu, Nali Zhu, Xuefu You, Finn Kirpekar, Fuquan Yang
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2020)
Article
Biochemistry & Molecular Biology
Simon Rose, Sylvie Auxilien, Jesper F. Havelund, Finn Kirpekar, Harald Huber, Henri Grosjean, Stephen Douthwaite
NUCLEIC ACIDS RESEARCH
(2020)
Article
Limnology
Clemens Schauberger, Mathias Middelboe, Morten Larsen, Logan M. Peoples, Douglas H. Bartlett, Finn Kirpekar, Ashley A. Rowden, Frank Wenzhoefer, Bo Thamdrup, Ronnie N. Glud
Summary: Research on prokaryotic and viral abundance in hadal trenches and abyssal regions revealed a high spatial heterogeneity in hadal sediments, indicating a higher relative importance of viruses in hadal settings compared to abyssal environments.
LIMNOLOGY AND OCEANOGRAPHY
(2021)
Article
Immunology
Marina Alexeeva, Marivi Nabong Moen, Xiang Ming Xu, Anette Rasmussen, Ingar Leiros, Finn Kirpekar, Arne Klungland, Lene Alsoe, Hilde Nilsen, Svein Bjelland
Summary: Uracil arises in DNA through deamination and replication errors, and its repair by uracil-DNA glycosylase and the base excision repair pathway are crucial in maintaining genomic stability. The mechanisms of DNA incision following uracil excision are still uncertain, but it has been shown that hUNG may play a role in this process and contribute to class switch recombination activity in cells deficient in other repair enzymes.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Microbiology
Rikke S. S. Thomasen, Magnus Ganer Jespersen, Katrine Jorgensen, Patricia T. dos Santos, Eva M. Sternkopf Lillebaek, Marianne N. Skov, Michael Kemp, Birgitte H. Kallipolitis
Summary: The study reveals that the regulatory activities of CcpA contribute to the sensitivity of L. monocytogenes to the antimicrobial activity of FFAs. However, strains with FFA-tolerance can still be targeted by the anti-virulent activity of FFAs.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Rikke S. S. Thomasen, Patricia T. dos Santos, Eva Sternkopf M. Lillebaek, Marianne N. Skov, Michael Kemp, Birgitte H. Kallipolitis
Summary: Free fatty acids (FFAs) have strong antimicrobial properties against pathogens, but the response of Listeria monocytogenes to FFAs is not fully understood. This study identified mutations in genes involved in wall teichoic acid (WTA) glycosylations that confer tolerance against several FFAs in L. monocytogenes. The FFA tolerant strains lack GlcNAc on their WTAs, resulting in a more hydrophilic surface and reduced binding of FFAs. Importantly, lack of GlcNAc on WTAs also confers tolerance toward acid stress.
FRONTIERS IN MICROBIOLOGY
(2022)