Article
Plant Sciences
Qiongli Jin, Linqi Zhang, Saiyan Hu, Guangbo Wei, Zhiye Wang
Summary: RNA transcripts have various secondary and tertiary structures that regulate biological functions. This study optimized DMS-MaPseq for analyzing RNA secondary structure in rice and profiled the structure of a gene involved in phosphate homeostasis. The results demonstrated the applicability of DMS-MaPseq in studying RNA structure-mediated regulation in crops.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Eleni Makraki, Sophia Miliara, Michalis Pagkalos, Michael Kokkinidis, Efstratios Mylonas, Vasiliki E. Fadouloglou
Summary: The non-coding 6S RNA binds to the RNA polymerase-s(70) holoenzyme to inhibit transcription during the stationary phase in bacteria. The binding is reversed upon outgrowth from the stationary phase. Structural characterization using Small Angle X-ray Scattering shows that binding to a small product RNA results in conformational changes of 6S, leading to compaction of its size and expansion of its central domain. This study improves our understanding of the structural basis of 6S regulation and provides insights into the mechanistic control of 6S transcription.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biology
Nils Peiter, Michael Rother
Summary: This study established a reporter system by engineering a bacterial enzyme into an archaeal selenoprotein to evaluate selenium insertion in Methanococcus maripaludis. The findings defined a minimal SECIS element required for Sec insertion and demonstrated the essentiality of a conserved structural motif for its function.
LIFE SCIENCE ALLIANCE
(2022)
Article
Agronomy
Zhifei Liu, Xinran Cao, Chengming Yu, Xuefeng Yuan
Summary: This study analyzed the structure of the viral satellite RNA of cucumber mosaic virus TA-Tb using the SHAPE method. Through optimization, the RNA structure was clearly elucidated, revealing the presence of non-structured, single-stranded flexible regions, particularly prominent at nucleotide positions 145 to 200. These findings provide insights into the mechanism by which satCMV TA-Tb regulates the pathogenicity and replication of its helper virus.
Article
Biochemistry & Molecular Biology
Elnaz Banijamali, Lorenzo Baronti, Walter Becker, Joanna J. Sajkowska-Kozielewicz, Ting Huang, Christina Palka, David Kosek, Lara Sweetapple, Juliane Mueller, Michael D. Stone, Emma R. Andersson, Katja Petzold
Summary: RNA regulation can be achieved by a second targeting RNA molecule, and SHAPE can be used to study the structure of RNA molecules and resolve RNA:protein interactions. In this study, SHAPE is applied to investigate RNA-mediated binding processes in RNA:RNA and RNA:RNA-RBP complexes. The results reveal the importance of seed and compensatory region interactions in the binding of microRNA to mRNA targets, providing complementary evidence for luciferase-assay-based evaluation.
Article
Multidisciplinary Sciences
Ryota Yamagami, Jacob P. Sieg, Sarah M. Assmann, Philip C. Bevilacqua
Summary: RNA structure is crucial for cellular events, and the study of tRNA structure is challenging. The tRNA structure-seq workflow accurately determines the in vivo secondary structure of tRNA and provides insights into tRNA abundance and natural modifications.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Immunology
Xuhua Xia
Summary: The design of Pfizer/BioNTech and Moderna mRNA vaccines involves various optimizations such as enhancing translation efficiency and improving mRNA stability. Different optimizations may conflict with each other, requiring compromises to be made.
Review
Biochemistry & Molecular Biology
Sharon Aviran, Danny Incarnato
Summary: RNA structure probing experiments are a straightforward way to determine RNA molecule structures. However, the dynamic nature of RNA poses challenges in interpreting the experimental data. Recent efforts have focused on developing computational methods to reconstruct alternative RNA conformations, enabling the study of RNA structure ensembles even in living cells.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Elizabeth A. Jolley, Helen Yakhnin, David C. Tack, Paul Babitzke, Philip C. Bevilacqua
Summary: RNA structure plays a role in regulating bacterial gene expression, including in response to temperature changes. By studying the response of Bacillus subtilis at different temperatures, the researchers found that RNA structure undergoes changes and exhibits nonmonotonic reactivity trends. They also discovered RNATs that control the expression of glpF and glpT, genes that are involved in thermoprotection.
Review
Pharmacology & Pharmacy
Dandan Shen, Bo Wang, Ya Gao, Lijuan Zhao, Yaping Bi, Jinge Zhang, Ning Wang, Huiqin Kang, Jingru Pang, Ying Liu, Luping Pang, Zhe-Sheng Chen, Yi-Chao Zheng, Hong-Min Liu
Summary: This review focuses on the studies of structure, inhibitors development, and biological function of FTO and ALKBH5.
ACTA PHARMACEUTICA SINICA B
(2022)
News Item
Chemistry, Multidisciplinary
Yifei Zhou, Chuanzheng Zhou
Summary: Therapeutic applications of DNAzymes are restricted due to their low effectiveness in vivo, but a promising approach has been developed to construct DNAzymes with high gene-silencing efficiency in mammalian cells by incorporating chemical modifications into an existing DNAzyme scaffold.
Article
Biochemistry & Molecular Biology
Kamilla Grzywacz, Agnieszka Chelkowska-Pauszek, Marianna Plucinska-Jankowska, Marek Zywicki
Summary: Chemical probing has long been used to study the secondary structure of RNA molecules. Recently, protocols for simultaneous analysis of multiple RNAs have been developed, allowing investigation of RNA structure dynamics in vivo. The SHAPE-MaP method is a popular approach for this purpose. In this study, we evaluated the protocol by examining the influence of reverse transcription enzymes, buffer conditions, and chemical probes on cDNA library properties and mutational profiling-derived structural signals.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Naoki Takizawa, Risa Karakida Kawaguchi
Summary: The global secondary structure map of the influenza A virus genome in virion was established using DMS-seq and SHAPE-seq methods. The study identified previously uncharacterized functional RNA structure motifs and validated predicted structures. The results provide evidence that these functional RNA structure motifs are associated with replication and packaging of the viral genome.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
Bo Yu, Pan Li, Qiangfeng Cliff Zhang, Lin Hou
Summary: DiffScan is a computational framework for normalization and differential analysis of RNA structure probing data, which can accurately identify SVRs at nucleotide resolution, demonstrating its compatibility with various structure probing platforms.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Sarah-Luisa Dulk, Silvia Rouskin
Summary: The role of RNA structure is crucial in biological processes. Traditional approaches for solving RNA structure are not high-throughput, while sequencing-based approaches using mutational profiling with dimethyl sulfate (DMS) can infer RNA structure.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Editorial Material
Genetics & Heredity
Darren J. Burgess
NATURE REVIEWS GENETICS
(2018)
Editorial Material
Genetics & Heredity
Darren J. Burgess
NATURE REVIEWS GENETICS
(2019)
Editorial Material
Genetics & Heredity
Darren J. Burgess
NATURE REVIEWS GENETICS
(2019)
Editorial Material
Genetics & Heredity
Darren J. Burgess
NATURE REVIEWS GENETICS
(2019)
Editorial Material
Genetics & Heredity
Darren J. Burgess
NATURE REVIEWS GENETICS
(2019)
Editorial Material
Genetics & Heredity
Darren J. Burgess
NATURE REVIEWS GENETICS
(2019)
Editorial Material
Genetics & Heredity
Darren J. Burgess
NATURE REVIEWS GENETICS
(2019)
Editorial Material
Genetics & Heredity
Darren J. Burgess
NATURE REVIEWS GENETICS
(2019)
Editorial Material
Genetics & Heredity
Darren J. Burgess
NATURE REVIEWS GENETICS
(2019)
Editorial Material
Genetics & Heredity
Darren J. Burgess
NATURE REVIEWS GENETICS
(2019)
Editorial Material
Genetics & Heredity
Darren J. Burgess
NATURE REVIEWS GENETICS
(2019)
Editorial Material
Genetics & Heredity
Darren J. Burgess
NATURE REVIEWS GENETICS
(2019)
Editorial Material
Genetics & Heredity
Darren J. Burgess
NATURE REVIEWS GENETICS
(2019)
Editorial Material
Genetics & Heredity
Darren J. Burgess
NATURE REVIEWS GENETICS
(2019)
Editorial Material
Genetics & Heredity
Darren J. Burgess
NATURE REVIEWS GENETICS
(2019)
