Article
Biochemistry & Molecular Biology
Casey S. Jacobsen, Prince Salvador, John F. Yung, Sabrina Kragness, Herra G. Mendoza, Gail Mandel, Peter A. Beal
Summary: Adenosine deaminases acting on RNA (ADARs) catalyze the hydrolytic deamination of adenosine to inosine in duplex RNA, resulting in an effective A-to-G edit. ADAR editing can lead to recoding events and alterations in RNA function. One limitation of ADAR is its preference for editing adenosines with specific neighboring nucleotides, but new strategies and approaches are being developed to overcome this.
ACS CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Analytical
Yafu Wang, Huiyu Niu, Kui Wang, Ge Wang, Junwei Liu, Tony D. James, Hua Zhang
Summary: This study developed a near-infrared fluorescent probe YON that can specifically and in real-time monitor and evaluate the health of mitochondrial DNA. YON exhibits ultra-sensitive detection ability and is suitable for interference-free imaging.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Loredana Frassinelli, Elisa Orecchini, Sofian Al-Wardat, Marco Tripodi, Carmine Mancone, Margherita Doria, Silvia Galardi, Silvia Anna Ciafre, Alessandro Michienzi
Summary: ADAR2 acts as a suppressor of L1 retrotransposition by inhibiting its activity, forming a complex with multiple non-ribosomal ADAR2-interacting factors.
Review
Biochemistry & Molecular Biology
Khadija Hajji, Jiri Sedmik, Anna Cherian, Damiano Amoruso, Liam P. P. Keegan, Mary A. A. O'Connell
Summary: The ADAR enzymes play important roles in neuronal function and innate immune control. This review focuses on ADAR2 proteins involved in efficient, highly site-specific RNA editing. The review covers the history of ADAR2 protein research, structural studies, disease models, and the use of ADAR RNA editing for gene therapy.
Article
Biochemistry & Molecular Biology
Hyung Joo Lee, Yiran Hou, Ju Heon Maeng, Nakul M. Shah, Yujie Chen, Heather A. Lawson, Hongbo Yang, Feng Yue, Ting Wang
Summary: This study systematically investigates the epigenomic and transcriptomic profile of transposable elements (TEs) in zebrafish tissues. The results show that TEs significantly contribute to gene regulation in zebrafish, with a portion of TEs being in active regulatory states. Specific TE subfamilies are found to be enriched in different tissues, and TE-derived transcriptional units are expressed across tissues.
Article
Biochemistry & Molecular Biology
Andrew T. M. Bagshaw, Neil J. Gemmell
Summary: In recent years, scientists have shifted their focus from studying the relationships between adjacent nucleotides to exploring the larger scale structure of DNA. A little-known technique called non-denaturing bisulfite modification of genomic DNA in conjunction with high-throughput sequencing has provided valuable insights. This technique has revealed a gradient in reactivity that increases towards the 5' end of poly-dC:dG mononucleotide repeats, suggesting the presence of positive-roll bending not predicted by existing models. Furthermore, these repeats are enriched at positions relative to the nucleosome dyad that bend towards the major groove, providing important information about DNA packaging.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Ananya Paul, Abdelbasset A. Farahat, David W. Boykin, W. David Wilson
Summary: This study aims to develop a detailed understanding of the binding thermodynamics of pyridine-based sequence-specific minor groove binders with different terminal cationic groups. The results reveal that the DNA sequence and compound structure play a crucial role in the molecular recognition and thermodynamics of minor groove complexes.
Article
Multidisciplinary Sciences
Juntaek Oh, Tiezheng Jia, Jun Xu, Jenny Chong, Peter B. Dervan, Dong Wang
Summary: It is found that hairpin pyrrole-imidazole (Py-Im) polyamides can cause transcriptional arrest of Pol II, which cannot be rescued by transcription factor TFIIS. Further structural studies revealed that the Py-Im oligomer directly interacts with RNA Pol II residues, inducing compression of the downstream DNA duplex, preventing Pol II forward translocation, and inducing Pol II backtracking.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Gang Xu, Yezi Wu, Tongyang Xiao, Furong Qi, Lujie Fan, Shengyuan Zhang, Jian Zhou, Yanhua He, Xiang Gao, Hongxiang Zeng, Yunfei Li, Zheng Zhang
Summary: This study reveals that SARS-CoV-2 infection activates a strong innate immune response in lung epithelial cells and uncovers the mechanism by which the virus disrupts the host immune system. Furthermore, it is found that SARS-CoV-2 proteins undergo ubiquitination during infection, and specific ubiquitination sites enhance viral infection. The identification of new antiviral targets is also provided.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Article
Plant Sciences
Jing Zhou, Siqi Chen, Wenjiao Shi, Rakefet David-Schwartz, Sutao Li, Fulin Yang, Zhanxi Lin
Summary: This study provides a comprehensive understanding of DEGs involved in drought stress at the transcriptome level in Giant Juncao, with insights into the molecular mechanisms of drought tolerance and diverse genetic resources for drought tolerance research. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed abiotic stress-responsive genes and pathways, and weighted gene co-expression network analysis predicted interrelationships between genes. The study identified important drought-rehydration-responsive protein families and modules involved in photosynthesis and plant hormone signal transduction under drought and rehydration conditions.
Article
Chemistry, Medicinal
Ke Li, Sarah B. Krueger, Steven C. Zimmerman
Summary: DM1 is a neuromuscular disorder caused by repeat expansion in the DMPK gene. A rationally designed small molecule has been found to selectively inhibit transcription and improve molecular features in DM1 model cells. This compound represents a new structure type for potential future optimization.
Article
Biology
Dhruva Katrekar, Yichen Xiang, Nathan Palmer, Anushka Saha, Dario Meluzzi, Prashant Mali
Summary: Adenosine deaminases acting on RNA (ADARs) have potential for programmable RNA editing, but their exogenous delivery leads to non-specific targeting and low enzymatic activity on certain RNA motifs. By performing a deep mutational scan of the ADAR2 deaminase domain, we improved enzymatic activity and developed a split-ADAR2 deaminase with significantly higher specificity for RNA editing. This systematic engineering of the ADAR2 deaminase domain has important implications for RNA biotechnology applications.
Article
Biochemistry & Molecular Biology
Devin P. Bendixsen, Tanner B. Pollock, Gianluca Peri, Eric J. Hayden
Summary: The study used a phylogenetic approach to evaluate the activity changes of self-cleaving ribozymes during mammalian evolution, finding that high activity ribozymes have been conserved in most lineages. Additionally, a reduction in ribozyme activity was observed multiple times throughout mammalian evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Cell Biology
Lokanand Koduru, Meiyappan Lakshmanan, Yi Qing Lee, Pooi-Leng Ho, Pei-Yu Lim, Wei Xuan Ler, Say Kong Ng, Dongseok Kim, Doo-Sang Park, Mazlina Banu, Dave Siak Wei Ow, Dong-Yup Lee
Summary: This study investigates the differences in growth, intestinal persistence, and postbiotic biosynthesis of six representative lactic acid bacteria (LAB) and their interactions with gut bacteria under different dietary regimes. The findings suggest that the attributes of probiotics are specific to both diet and species, and cannot be solely explained by genomics. Additionally, high-fat/low-carb diets may have detrimental effects on most LAB. The results highlight the importance of personalized probiotic design.
Article
Biochemistry & Molecular Biology
Matthew Dukeshire, David Schaeper, Pravina Venkatesan, Amirhossein Manzourolajdad
Summary: Understanding the life cycle and pathogenicity of SARS-CoV-2 variants is crucial during the COVID-19 pandemic. In this study, researchers identified variant-specific evolutionary changes in long-range RNA-RNA interactions, providing insights into novel interactions. Variant-specific analyses are important for identifying potential interactions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Neurosciences
Chengwen Zhou, Li Ding, M. Elizabeth Deel, Elizabeth A. Ferrick, Ronald B. Emeson, Martin J. Gallagher
NEUROBIOLOGY OF DISEASE
(2015)
Article
Medicine, Research & Experimental
Zhaiyi Zhang, Manli Shen, Paul J. Gresch, Masoud Ghamari-Langroudi, Alexander G. Rabchevsky, Ronald B. Emeson, Stefan Stamm
EMBO MOLECULAR MEDICINE
(2016)
Review
Genetics & Heredity
Stefan Stamm, Samuel B. Gruber, Alexander G. Rabchevsky, Ronald B. Emeson
Article
Multidisciplinary Sciences
Olga Jasnovidova, Tomas Klumpler, Karel Kubicek, Sergei Kalynych, Pavel Plevka, Richard Stefl
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2017)
Article
Neurosciences
Richard T. O'Neil, Xiaojing Wang, Michael V. Morabito, Ronald B. Emeson
Article
Multidisciplinary Sciences
Elizabeth A. Ferrick-Kiddie, Joshua J. C. Rosenthal, Gregory D. Ayers, Ronald B. Emeson
SCIENTIFIC REPORTS
(2017)
Article
Biochemical Research Methods
Pavel Brazda, Ondrej Sedo, Karel Kubicek, Richard Stefl
Article
Biochemistry & Molecular Biology
Zhong Han, Olga Jasnovidova, Nouhou Haidara, Agnieszka Tudek, Karel Kubicek, Domenico Libri, Richard Stefl, Odil Porrua
Article
Biochemistry & Molecular Biology
Pavel Brazda, Magdalena Krejcikova, Aiste Kasiliauskaite, Eliska Smirakova, Tomas Klumpler, Robert Vacha, Karel Kubicek, Richard Stefl
JOURNAL OF MOLECULAR BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Kayla M. Shumate, Sadik T. Tas, Ege T. Kavalali, Ronald B. Emeson
Summary: Caps editing plays a crucial role in modulating neurotransmission and synaptic plasticity, particularly at inhibitory synapses. The edited Cadps transcripts increase the proportion of synapses containing CAPS1, and editing is regulated by neuronal activity.
JOURNAL OF NEUROCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Turnee N. Malik, Erin E. Doherty, Vandana M. Gaded, Theodore M. Hill, Peter A. Beal, Ronald B. Emeson
Summary: ADAR-mediated RNA editing modulates various cellular pathways such as innate immunity and protein recoding and is considered as a strategy for treating genetic disorders. Research has shown that intracellular acidification increases RNA editing, mainly due to enhanced ADAR base-flipping and deamination rate under acidic pH conditions.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Lisa-Marie Appel, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, Martin G. Puchinger, Sebastian Kostrhon, Carmen Ebenwaldner, Marek Sebesta, Etienne Beltzung, Karl Mechtler, Gen Lin, Anna Vlasova, Martin Leeb, Rushad Pavri, Alexander Stark, Altuna Akalin, Richard Stefl, Carrie Bernecky, Kristina Djinovic-Carugo, Dea Slade
Summary: The study reveals that PHF3 acts as a reader of the phosphorylated RNA polymerase II C-terminal domain through its SPOC domain, regulating transcription, mRNA stability, and neuronal gene expression.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Aiste Kasiliauskaite, Karel Kubicek, Tomas Klumpler, Martina Zanova, David Zapletal, Eliska Koutna, Jiri Novacek, Richard Stefl
Summary: This study visualized the architecture of Spt6 from Saccharomyces cerevisiae using cryo-electron microscopy and small-angle X-ray scattering, and found that the flexible N- and C-termini of Spt6 are critical for its function. The N-terminal region of Spt6 prevents its binding to Pol II CTD, Pol II CTD-linker, pre-formed intact nucleosomes and nucleosomal DNA. Additionally, Spt6 promotes nucleosome assembly in vitro through the cooperation between its intrinsically disordered and structured regions.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
David Zapletal, Eliska Taborska, Josef Pasulka, Radek Malik, Karel Kubicek, Martina Zanova, Christian Much, Marek Sebesta, Valeria Buccheri, Filip Horvat, Irena Jenickova, Michaela Prochazkova, Jan Prochazka, Matyas Pinkas, Jiri Novacek, Diego F. Joseph, Radislav Sedlacek, Carrie Bernecky, Donal O'Carroll, Richard Stefl, Petr Svoboda
Summary: The DExD/H domain of Dicer plays a crucial structural role in mammalian miRNA biogenesis. It locks Dicer in a closed state, facilitating miRNA precursor selection. Absence or mutations of the DExD/H domain unlock Dicer and activate RNAi.
Article
Biochemistry & Molecular Biology
Olga Jasnovidova, Magdalena Krejcikova, Karel Kubicek, Richard Stefl