Article
Oncology
Catherine E. Scull, Guy Twa, Yinfeng Zhang, Naiheng J. Yang, Robert N. Hunter III, Corinne E. Augelli-szafran, David A. Schneider
Summary: A newly identified ribosome biogenesis inhibitor, RBI2, has been shown to inhibit multiple types of cancer cells by inducing rapid polyadenylation and degradation of ribosomal RNA. This mechanism of action is distinct from previously described compounds and offers a potential novel pathway for cancer therapeutics targeting ribosome synthesis. This study reveals the importance of ribosome biogenesis in cancer cell growth and highlights the potential of RBI2 as a promising cancer therapeutic.
Article
Multidisciplinary Sciences
Craig J. Marshall, M. Zuhaib Qayyum, Julie E. Walker, Katsuhiko S. Murakami, Thomas J. Santangelo
Summary: Transcription termination is an important process in regulating gene expression, and the protein Eta has been identified as one of the factors involved in disrupting transcription elongation complexes. By studying the biochemical activities and crystal structure of Eta, researchers have gained insight into its role in transcription termination. The susceptibility of transcription elongation complexes to disruption by termination factors highlights the common features of transcription termination mechanisms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Microbiology
Simona Pilotto, Finn Werner
Summary: Multisubunit RNA polymerases (RNAPs) carry out transcription in all domains of life. During virus infection, RNAPs are targeted by transcription factors encoded by either the cell or the virus, resulting in the global repression of transcription. These repressors serve as versatile molecular probes to study RNAP mechanisms and aid in the development of new antibiotics.
Article
Oncology
Ruth Q. Jacobs, Kaila B. Fuller, Stephanie L. Cooper, Zachariah Carter, Marikki Laiho, Aaron L. Lucius, David A. Schneider
Summary: This study evaluates the specificity of the compound BMH-21 on transcription by Pols I, II, and III. The results show that Pol I is more sensitive to inhibition by BMH-21 compared to Pols II and III. These findings support the ongoing development of BMH-21 and its derivatives as potential therapeutic agents.
Article
Developmental Biology
Zuhui Wang, Wulan Deng
Summary: This review focuses on the single-molecule dynamic features of transcription regulatory events observed in living cells using live-cell single-molecule imaging techniques, and discusses their biological relevance and interpretation in understanding the mechanisms of transcription regulation.
DEVELOPMENTAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Xizi Chen, Xinxin Wang, Weida Liu, Yulei Ren, Xuechun Qu, Jiabei Li, Xiaotong Yin, Yanhui Xu
Summary: RNA polymerase II-mediated eukaryotic transcription begins with the assembly of the preinitiation complex (PIC) on core promoters. The +1 nucleosome, positioned about 40 base pairs downstream of the transcription start site (TSS), acts as a barrier to transcription. The study shows that the PIC-Mediator prefers binding to the T40N nucleosome located at the 40 base pairs downstream of the TSS and contacts the T50N nucleosome, but not the T70N nucleosome. The nucleosome facilitates the organization of PIC-Mediator on the promoter and may contribute to transcription initiation. The study reveals the molecular mechanism of PIC-Mediator organization on chromatin and emphasizes the significance of the +1 nucleosome in regulating transcription initiation.
Article
Biochemical Research Methods
Hannah Spitzer, Scott Berry, Mark Donoghoe, Lucas Pelkmans, Fabian J. Theis
Summary: CAMPA is a deep learning framework that learns representations of molecular pixel profiles from multiplexed images. It clusters these representations to quantify subcellular landmarks and captures interpretable cellular phenotypes. Using this framework, the study reveals the changes in subcellular organization upon perturbation of RNA synthesis, RNA processing, or cell size, and uncovers the links between the molecular composition of membraneless organelles and cell-to-cell variability in bulk RNA synthesis rates.
Article
Cell Biology
Mattia Marenda, Elena Lazarova, Sebastian van de Linde, Nick Gilbert, Davide Michieletto
Summary: Understanding biological function involves identifying and characterizing complex patterns of molecules, which can be quantitatively measured by single-molecule localization microscopy. Interconnected protein clusters are common within nuclear proteins, suggesting an important role in genome organization and function, while absent in ceramides located in the plasma membrane.
JOURNAL OF CELL BIOLOGY
(2021)
Review
Developmental Biology
Alan P. Boka, Apratim Mukherjee, Mustafa Mir
Summary: This article provides an accessible overview of the rapidly expanding family of technologies for single-molecule tracking (SMT), covering the basics, motivation, key technologies, and data analysis of SMT experiments. It aims to enable readers to critically analyze single-molecule studies and inspire the application of SMT to their own work by explaining the trade-offs involved in optimizing parameters.
Review
Chemistry, Multidisciplinary
Wei Chen, Xiaoying Zhao, Nanyang Yang, Xing Li
Summary: Messenger RNA (mRNA) serves as the fundamental information transfer system in cells. Tracking single mRNA from transcription to degradation using fluorescent probes provides spatiotemporal information about how genetic information is transferred from DNA to proteins. RNA aptamers: small-molecule fluorophores (SFs) systems, as exciting alternatives for single mRNA imaging, offer advantages such as fluorogenic ability and minimal perturbation. This review summarizes the five reported RNA aptamers: SFs systems for single mRNA imaging in living cells so far, discusses challenges, and provides prospects for single mRNA imaging applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Biochemistry & Molecular Biology
Mohamed A. Sobhy, Muhammad Tehseen, Masateru Takahashi, Amer Bralic, Alfredo De Biasio, Samir M. Hamdan
Summary: FEN1 is a key component in the molecular machinery of DNA replication and repair. The study reviewed in this article focuses on using single-molecule fluorescence to study important mechanistic details of FEN1 enzymatic reaction, providing a guide for studying other biomolecular enzymatic reactions. The research shows that FEN1 actively bends the substrate to control active site assembly, preventing off-target cleavage.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Multidisciplinary Sciences
Rishi K. Vishwakarma, M. Zuhaib Qayyum, Paul Babitzke, Katsuhiko S. Murakami
Summary: NusG is a transcription elongation factor that induces transcription pausing in bacteria by interacting with a specific sequence in the non-template DNA strand. The interaction between NusG and the DNA rearranges the transcription bubble and affects the conformational changes of RNA polymerase, leading to the inhibition of RNA synthesis. This mechanism of pausing is widely conserved in bacteria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Aleksandr Barulin, Prithu Roy, Jean-Benoit Claude, Jerome Wenger
Summary: The authors introduce optical horn antennas, a nanophotonic platform, for the label-free detection of UV autofluorescence from single proteins. This technique allows for real-time monitoring of protein unfolding and dissociation.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Keyan Bao, Xueli Zhang, Dongyu Li, Wei Sun, Zhenzhao Sun, Jingfei Wang, Ping Zhu
Summary: By studying the structure of reovirus, we have identified the structures of its transcriptase complex in different states and proposed a transcriptional model with five states. Our findings reveal the key regulatory mechanisms during the transcription process of reovirus.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Robert Reichelt, Tamara Rothmeier, Felix Gruenberger, Sarah Willkomm, Astrid Bruckmann, Winfried Hausner, Dina Grohmann
Summary: Posttranscriptional processes in Bacteria include the association of small regulatory RNAs with a target mRNA. This study focuses on the protein interaction partners of archaeal Sm-like proteins and their binding sites. The results show that the archaeal Sm-like protein PfuSmAP1 preferentially binds messenger RNAs and antisense RNAs, and is co-transcriptionally associated with target RNAs.
BIOLOGICAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Fabian Blombach, Katherine L. Smollett, Dina Grohmann, Finn Werner
JOURNAL OF MOLECULAR BIOLOGY
(2016)
Article
Multidisciplinary Sciences
Sarah Schulz, Andreas Gietl, Katherine Smollett, Philip Tinnefeld, Finn Werner, Dina Grohmann
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Multidisciplinary Sciences
Carol Sheppard, Fabian Blombach, Adam Belsom, Sarah Schulz, Tina Daviter, Katherine Smollett, Emilie Mahieu, Susanne Erdmann, Philip Tinnefeld, Roger Garrett, Dina Grohmann, Juri Rappsilber, Finn Werner
NATURE COMMUNICATIONS
(2016)
Review
Biochemistry & Molecular Biology
Carol Sheppard, Finn Werner
Editorial Material
Multidisciplinary Sciences
Thomas Fouqueau, Finn Werner
Article
Multidisciplinary Sciences
Thomas Fouqueau, Fabian Blombach, Ross Hartman, Alan C. M. Cheung, Mark J. Young, Finn Werner
NATURE COMMUNICATIONS
(2017)
Article
Microbiology
Adrian Zander, Sarah Willkomm, Sapir Ofer, Marleen van Wolferen, Luisa Egert, Sabine Buchmeier, Sarah Stoeckl, Philip Tinnefeld, Sabine Schneider, Andreas Klingl, Sonja-Verena Albers, Finn Werner, Dina Grohmann
NATURE MICROBIOLOGY
(2017)
Article
Microbiology
Katherine Smollett, Fabian Blombach, Robert Reichelt, Michael Thomm, Finn Werner
NATURE MICROBIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Fabian Blombach, Darya Ausiannikava, Angelo Miguel Figueiredo, Zoja Soloviev, Tanya Prentice, Mark Zhang, Nanruoyi Zhou, Konstantinos Thalassinos, Thorsten Allers, Finn Werner
NUCLEIC ACIDS RESEARCH
(2018)
Review
Biochemistry & Molecular Biology
Gwenny Cackett, Michal Sykora, Finn Werner
BIOCHEMICAL SOCIETY TRANSACTIONS
(2020)
Article
Biochemistry & Molecular Biology
Isabelle Anna Zink, Thomas Fouqueau, Gabriel Tarrason Risa, Finn Werner, Buzz Baum, Udo Blasi, Christa Schleper
Summary: CRISPR type III systems in archaea can be utilized for gene knockdown technologies to study essential genes, with results showing gene-specific silencing thresholds which can induce growth retardation phenotypes. Strong miniCRISPR constructs exceeding these thresholds can lead to specific mutation of the silencing miniCRISPR array and phenotypical reversion in cultures, with over two thirds of sequenced reverted cultures exhibiting precise excision of targeting spacers from the miniCRISPR array, suggesting an active recombination system acting on CRISPR arrays.
Article
Multidisciplinary Sciences
Fabian Blombach, Thomas Fouqueau, Dorota Matelska, Katherine Smollett, Finn Werner
Summary: Recruitment of RNA polymerase and initiation factors to the promoter is crucial for transcription activation and repression in archaea. The escape of the transcription elongation complex (TEC) is rate-limiting for transcription output during exponential growth, and changes in TEC escape correlate with changes in the transcriptome under oxidative stress. Impaired TEC escape may lead to premature termination of early TECs and accumulation of initiation factors at the promoter.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Simona Pilotto, Thomas Fouqueau, Natalya Lukoyanova, Carol Sheppard, Soizick Lucas-Staat, Luis Miguel Diaz-Santin, Dorota Matelska, David Prangishvili, Alan C. M. Cheung, Finn Werner
Summary: The study investigates two complexes that inhibit RNA polymerase, from Acidianus two-tailed virus and Sulfolobus Turreted Icosahedral Virus, revealing their mechanisms of transcription inhibition. The findings are important for understanding the inhibitory effects of archaeal eukaryotic-like RNA polymerases in virus infection.
NATURE COMMUNICATIONS
(2021)
Article
Virology
Gwenny Cackett, Raquel Portugal, Dorota Matelska, Linda Dixon, Finn Werner
Summary: African swine fever virus (ASFV) causes hemorrhagic fever in domestic pigs, with high mortality rates and no approved vaccines or antivirals. A study on the ASFV genotype II Georgia 2007/1 (GRG) identified molecular determinants for virulence and found differential gene regulation in infected host macrophages.
JOURNAL OF VIROLOGY
(2022)
Review
Biochemistry & Molecular Biology
Thomas Fouqueau, Fabian Blombach, Gwenny Cackett, Alice E. Carty, Dorota M. Matelska, Sapir Ofer, Simona Pilotto, Duy Khanh Phung, Finn Werner
EMERGING TOPICS IN LIFE SCIENCES
(2018)
Article
Biochemical Research Methods
K. Ramki, G. Thiruppathi, Selva Kumar Ramasamy, P. Sundararaj, P. Sakthivel
Summary: A chromone-based ratiometric fluorescent probe L2 was developed for the selective detection of Hg(II) in a semiaqueous solution. The probe exhibited enhanced fluorescence in its aggregated state and even higher fluorescence when chelated with Hg(II). The probe demonstrated high sensitivity and specificity for Hg(II) detection and was successfully applied for imaging Hg(II) in a living model.
Article
Biochemical Research Methods
Qun Zhang, Rui Yang, Gang Liu, Shiyan Jiang, Jiarui Wang, Juqiang Lin, Tingyin Wang, Jing Wang, Zufang Huang
Summary: This research aims to develop a cost-effective and portable method for measuring creatinine levels using the enhanced Tyndall effect phenomenon. The method offers a promising solution for monitoring renal healthcare in resource-limited settings.