Article
Multidisciplinary Sciences
Carlo Yague-Sanz, Valerie Migeot, Marc Larochelle, Francois Bachand, Maxime Wery, Antonin Morillon, Damien Hermand
Summary: Transcription of RNA polymerase II is coupled with remodeling of chromatin, and this study reveals that transcription of RNA polymerase II is also required to maintain nucleosome depletion at RNA polymerase III loci. The mechanism involves the involvement of the Pcr1 transcription factor, which affects local histone occupancy through the associated SAGA complex and a Pol II phospho-S2 CTD / Mst2 pathway. These findings expand our understanding of the role of RNA polymerase II in gene expression.
NATURE COMMUNICATIONS
(2023)
Editorial Material
Genetics & Heredity
Kevin M. Brindle
Summary: MRI-based gene reporters can image gene expression at depth and high resolution, and may be translated to clinical applications. They exploit either endogenous contrast mechanisms or modulate the response to an introduced exogenous contrast agent.
TRENDS IN GENETICS
(2022)
Article
Microbiology
Caetanie F. Tchagang, Thien-Fah Mah, Francois-Xavier Campbell-Valois
Summary: Pseudomonas aeruginosa, a bacteria commonly found in the airways of individuals with cystic fibrosis, forms biofilms resistant to immune clearance and antibiotic treatment. In low-oxygen conditions, P. aeruginosa can use nitrate instead of oxygen to grow. Current fluorescent reporters for studying P. aeruginosa require oxygen for their chromophore maturation, limiting their use in anaerobic conditions. This study evaluated alternative fluorescent proteins and identified two that successfully labeled P. aeruginosa in anoxic environments, enabling the study of P. aeruginosa in biofilms and similar low-oxygen niches.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Cell Biology
Satoshi Uchino, Yuma Ito, Yuko Sato, Tetsuya Handa, Yasuyuki Ohkawa, Makio Tokunaga, Hiroshi Kimura
Summary: A genetically encoded modification-specific intracellular antibody probe was developed to detect RNAP2 Ser2 phosphorylation in living cells, revealing its specific role in transcription complexes and providing insights into genome and cell function.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Jeremy Dufourt, Maelle Bellec, Antonio Trullo, Matthieu Dejean, Sylvain De Rossi, Cyril Favard, Mounia Lagha
Summary: By using the SunTag method, researchers visualized and quantified the translation of single mRNAs in living Drosophila embryos, revealing spatial heterogeneity in mRNA translation efficiency and the presence of translation factories. These findings open up new avenues for understanding the role of gene regulation during development in living multicellular organisms.
Article
Biology
Yucen Hu, Jingxiu Xu, Erqing Gao, Xueyuan Fan, Jieli Wei, Bingcheng Ye, Suhong Xu, Weirui Ma
Summary: Imaging endogenous mRNAs in live animals is achieved using the MS2-based signal amplification with the Suntag system. This technique has high temporal resolution and utilizes 8xMS2 stem-loops, eliminating the need to insert a 1300 nt 24xMS2 into the genome for imaging endogenous mRNAs. By utilizing this tool, gene expression activation and dynamics of endogenous mRNAs in live C. elegans epidermis can be imaged.
Article
Chemistry, Multidisciplinary
Jingfang Zhao, Limin Xiang
Summary: This article introduces the latest advances in three main RNA imaging tools based on the species of interacting molecules, and discusses their advantages from a technical viewpoint. It also explores future directions and states that this emerging field will bring new insights to RNA biology research.
CHINESE JOURNAL OF CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Hyla Allouche-Arnon, Olga Khersonsky, Nishanth D. Tirukoti, Yoav Peleg, Orly Dym, Shira Albeck, Alexander Brandis, Tevie Mehlman, Liat Avram, Talia Harris, Nirbhay N. Yadav, Sarel J. Fleishman, Amnon Bar-Shir
Summary: This research utilizes the MRI system GeneREFORM for two-color imaging, improving the detection of transgene expression in live animals. By designing orthogonal reporter genes and reporter probes, dynamic proton exchange MRI imaging is achieved, paving the way for future deep-tissue multiplexed imaging of gene expression in live animals.
NATURE BIOTECHNOLOGY
(2022)
Article
Chemistry, Analytical
Xiaorui Shi, Chong Hu, Yiyi Jiang, Bin Guo, Chu Tang, Beilei Zhang, Fu Wang
Summary: In this study, we developed a PUF protein-based luciferase reporter system called PUF/miR, which can quantitatively and non-invasively detect miRNA activity in living cells and animal models. The feasibility of this system was validated by monitoring the expression of several types of miRNAs in different cell types and tissues in mice. The reliability and quantitative consistency of the system were further confirmed by quantitative RT-PCR. This innovative approach provides a potential means for noninvasive monitoring of disease-related miRNAs and can contribute to a deeper understanding of miRNA biology.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Virginia L. Pimmett, Matthieu Dejean, Carola Fernandez, Antonio Trullo, Edouard Bertrand, Ovidiu Radulescu, Mounia Lagha
Summary: TATA-containing and INR-containing promoters exhibit distinct dynamics in early Drosophila development, requiring one or two separate rate-limiting steps respectively, with TATA-driven promoters requiring more steps. Core promoter elements play an important role in regulating the rate limiting steps of transcription.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Yujie Li, Lihua Zhang, Haiquan Yang, Yuanyuan Xia, Liming Liu, Xianzhong Chen, Wei Shen
Summary: In this study, a tRNA:gRNA platform was developed to enhance gene editing and silencing efficiency in C. tropicalis. The platform was proven to be effective in single-gene and multi-gene editing using the CRISPR-Cas9 system. Additionally, a CRISPRi system was successfully constructed to regulate gene expression in C. tropicalis. The tRNA:gRNA platform and the CRISPRi system hold great potential for metabolic engineering in C. tropicalis.
MICROBIOLOGY SPECTRUM
(2022)
Article
Medicine, Research & Experimental
Masayuki Sano, Kana Morishita, Satoshi Oikawa, Takayuki Akimoto, Kimio Sumaru, Yoshio Kato
Summary: MicroRNAs are small RNAs that regulate gene expression in eukaryotic cells, and their unique expression patterns make them potential molecular markers for specific cell states. A new miR-ON sensor, Csy4-miR-ON, has been developed for sensitive and high-contrast fluorescent detection of miRNAs in human cells, enabling imaging of various miRNAs in vitro and in vivo. This tool can be used for evaluating miRNA expression in diverse biological and medical applications.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2021)
Article
Biochemistry & Molecular Biology
Adity Gupta, Ashutosh Kumar, Neha Singh, Madhu Patel, Vasily M. Studitsky, Kam Y. J. Zhang, Md. Sohail Akhtar
Summary: This study reveals the function of Cdc73 during mRNA transcription and identifies its interaction with CTD phosphorylation marks.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Marianna Rossetti, Rosa Merlo, Neda Bagheri, Danila Moscone, Anna Valenti, Aakash Saha, Pablo R. Arantes, Rudy Ippodrino, Francesco Ricci, Ida Treglia, Elisabetta Delibato, John van der Oost, Giulia Palermo, Giuseppe Perugino, Alessandro Porchetta
Summary: By using hairpin DNA as FRET-based reporters, we have enhanced the trans-cleavage activity of Cas12a enzymes, allowing for faster detection of clinically relevant double stranded DNA targets.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Analytical
Fang Yang, Shunmei Li, Xia Li, Ruo Yuan, Yun Xiang
Summary: In this study, DNA-cross-linked polymeric lighting-up nanogels (DPLNs) were synthesized for high sensitivity monitoring and imaging of miRNA-21 in live cells through DNA hairpin-based hybridization chain reaction within nanoscale-confined space. The results showed that DPLNs exhibited low cytotoxicity and highly enhanced nuclease resistance, and could be successfully delivered into live cells for imaging low levels of miRNA-21.
ANALYTICAL CHEMISTRY
(2022)
Article
Biophysics
Agnivo Gosai, Brendan Shin Hau Yeah, Marit Nilsen-Hamilton, Pranav Shrotriya
BIOSENSORS & BIOELECTRONICS
(2019)
Article
Chemistry, Physical
Kalyan Santra, Ivan Geraskin, Marit Nilsen-Hamilton, George A. Kraus, Jacob W. Petrich
JOURNAL OF PHYSICAL CHEMISTRY B
(2019)
Article
Multidisciplinary Sciences
Judhajeet Ray, Paul R. Munn, Anniina Vihervaara, James J. Lewis, Abdullah Ozer, Charles G. Danko, John T. Lis
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biochemistry & Molecular Biology
Muslum Ilgu, Shuting Yan, Ryan M. Khounlo, Monica H. Lamm, Marit Nilsen-Hamilton
Article
Biochemistry & Molecular Biology
Judhajeet Ray, Angela Kruse, Abdullah Ozer, Takuya Kajitani, Richard Johnson, Michael MacCoss, Michelle Heck, John T. Lis
NUCLEIC ACIDS RESEARCH
(2020)
Article
Chemistry, Multidisciplinary
Shuting Yan, Jason M. Peck, Muslum Ilgu, Marit Nilsen-Hamilton, Monica H. Lamm
Article
Chemistry, Medicinal
Meric Ozturk, Marit Nilsen-Hamilton, Muslum Ilgu
Summary: Neurological diseases are a major global health concern affecting over a billion people, with limited diagnosis and treatment options available. Aptamers, as small nucleic acid molecules that are easy to modify chemically, hold promise for future diagnostics and therapeutics for these diseases.
Article
Biochemistry & Molecular Biology
Sharif Anisuzzaman, Ivan M. Geraskin, Muslum Ilgu, Lee Bendickson, George A. Kraus, Marit Nilsen-Hamilton
Summary: The interaction between nucleic acids and molecular targets involves structural reorganization. Understanding this interaction is important for drug development. Polyfluorophenyl modifications have been found to enhance the ability of small molecule drugs to disrupt local RNA structures and promote remodeling.
Article
Multidisciplinary Sciences
Drew T. Bergman, Thouis R. Jones, Vincent Liu, Judhajeet Ray, Evelyn Jagoda, Layla Siraj, Helen Y. Kang, Joseph Nasser, Michael Kane, Antonio Rios, Tung H. Nguyen, Sharon R. Grossman, Charles P. Fulco, Eric S. Lander, Jesse M. Engreitz
Summary: Gene regulation in the human genome is controlled by distal enhancers and this study examines the combinatorial compatibilities of enhancer-promoter interactions in human cells. The results show that most enhancers activate all promoters similarly and that enhancer and promoter activities combine multiplicatively to determine RNA output.
Article
Biochemistry & Molecular Biology
Dilini Singappuli-Arachchige, Shuren Feng, Lijun Wang, Pierre E. Palo, Samuel O. Shobade, Michelle Thomas, Marit Nilsen-Hamilton
Summary: Magnetosomes of magnetotactic bacteria contain magnetic nanocrystals enclosed in vesicles. Mms6, a single magnetosome protein, has been found to direct the crystallization of magnetite nanoparticles in vitro. This study shows that Mms6 acts as a ferric reductase, reducing Fe3+ to Fe2+ to promote magnetite formation. The structure and multimeric state of Mms6 play a role in its iron reduction ability and iron binding characteristics.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Soma Banerjee, Mahsa Askary Hemmat, Shambhavi Shubham, Agnivo Gosai, Sivaranjani Devarakonda, Nianyu Jiang, Charith Geekiyanage, Jacob A. Dillard, Wendy Maury, Pranav Shrotriya, Monica H. Lamm, Marit Nilsen-Hamilton
Summary: The Ebola virus glycoprotein (GP) gene produces several mRNAs that generate different proteins, including a transmembrane protein and two secreted glycoproteins. Three structurally distinct aptamers were selected to bind with the secreted glycoprotein (sGP) and the transmembrane protein (GP1,2). These aptamers showed high affinity and selectivity for sGP and GP1,2 and could detect them with high sensitivity in the presence of serum.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Alejandro Londono-Calderon, Md Mir Hossen, Pierre E. Palo, Lee Bendickson, Sandra Vergara, Marit Nilsen-Hamilton, Andrew C. Hillier, Tanya Prozorov