Article
Multidisciplinary Sciences
Zachery Mielko, Yuning Zhang, Harshit Sahay, Yiling Liu, Matthew A. Schaich, Brittani Schnable, Abigail M. Morrison, Debbie Burdinski, Sheera Adar, Miles Pufall, Bennett Van Houten, Raluca Gordan, Ariel Afek
Summary: Somatic mutations are highly concentrated at transcription factor binding sites, particularly in melanomas with UV-induced mutations. The inefficient repair of UV lesions within TF-binding sites is proposed as one of the main mechanisms for this hypermutation pattern due to competition between TFs and DNA repair proteins. However, the impact of UV irradiation on TF binding to DNA and whether TFs maintain specificity for their DNA sites after UV exposure remain unclear. Using a high-throughput approach called UV-Bind, researchers found that UV lesions significantly altered the DNA binding preferences of all tested TFs, with a decrease in binding specificity. Despite the overall reduction in DNA-binding specificity, TFs can still compete with repair proteins for lesion recognition, consistent with their specificity for UV-irradiated DNA.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Yizhao Luan, Zehua Tang, Yao He, Zhi Xie
Summary: In this study, evidence was provided showing that coevolving residues in TF domains contribute to DNA binding specificity. It was demonstrated that the coevolving residues are more likely to coevolve with other TF subclass-determining sites and mutation of these coevolving residues could significantly reduce the stability of the TF-DNA complex. Overall, this study expands our understanding of the interaction among coevolving residues in TFs and their importance in transcriptional regulation.
MICROBIOLOGY SPECTRUM
(2023)
Article
Cell Biology
Yihao Yang, Nicholas Gomez, Nicole Infarinato, Rene C. Adam, Megan Sribour, Inwha Baek, Melanie Laurin, Elaine Fuchs
Summary: This study reveals the crucial role of SOX9 in diverting embryonic epidermal stem cells into hair follicle stem cells. By re-activating SOX9 in adult epidermal stem cells, the researchers induce fate switching. They show that SOX9 binds and opens hair follicle enhancers in epidermal stem cells, while recruiting epigenetic factors away from epidermal enhancers, leading to their silencing. This sustained expression of SOX9 subsequently activates oncogenic transcriptional regulators and contributes to the development of cancer.
NATURE CELL BIOLOGY
(2023)
Review
Plant Sciences
Lucia Strader, Dolf Weijers, Doris Wagner
Summary: This article reviews new findings on the function of plant transcription factors and their role in shaping transcription in the context of chromatin.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Review
Plant Sciences
Juriaan Rienstra, Jorge Hernandez-Garcia, Dolf Weijers
Summary: Most plant growth and development processes are regulated by auxin, with the nuclear auxin pathway (NAP) being the most well-studied mechanism. In this pathway, Auxin Response Factors (ARFs) determine which genes become auxin regulated by binding to specific DNA sequences. Recent studies have revealed the DNA binding specificities of different ARFs and the minimal functional system of the NAP system. This review provides an overview of key aspects of ARF DNA binding and highlights the importance of studying minimal NAP systems and algal ARFs, as well as using cutting-edge techniques and structural biology to further understand ARF function.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Genetics & Heredity
Alexios-Fotios A. Mentis, Kostas A. Papavassiliou, Athanasios G. Papavassiliou
Summary: Transcription factors play a key role in gene regulation, and their study and therapeutic targeting are still challenging. DNA origami, a synthetic biology/medicine tool, shows potential in studying transcription factor dynamics and designing drugs targeting transcription factors.
JOURNAL OF MOLECULAR MEDICINE-JMM
(2023)
Article
Chemistry, Multidisciplinary
Bingchen Che, Dan Sun, Chen Zhang, Jiaqing Hou, Wei Zhao, Guangyin Jing, Yuguang Mu, Yaoyu Cao, Liang Dai, Ce Zhang
Summary: Mechanically induced chromosome reorganization is important in transcriptional regulation, but the interplay between chromosome reorganization and transcription activities is complicated. By introducing DNA, packaging proteins, and transcription factor NF-KB into a fluidic chip with varying spatial confinement, it was found that strong nanoconfinement suppresses higher-order folding of protein-DNA complexes and leads to increased NF-KB binding. Overall, these results reveal a pathway of how intranuclear geometrical cues alter the open/closed state of a DNA-protein complex and affect transcription activities.
Article
Immunology
Upalabdha Dey, Kaushika Olymon, Anikesh Banik, Eshan Abbas, Venkata Rajesh Yella, Aditya Kumar
Summary: Mycobacterium tuberculosis, the causative agent of tuberculosis, has evolved into a multidrug resistance strain, posing a severe global health threat. The survival and dormancy of the bacteria within the host macrophage rely on multiple transcription factors (TFs) contributing to virulence. This study analyzed the compositional and conformational preferences of 21 mycobacterial TFs in their DNA binding sites, revealing nuanced DNA shape and structural preferences.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Review
Medicine, General & Internal
Aleksandra Rapacka-Zdonczyk, Agata Wozniak, Klaudia Michalska, Michal Pieranski, Patrycja Ogonowska, Mariusz Grinholc, Joanna Nakonieczna
Summary: Photodynamic inactivation of microorganisms (aPDI) is an effective method to destroy antibiotic-resistant microbial isolates, but research on different photosensitizers, target microorganisms, and light delivery systems mostly shows efficacy in vitro models. Investigating different bacterial subpopulations' responses to aPDI is essential to identifying molecular features driving antimicrobial photodynamic inactivation effectiveness.
FRONTIERS IN MEDICINE
(2021)
Article
Cell Biology
Camila Oses, Marcos Gabriel Francia, Paula Verneri, Camila Vazquez Echegaray, Alejandra Sonia Guberman, Valeria Levi
Summary: DNA replication in stem cells is a challenging process that involves significant changes in chromatin structure and transcription-related molecules. The master transcription factors OCT4, SOX2, and NANOG play crucial roles in pluripotency regulation. This study investigates the dynamic distribution of these transcription factors during the cell cycle and reveals spatial redistribution during DNA replication. Additionally, differentiation cues in the G1 phase trigger reorganization of pluripotency transcription factors in early-S phase, indicating their distinct roles in early differentiation stages.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Chemistry, Physical
Reman Kumar Singh, Arnab Mukherjee
Summary: The study investigates the molecular mechanism of the interaction between the transcription factor SOX4 and DNA, revealing that the protein primarily binds to the DNA backbone and rotates around it to form an intercalative state. It demonstrates that, although there are multiple pathways for intercalation, the deintercalation pathway matches with the most probable intercalation pathway, leading to simultaneous bending and kinking of DNA.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biophysics
Bingzhi Li, Anqi Xia, Shilin Zhang, Tiying Suo, Yujie Ma, He Huang, Xing Zhang, Yue Chen, Xuemin Zhou
Summary: Transcription factors (TFs) are crucial proteins for cell fate determination and have potential applications in disease diagnostics and treatment. A highly sensitive biosensor based on the CRISPR/Cas12a system was developed for TF detection, utilizing competitive binding between Cas12a-crRNA and TFs to a specific dsDNA activator. This study demonstrates a novel approach in applying CRISPR technology for TF sensing and highlights the potential of using blocking mechanisms as a new sensing strategy for CRISPR-based biosensors.
BIOSENSORS & BIOELECTRONICS
(2021)
Review
Immunology
Eva Neugebauer, Aura M. Bastidas-Quintero, Daniel Weidl, Florian Full
Summary: This article reviews the current research progress on how viruses utilize pioneer factors for viral replication and persistence in the host, as well as for the development of viral cancer.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemical Research Methods
Hongfei Li, Yue Gong, Yifeng Liu, Hao Lin, Guohua Wang
Summary: Transcription factors (TFs) are proteins involved in gene expression regulation, and recent studies have shown that some TFs can interact with methylated DNA fragments. This study presents a machine learning-based approach to quickly identify TFs that can bind to methylated DNA. The proposed model, based on tripeptide word vector feature and recurrent neural network, achieves high accuracy in predicting TFs and their binding to methylated DNA.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Biochemistry & Molecular Biology
Ian G. Cowell, John W. Casement, Caroline A. Austin
Summary: Transcription and its regulation are affected by DNA torsion and supercoiling, which are resolved by DNA topoisomerases. This review focuses on one type of DNA topoisomerase II beta, which plays a critical role in developmental transcription and signal-induced transcription.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Matthew D. Newton, Benjamin J. Taylor, Rosalie P. C. Driessen, Leonie Roos, Nevena Cvetesic, Shenaz Allyjaun, Boris Lenhard, Maria Emanuela Cuomo, David S. Rueda
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2019)
Article
Immunology
Ludovica Bruno, Vijendra Ramlall, Romain A. Studer, Stephan Sauer, David Bradley, Gopuraja Dharmalingam, Thomas Carroll, Mohamed Ghoneim, Michael Chopin, Stephen L. Nutt, Sarah Elderkin, David S. Rueda, Amanda G. Fisher, Trevor Siggers, Pedro Beltrao, Matthias Merkenschlager
Article
Multidisciplinary Sciences
Julianna Volko, Adam Kenesei, Meili Zhang, Peter Varnai, Gabor Mocsar, Michael N. Petrus, Karoly Jambrovics, Zoltan Balajthy, Gabriele Mueller, Andrea Bodnar, Katalin Toth, Thomas A. Waldmann, Gyorgy Vamosi
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Multidisciplinary Sciences
Marcus D. Wilson, Ludovic Renault, Daniel P. Maskell, Mohamed Ghoneim, Valerie E. Pye, Andrea Nans, David S. Rueda, Peter Cherepanov, Alessandro Costa
NATURE COMMUNICATIONS
(2019)
Article
Microbiology
Michi Miura, Supravat Dey, Saumya Ramanayake, Abhyudai Singh, David S. Rueda, Charles R. M. Bangham
Article
Chemistry, Analytical
Balint Reho, Lukas Lau, Gabor Mocsar, Gabriele Mueller, Lina Fadel, Peter Brazda, Laszlo Nagy, Katalin Toth, Gyorgy Vamosi
ANALYTICAL CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Ferenc Papp, Peter Hajdu, Gabor Tajti, Agnes Toth, Eva Nagy, Zsolt Fazekas, Sandor Kovacs, Gyorgy Vamosi, Zoltan Varga, Gyorgy Panyi
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Multidisciplinary Sciences
Adam D. Cawte, Peter J. Unrau, David S. Rueda
NATURE COMMUNICATIONS
(2020)
Article
Biology
Radek Kana, Gabor Steinbach, Roman Sobotka, Gyorgy Vamosi, Josef Komenda
Summary: The study revealed that unbound proteins in cyanobacterial thylakoid membranes can diffuse very fast, comparable to free lipids. This highlights the crucial role of protein-protein interactions in restricting the mobility of large thylakoid protein complexes.
Article
Chemistry, Multidisciplinary
Matthew D. Newton, Simon D. Fairbanks, Jim A. Thomas, David S. Rueda
Summary: The study demonstrates that the dinuclear ruthenium(II) complex can thread and lock into force-extended DNA in a two-step mechanism, with one stereoisomer showing the highest binding affinity reported. Interestingly, the complex behaves differently on torsionally constrained DNA and negatively supercoiled DNA, making it a potential long-lived luminescent label for biological applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Istvan Csomos, Peter Nagy, Csenge Filep, Istvan Rebenku, Eniko Nizsaloczki, Tamas Kovacs, Gyoergy Vamosi, Laszlo Matyus, Andrea Bodnar
Summary: STAT3 is a crucial transcription factor involved in cancer development, with its activation playing a key role. Interleukin-6 is a major activator of STAT3, while chelidonine exerts regulatory effects on STAT3 signaling in treating uveal melanoma cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Roopesh Anand, Erika Buechelmaier, Ondrej Belan, Matthew Newton, Aleksandra Vancevska, Artur Kaczmarczyk, Tohru Takaki, David S. Rueda, Simon N. Powell, Simon J. Boulton
Summary: HELQ is a superfamily 2 helicase with 3' to 5' polarity, and disruption in mice causes germ cells loss, infertility, and increased predisposition to ovarian and pituitary tumors. Defects in HELQ result in cellular hypersensitivity to cisplatin and mitomycin C, as well as persistence of RAD51 foci after DNA damage. HELQ possesses an intrinsic ability to capture RPA-bound DNA strands and facilitate annealing of complementary sequences.
Article
Multidisciplinary Sciences
Artur P. Kaczmarczyk, Anne-Cecile Declais, Matthew D. Newton, Simon J. Boulton, David M. J. Lilley, David S. Rueda
Summary: This study captures the entire reaction trajectory of a nuclease targeting and resolving a DNA junction at single-molecule level. The results show that the enzyme first binds remotely to dsDNA and undergoes 1D diffusion before cleaving the junction upon encountering it.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Aris E. N. R. Aristodemou, David Rueda, Graham R. Taylor, Charles R. M. Bangham, Patrick L. R. Green
Summary: This study analyzed the expression changes of host and viral genes during HTLV-1 reactivation in cells isolated from patients' blood. The study found that changes in viral expression may be related to changes in a group of epigenetic modifiers, which may contribute to the virus returning to a latent state after activation. In addition, the study also identified three deubiquitinases that can promote viral expression. These findings are of great importance for further understanding the lifecycle and infection mechanisms of HTLV-1.
Article
Chemistry, Physical
Marialucrezia Losito, Quentin M. Smith, Matthew D. Newton, Maria Emanuela Cuomo, David S. Rueda
Summary: Using optical tweezers, researchers studied target search and cleavage by CRISPR-Cas12a on lambda-DNA under force stretching. Cas12a employs fast one-dimensional hopping to locate its target, with binding and cleavage occurring rapidly and specifically at low forces (<= 5 pN), involving a 1.8 nm rate-limiting conformational change. Mechanical distortion slows diffusion, increases off-target binding, but hinders cleavage.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
