Article
Biochemistry & Molecular Biology
Qiang Lu, Taiyu Chen, Jiening Wang, Feng Wang, Wenlong Ye, Lixin Ma, Shan Wu
Summary: This study presents a cryo-EM structure of an RNA polymerase transcription complex containing a temperature-sensitive bacterial sigma factor, sigma(32) (sigma(32)-RPo). The structure reveals key interactions essential for the assembly of E. coli sigma(32)-RNAP holoenzyme and for promoter recognition and unwinding by sigma(32). These unique structural features advance our understanding of the mechanism of transcription initiation mediated by different sigma factors.
Article
Multidisciplinary Sciences
Yu Liu, Libing Yu, Chirangini Pukhrambam, Jared T. Winkelman, Emre Firlar, Jason T. Kaelber, Yu Zhang, Bryce E. Nickels, Richard H. Ebright
Summary: This study reveals the mechanism of RNA extension in reiterative transcription initiation, showing that it differs from the mechanism of RNA extension in standard transcription initiation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Yuli Zhang, Linlin Hou
Summary: Sox proteins, known as crucial transcription factors, are not limited to transcription initiation but also involved in regulating alternative splicing networks and translational control.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Chirangini Pukhrambam, Vadim Molodtsov, Mahdi Kooshkbaghi, Ammar Tareen, Hoa Vu, Kyle S. Skalenko, Min Su, Zhou Yin, Jared T. Winkelman, Justin B. Kinney, Richard H. Ebright, Bryce E. Nickels
Summary: In sigma-dependent transcriptional pausing, the presence or absence of GreB determines whether the paused state involves backtracking or scrunched by 2-4 base pairs or 2-3 base pairs respectively. The consensus sequence T(-3)N(-2)Y(-1)G(+1) is associated with pausing in both initial transcription and transcription elongation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Hyung-Woo Jeon, Mary E. Byrne
Summary: Plant leaves have various shapes due to different species, developmental stages, and environments. Mutations in the homeodomain transcription factors Saw1 and Saw2 can lead to earlier appearance of leaf margin serrations.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biotechnology & Applied Microbiology
Yang Liu, Chen Ai, Tingting Gan, Jinchun Wu, Yongpeng Jiang, Xuhao Liu, Rusen Lu, Ning Gao, Qing Li, Xiong Ji, Jiazhi Hu
Summary: The study revealed that RNA polymerase II redistributes MCM complexes to prevent early DNA replication initiation within transcribed regions, spatially separating transcription and early DNA replication events to avoid collisions and preserve genome stability.
Article
Biochemistry & Molecular Biology
Genki Shino, Shoji Takada
Summary: This study used multiscale molecular dynamics simulations based on cryo-electron microscopy structures to investigate the dynamic processes of DNA opening in transcription initiation. An intermediate state in Pol II was identified during the transition from open to initially transcribing complexes, shedding light on the mechanism of promoter DNA opening. Additionally, atomic models provided insights into atomistic interactions for future simulations.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
Liqiang Shen, Giorgio Lai, Linlin You, Jing Shi, Xiaoxian Wu, Maria Puiu, Zhanxi Gu, Yu Feng, Yulia Yuzenkova, Yu Zhang
Summary: This study presents the cryo-EM structures of cyanobacterial transcription initiation complexes, revealing the role of SI3-& sigma; arch interaction in transcription initiation of cyanobacteria. Disruption of this structure affects the growth and stress response of cyanobacteria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
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)
Review
Microbiology
Cheyenne D. Lee, Arshad Rizvi, Adrianne N. Edwards, Michael A. DiCandia, German G. Vargas Cuebas, Marcos P. Monteiro, Shonna M. McBride
Summary: Clostridioides difficile relies on dormant spore formation to survive and transmit between hosts. Its genome lacks many known regulatory factors for sporulation found in other bacteria, suggesting it has evolved unique mechanisms to control sporulation initiation in response to its specific ecological niche and host environment.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Review
Plant Sciences
Qingqing Yang, Cunquan Yuan, Tianci Cong, Qixiang Zhang
Summary: The branching phenotype is a crucial agronomic trait of plants, with significance in both fruit trees' yield and the ornamental value of landscape trees and flowers. The regulation of meristem initiation by plant hormones and transcription factors plays a significant role in determining the branching characteristics. However, research on meristem initiation in horticultural plants is limited, and the mechanism of regulation is not well understood. This review summarizes recent progress in understanding the regulatory networks and mechanisms of axillary meristem and floral meristem initiation, and suggests the need for future studies to improve the branching trait in horticultural plants.
Article
Chemistry, Multidisciplinary
Zhenyu Zou, Jialun Liang, Qian Jia, Di Bai, Wei Xie, Wenqiang Wu, Chuang Tan, Jie Ma
Summary: “The flow-cell system, developed in this work, combines gas-pumped calibration and fluorescence imaging to enable simultaneous single-molecule force measurement and visualization. It offers high force stability and tuning accuracy, allowing for precise force application and measurement. The system also facilitates real-time tracking of protein motors and monitoring of biomolecular conformational changes under controlled forces. The findings from this work lay down a valuable foundation for the flow-cell to be utilized as a versatile, quantitative, and high-throughput tool for single-molecule manipulation and visualization.”
Article
Genetics & Heredity
William J. Andrews, Swagat Ray, Tatiana Panova, Christoph Engel, Konstantin Panov
Summary: The study found that DNA intercalators/groove binders can effectively inhibit Pol-I specific transcription without affecting its synthetic ability. These compounds have limited effect on transcription by Pol-II and III, demonstrating the hypersensitivity of Pol-I transcription. The research suggests that alterations in the 3D structure of the rDNA promoter may affect the stability of the pre-initiation complex and initiation.
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
Biochemistry & Molecular Biology
Juntaek Oh, Jun Xu, Jenny Chong, Dong Wang
Summary: This review summarizes recent research progress on the molecular basis of transcriptional pausing and stalling caused by different types of obstacles, and discusses new insights into Pol II-mediated lesion recognition and the roles of CSB in TC-NER.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2021)
Meeting Abstract
Biophysics
Jun Fan, Nigel Savery, Nicolas Joly, Terence Strick
BIOPHYSICAL JOURNAL
(2015)
Article
Developmental Biology
Nicolas Joly, Lisa Martino, Emmanuelle Gigant, Julien Dumont, Lionel Pintard
Article
Cell Biology
Yann Thomas, Luca Cirillo, Costanza Panbianco, Lisa Martino, Nicolas Tavernier, Francoise Schwager, Lucie Van Hove, Nicolas Joly, Anna Santamaria, Lionel Pintard, Monica Gotta
Article
Multidisciplinary Sciences
Gilbert Richarme, Cailing Liu, Mouadh Mihoub, Jad Abdallah, Thibaut Leger, Nicolas Joly, Jean-Claude Liebart, Ula V. Jurkunas, Marc Nadal, Philippe Bouloc, Julien Dairou, Aazdine Lamouri
Article
Biochemistry & Molecular Biology
Nan Zhang, Timothy Simpson, Edward Lawton, Povilas Uzdavinys, Nicolas Joly, Patricia Burrows, Martin Buck
JOURNAL OF MOLECULAR BIOLOGY
(2013)
Article
Biochemistry & Molecular Biology
Nan Zhang, Yuliya Gordiyenko, Nicolas Joly, Edward Lawton, Carol V. Robinson, Martin Buck
JOURNAL OF MOLECULAR BIOLOGY
(2014)
Article
Biochemistry & Molecular Biology
Edward Lawton, Milija Jovanovic, Nicolas Joly, Christopher Waite, Nan Zhang, Baojun Wang, Patricia Burrows, Martin Buck
JOURNAL OF MOLECULAR BIOLOGY
(2014)
Article
Biochemistry & Molecular Biology
Nicolas Joly, Nan Zhang, Martin Buck
Article
Biochemistry & Molecular Biology
Vidya C. Darbari, Ed Lawton, Duo Lu, Patricia C. Burrows, Simone Wiesler, Nicolas Joly, Nan Zhang, Xiaodong Zhang, Martin Buck
NUCLEIC ACIDS RESEARCH
(2014)
Article
Cell Biology
Nicolas Joly, Eva Beaumale, Lucie Van Hove, Lisa Martino, Lionel Pintard
JOURNAL OF CELL BIOLOGY
(2020)
Article
Biology
Griselda Velez-Aguilera, Sylvia Nkombo Nkoula, Batool Ossareh-Nazari, Jana Link, Dimitra Paouneskou, Lucie Van Hove, Nicolas Joly, Nicolas Tavernier, Jean-Marc Verbavatz, Verena Jantsch, Lionel Pintard
Article
Multidisciplinary Sciences
N. Tavernier, Y. Thomas, S. Vigneron, P. Maisonneuve, S. Orlicky, P. Mader, S. G. Regmi, L. Van Hove, N. M. Levinson, G. Gasmi-Seabrook, N. Joly, M. Poteau, G. Velez-Aguilera, O. Gavet, A. Castro, M. Dasso, T. Lorca, F. Sicheri, L. Pintard
Summary: The research uncovers the activation mechanism of AURKA crucial for mitotic entry, showing that phosphorylated Bora directly activates AURKA kinase activity. Through specific amino acid regions, Bora binds AURKA and substitutes for a key phospho-regulatory site, highlighting the importance of this mechanism for timely mitotic entry in Xenopus and human cells.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Jessica Knox, Nicolas Joly, Edmond M. Linossi, Jose A. Carmona-Negron, Natalia Jura, Lionel Pintard, William Zuercher, Peter J. Roy
Summary: Over one billion people are currently infected with a parasitic nematode, leading to various symptoms. Resistance is emerging to current anthelmintics, prompting the need for new drugs. Studies have identified nematode EGFR, MEK1, and PLK1 as potential key targets for the development of new anthelmintics.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Lisa Martino, Stephanie Morchoisne-Bolhy, Dhanya K. Cheerambathur, Lucie Van Hove, Julien Dumont, Nicolas Joly, Arshad Desai, Valerie Doye, Lionel Pintard
DEVELOPMENTAL CELL
(2017)
Article
Biochemistry & Molecular Biology
Jordan Monnet, Wilfried Grange, Terence R. Strick, Nicolas Joly
TRANSCRIPTION-AUSTIN
(2013)