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)
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
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)
Article
Microbiology
Kevin S. Myers, Daniel R. Noguera, Timothy J. Donohue
Summary: Bioinformatic analysis of promoter sequences from nine bacterial species revealed previously unreported differences in sigma(70)-dependent promoters, suggesting potential species-specific transcription regulation mechanisms. The study also proposed a new role for the transcription factor CarD in transcription of sigma(70)-dependent promoters in certain bacterial species, expanding our understanding of bacterial transcription regulation.
Review
Biochemistry & Molecular Biology
Matthew D. Gibbons, Yu Fang, Austin P. Spicola, Niko Linzer, Stephen M. Jones, Breanna R. Johnson, Lu Li, Mingyi Xie, Jorg Bungert
Summary: Enhancers in higher eukaryotes and upstream activating sequences (UASs) in yeast recruit components of the RNA polymerase II transcription machinery. Pol II recruited to enhancers in higher eukaryotes initiates transcription and generates enhancer RNA (eRNA), while UASs in yeast do not recruit the required transcription factor TFIIH. In both systems, Pol II is transferred from enhancers/UASs to promoters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(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)
Review
Microbiology
Alexander S. F. Berry, Camila Farias Amorim, Corbett L. Berry, Camille M. Syrett, Elise D. English, Daniel P. Beiting
Summary: With the increasing accessibility to high-throughput sequencing technology, the bottleneck in biomedical research has shifted to data analysis. This study describes a modular framework for teaching bioinformatics using publicly available RNA sequencing data sets from infectious disease studies, focusing on host-parasite interactions. Lessons learned from adapting the course for virtual learners during the COVID-19 pandemic are highlighted.
Article
Multidisciplinary Sciences
Shintaro Aibara, Sandra Schilbach, Patrick Cramer
Summary: The initiation of transcription is a crucial step in the regulation of gene activity during mammalian cell differentiation and development. The high-resolution cryo-electron microscopy structure of the human pre-initiation complex provides insight into the mechanisms of DNA opening and transcription initiation.
Article
Cell Biology
Chih-Chien Wang, Jen-Jie Weng, Hsiang-Cheng Chen, Meng-Chang Lee, Pi-Shao Ko, Sui-Lung Su
Summary: This study identified SNPs of TFBSs influencing osteoporosis and validated the association between the rs130347 genotype and downstream gene expression. The findings provide new insights into the genetic basis of osteoporosis and suggest that this strategy can be expanded to other diseases for personalized precision medicine.
Article
Biochemistry & Molecular Biology
Christopher Hennecker, Lynn Yamout, Chuyang Zhang, Chenzhi Zhao, David Hiraki, Nicolas Moitessier, Anthony Mittermaier
Summary: This study provides new evidence linking G4 polymorphism to biological function. The analysis of G4-containing regions in human gene promoter regions revealed that G4CRs with higher degrees of polymorphism are more tightly clustered near transcription sites and tend to contain G4s with shorter loops and bulges. Furthermore, G4CRs with well-characterized biological functions tended to be longer and more polymorphic than genome-wide averages.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Heung Jin Jeon, Monford Paul N. Abishek, Yonho Lee, Heon M. Lim
Summary: In this study, we demonstrate that Rho-dependent termination of transcription occurs stochastically at cistron junctions, generating a stable mRNA that is shorter than the full-length mRNA. We further show that the failure in translation initiation of the next gene, rather than the failure of translation termination of the preceding gene, causes the Rho-dependent termination. Additionally, we find that transcription pauses 130 nucleotides downstream from the site of translation termination, and this pause is necessary for Rho-dependent termination.
Article
Biochemistry & Molecular Biology
Sandra Schilbach, Shintaro Aibara, Christian Dienemann, Frauke Grabbe, Patrick Cramer
Summary: This study reveals the high-resolution structure of the transcription initiation complex and the mechanism of DNA opening, crucial for promoter-initiated transcription. TFIIE facilitates initiation by supporting the clamp head loop and regulating the TFIIH translocase.
Article
Cell Biology
Xinyi Lu, Wenting Xuan, Juanjuan Li, Hongwei Yao, Cheng Huang, Jun Li
Summary: Recent research has shown that AMPK can significantly reduce alcohol-induced liver injury and enhance hepatocytes' mitophagy levels. AMPK indirectly upregulates the protein level of UQCRC2 by promoting NFE2L2/NRF2, thus improving mitophagy and alleviating liver damage.
Article
Microbiology
Megan R. Edwards, Olivia A. Vogel, Hiroyuki Mori, Robert A. Davey, Christopher F. Basler
Summary: This study investigates the role of VP30 in Marburg virus transcription. It demonstrates that VP30 is essential for the transcription reinitiation at the GP gene start site, resulting in the loss of expression of GP and downstream genes when VP30 is absent. The study also identifies a region at the GP gene start site and a zinc binding motif in VP30 as critical factors for transcription reinitiation. These findings enhance our understanding of Marburg virus gene expression regulation.
Article
Computer Science, Information Systems
J. Castell-Diaz, F. Abad-Navarro, M. E. de la Morena-Barrio, J. Corral, J. T. Fernandez-Breis
Summary: Traditional methods are ineffective in predicting mutations in the translation initiation codon, therefore we propose a method to predict the effect of such mutations using a biological model and machine learning algorithms.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
(2022)
Review
Biochemistry & Molecular Biology
Amanda C. Raimer, Kelsey M. Gray, A. Gregory Matera
Article
Genetics & Heredity
Taylor J. R. Penke, Daniel J. McKay, Brian D. Strahl, A. Gregory Matera, Robert J. Duronio
Article
Genetics & Heredity
Taylor J. R. Penke, Daniel J. McKay, Brian D. Strahl, A. Gregory Matera, Robert J. Duronio
Article
Cell Biology
Kelsey M. Gray, Kevin A. Kaifer, David Baillat, Ying Wen, Thomas R. Bonacci, Allison D. Ebert, Amanda C. Raimer, Ashlyn M. Spring, Sara ten Have, Jacqueline J. Glascock, Kushol Gupta, Gregory D. Van Duyne, Michael J. Emanuele, Angus I. Lamond, Eric J. Wagner, Christian L. Lorson, A. Gregory Matera
MOLECULAR BIOLOGY OF THE CELL
(2018)
Article
Biology
Ingo D. Meier, Michael P. Walker, A. Gregory Matera
Article
Genetics & Heredity
Mary Leatham-Jensen, Christopher M. Uyehara, Brian D. Strahl, A. Gregory Matera, Robert J. Duronio, Daniel J. McKay
Article
Biochemistry & Molecular Biology
Casey A. Schmidt, Joseph D. Giusto, Alicia Bao, Anita K. Hopper, A. Gregory Matera
NUCLEIC ACIDS RESEARCH
(2019)
Review
Cell Biology
Casey A. Schmidt, A. Gregory Matera
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2020)
Article
Biochemistry & Molecular Biology
Cassandra K. Hayne, Casey A. Schmidt, Maira Haque, A. Gregory Matera, Robin E. Stanley
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Kushol Gupta, Ying Wen, Nisha S. Ninan, Amanda C. Raimer, Robert Sharp, Ashlyn M. Spring, Kathryn L. Sarachan, Meghan C. Johnson, Gregory D. Van Duyne, A. Gregory Matera
Summary: Protein oligomerization is a mechanism for separating homogeneous solutions into distinct liquid phases to facilitate the assembly of membraneless organelles. The SMN protein is a key component in a macromolecular complex and mutations in its YG box domain can lead to disease. Through various research methods, it was found that the formation of higher-order SMN oligomers depends on a new structural motif.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Casey A. Schmidt, Lucy Y. Min, Michelle H. McVay, Joseph D. Giusto, John C. Brown, Harmony R. Salzler, A. Gregory Matera
Summary: Mature transfer (t)RNAs are generated through multiple RNA processing events, including the excision of intervening sequences. Mutations in CLP1 and TSEN genes, which are involved in tRNA splicing, have been found to cause neurological diseases in humans and fruit flies. These findings provide insights into the mechanisms of Pontocerebellar Hypoplasia (PCH) and allow for further research using the fruit fly model.
Article
Genetics & Heredity
Aaron T. Crain, Stephen Klusza, Robin L. Armstrong, Priscila Santa Rosa, Brenda R. S. Temple, Brian D. Strahl, Daniel J. McKay, A. Gregory Matera, Robert J. Duronio
Summary: KMT5A and Set8 enzymes have functional conservation in Drosophila development, and the N-terminal domain of Set8 has a specific role in eye development, which is distinct from H4K20me1.
Editorial Material
Cell Biology
Ling-Ling Chen, Albrecht Bindereif, Irene Bozzoni, Howard Y. Y. Chang, A. Gregory Matera, Myriam Gorospe, Thomas B. B. Hansen, Jorgen Kjems, Xu-Kai Ma, Jun Wei Pek, Nikolaus Rajewsky, Julia Salzman, Jeremy E. E. Wilusz, Li Yang, Fangqing Zhao
Summary: This Comment calls for a common nomenclature for naming circRNAs to ensure clarity and reproducibility in studies.
NATURE CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Cassandra K. Hayne, Kevin John U. Butay, Zachary D. Stewart, Juno M. Krahn, Lalith Perera, Jason G. Williams, Robert M. Petrovitch, Leesa J. Deterding, A. Gregory Matera, Mario J. Borgnia, Robin E. Stanley
Summary: The authors used cryo-electron microscopy to investigate the recognition and processing of pre-tRNA by the human tRNA splicing endonuclease complex TSEN. They reported the structures of the TSEN-pre-tRNA complex, which reveal the overall architecture of the complex and the tRNA binding interfaces. These structures provide insights into the mechanism of pre-tRNA splicing and the neurodevelopmental disorders associated with mutations in the TSEN complex.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)