Article
Cell Biology
Jia Fei, Jun Xu, Ziwei Li, Kevin Xu, Dong Wang, George A. Kassavetis, James T. Kadonaga
Summary: NDF is a transcription elongation factor that binds to Pol II and enhances gene expression elongation by a different mechanism than TFIIS.
GENES & DEVELOPMENT
(2022)
Review
Biochemistry & Molecular Biology
Niko Linzer, Alexis Trumbull, Rukiye Nar, Matthew D. Gibbons, David T. Yu, John Strouboulis, Joerg Bungert
Summary: TFII-I, a key transcription factor, plays crucial roles in regulating Pol II transcription at the stages of initiation and elongation by interacting with various co-regulators and influencing transcription positively or negatively. Its expression changes are associated with a range of diseases and developmental processes, highlighting its important role in gene regulation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(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
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
Biochemistry & Molecular Biology
Soren Lykke-Andersen, Kristina Zumer, Ewa Smidova Molska, Jerome O. Rouviere, Guifen Wu, Carina Demel, Bjoern Schwalb, Manfred Schmid, Patrick Cramer, Torben Heick Jensen
Summary: The termination of RNA polymerase II transcription in metazoans largely depends on the cleavage and poly-adenylation (CPA) and integrator (INT) complexes. The CPA shows global activity at pA sites regardless of their positioning relative to the TU promoter, while the INT has a global activity mainly restricted to a 3kb promoter-proximal region. The INT functions in dampening transcriptional output from weak promoters and providing quality control of RNAPII complexes unfavorably configured for transcriptional elongation, with its stable snRNA production role being an exception.
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.
Review
Biochemistry & Molecular Biology
Joseph C. Reese
Summary: RNA polymerase II encounters various obstacles during mRNA synthesis. Elongation factors are responsible for reactivating or rescuing paused or arrested RNAPII. However, when RNAPII fails to resume transcription, it is degraded by the ubiquitin-proteasome system. This review focuses on the latest developments in understanding this process and the role of elongation factors in the removal and degradation of RNAPII.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2023)
Article
Biology
Shao-Pei Chou, Adriana K. Alexander, Edward J. Rice, Lauren A. Choate, Charles G. Danko
Summary: This study investigates how DNA sequence differences affect the dynamics and position of RNA polymerase II (Pol II) during transcription. The researchers found that DNA sequence motifs are key determinants of Pol II initiation and pause positions, and that initiation site selection follows a stochastic process similar to Brownian motion. Additionally, they discovered that differences in transcription termination impact the structure and stability of mature mRNA, and that allelic changes in transcription affect mRNA and ncRNA expression across genomic domains.
Article
Biochemistry & Molecular Biology
Yuanjun Li, Jie Huang, Junyi Zhu, Lijun Bao, Hui Wang, Yongpeng Jiang, Kai Tian, Rui Wang, Haonan Zheng, WenJia Duan, Weifeng Lai, Xiao Yi, Yi Zhu, Tiannan Guo, Xiong Ji
Summary: The study revealed that different RNA Pol II subunits play distinct roles in transcription regulation, with a preference for RNA processing. Depletion of different RNA Pol II subunits leads to differential gene expression, involving diverse biological functions.
Article
Medicine, Research & Experimental
Shane D. Falcinelli, Jackson J. Peterson, Anne-Marie W. Turner, David Irlbeck, Jenna Read, Samuel L. M. Raines, Katherine S. James, Cameron Sutton, Anthony Sanchez, Ann Emery, Gavin Sampey, Robert Ferris, Brigitte Allard, Simon Ghofrani, Jennifer L. Kirchherr, Caroline Baker, JoAnn D. Kuruc, Cynthia L. Gay, Lindsey I. James, Guoxin Wu, Paul Zuck, Inmaculada Rioja, Rebecca C. Furze, Rab K. Prinjha, Bonnie J. Howell, Ronald Swanstrom, Edward P. Browne, Brian D. Strahl, Richard M. Dunham, Nancie M. Archin, David M. Margolis
Summary: This study demonstrates the synergy in latent reservoir activation when using inhibitor of apoptosis protein (IAP) antagonists in combination with bromodomain and extraterminal domain protein inhibitors (BETi). It also highlights the importance of HIV transcriptional elongation and splicing as barriers to latent HIV protein expression, providing a rationale for further exploration of IAPi+BETi in animal models of HIV latency.
JOURNAL OF CLINICAL INVESTIGATION
(2022)
Article
Biochemistry & Molecular Biology
Cecile Evrin, Albert Serra-Cardona, Shoufu Duan, Progya P. Mukherjee, Zhiguo Zhang, Karim P. M. Labib
Summary: In eukaryotes, the essential factor Spt5 plays a direct role in the process of re-deposition of nucleosomal histones during transcription. It contains an acidic amino terminal tail called Spt5N, which has a histone-binding motif that is essential for yeast cell viability.
Article
Genetics & Heredity
Andrew M. Clarke, Abigail K. Huffines, Yvonne J. K. Edwards, Chad M. Petit, David A. Schneider
Summary: Saccharomyces cerevisiae has approximately 200 copies of the 35S rDNA gene, transcribed by RNA polymerase I (Pol I) with the A12.2 subunit playing a crucial role. Investigating Pol I occupancy changes in the 35S gene and IGS in an rpa12 Delta strain, we found that the A12.2 subunit is important for transcription elongation and termination.
Article
Biochemistry & Molecular Biology
Kai Zhou, Songkuan Zhuang, Fulong Liu, Yanheng Chen, You Li, Shihui Wang, Yuxuan Li, Huixin Wen, Xiaohua Lin, Jie Wang, Yue Huang, Cailing He, Nan Xu, Zongshu Li, Lang Xu, Zixuan Zhang, Lin-Feng Chen, Ruichuan Chen, Min Liu
Summary: P-TEFb modulates RNA polymerase II elongation through interaction with Brd4 and SEC. This study uncovers a novel mechanism for the reassembly of Cdk9 and CycT1 monomers on chromatin to form active P-TEFb.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Zhou Yin, Jeremy G. Bird, Jason T. Kaelber, Bryce E. Nickels, Richard H. Ebright
Summary: The article investigates the mechanism of action of Q proteins in transcription in Lambdoid bacteriophage. The results show that Q proteins form a nozzle-like structure to prevent pause and termination of RNA polymerase during transcription. Compared to previous studies, this research reveals the structural and functional differences of Q proteins in different bacteriophages.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Genetics & Heredity
Cecilia Studniarek, Sylvain Egloff, Shona Murphy
Summary: Effective synthesis of mammalian mRNAs relies on various factors, including transcription initiation, elongation, and termination, as well as the global regulatory role of noncoding RNAs. These non-protein regulators play critical roles in gene expression by directly associating with pol II or modulating the activity of transcription or RNA processing factors.
TRENDS IN GENETICS
(2021)
Article
Clinical Neurology
Raquel Pinacho, Gregory Saia, J. Javier Meana, Grace Gill, Belen Ramos
EUROPEAN NEUROPSYCHOPHARMACOLOGY
(2015)
Article
Biochemistry & Molecular Biology
Jian Ouyang, Elizabeth Garner, Alexander Hallet, Hai Dang Nguyen, Kimberly A. Rickman, Grace Gill, Agata Smogorzewska, Lee Zou
Article
Multidisciplinary Sciences
Raquel Pinacho, Gregory Saia, Montserrat Fuste, Iria Melendez-Perez, Victoria Villalta-Gil, Josep Maria Haro, Grace Gill, Belen Ramos
Article
Clinical Neurology
Raquel Pinacho, Nuria Villalmanzo, Jasmin Lalonde, Josep Maria Haro, J. Javier Meana, Grace Gill, Belen Ramos
Article
Cell Biology
Alvaro Valin, Grace Gill
Article
Developmental Biology
Xinxin Sun, Raquel Pinacho, Gregory Saia, Diana Punko, J. Javier Meana, Belen Ramos, Grace Gill
DEVELOPMENTAL NEUROBIOLOGY
(2015)
Article
Biochemistry & Molecular Biology
Gregory Saia, Jasmin Lalonde, Xinxin Sun, Belen Ramos, Grace Gill
JOURNAL OF NEUROCHEMISTRY
(2014)
Article
Psychiatry
Raquel Pinacho, Nuria Villalmanzo, Mercedes Roca, Raquel Iniesta, Alfonso Monje, Josep Maria Haro, J. Javier Meana, Isidre Ferrer, Grace Gill, Belen Ramos
JOURNAL OF PSYCHIATRIC RESEARCH
(2013)
Editorial Material
Biochemistry & Molecular Biology
Grace Gill
Article
Biochemistry & Molecular Biology
Moon Hee Lee, Angela M. Mabb, Grace B. Gill, Edward T. H. Yeh, Shigeki Miyamoto
Article
Biochemistry & Molecular Biology
Peter Mulligan, Fajun Yang, Luisa Di Stefano, Jun-Yuan Ji, Jian Ouyang, Joy L. Nishikawa, Debra Toiber, Madhura Kulkarni, Qun Wang, S. Hani Najafi-Shoushtari, Raul Mostoslavsky, Steven P. Gygi, Grace Gill, Nicholas J. Dyson, Anders M. Naeaer
Article
Multidisciplinary Sciences
Sohini Mazumdar, Lisa M. Arendt, Sarah Phillips, Maja Sedic, Charlotte Kuperwasser, Grace Gill
Article
Biochemistry & Molecular Biology
Jasmin Lalonde, Gregory Saia, Grace Gill
Article
Cell & Tissue Engineering
Sarah Phillips, Aleix Prat, Maja Sedic, Theresa Proia, Ania Wronski, Sohini Mazumdar, Adam Skibinski, Stephanie H. Shirley, Charles M. Perou, Grace Gill, Piyush B. Gupta, Charlotte Kuperwasser