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
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
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
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.
Review
Biochemistry & Molecular Biology
Emmanuel Compe, Jean-Marc Egly
Summary: In eukaryotes, transcription of protein-coding genes requires the assembly of a preinitiation machinery at core promoters containing RNAPII and GTFs. Transcription is enhanced by regulatory elements called enhancers, recognized by specific DNA-binding transcription factors. Understanding the transcription initiation mechanism has benefited from the study of altered transcription components associated with human diseases.
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 90, 2021
(2021)
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)
Article
Biology
Natalia Petrenko, Kevin Struhl
Summary: Differences in the transcriptional initiation process exist among eukaryotic species, such as the dynamic bridge of Mediator and variations in TBP occupancy. TFIID interacts strongly at downstream regions of the initiation site in flies, contrasting with yeast and mammals. The Mediator subunit Med26 and Taf7 interact near the Pol II pause region, but only in subsets of genes.
Article
Nanoscience & Nanotechnology
A. Nemashkalo, M. E. Phipps, S. P. Hennelly, P. M. Goodwin
Summary: This article introduces the application of single-molecule microscopy and spectroscopy in studying molecular interactions within cells. The low throughput of conventional methods hinders the progress of research. The RS2 sequencer, utilizing nanofabrication and single-molecule spectroscopy, offers high throughput and real-time observation of transcription and interactions. This instrument enables the study of biological assembly and interaction questions at the single-molecule level.
Article
Biology
Abhishek Mazumder, Richard H. Ebright, Achillefs N. Kapanidis
Summary: This study used single-molecule techniques to investigate the unwinding process of bacterial promoters, and found that the RNAP clamp remains closed during binding to the promoter, continues to stay closed during unwinding, and further closes after unwinding, locking the DNA in the active center cleft of the RNAP.
Article
Biochemistry & Molecular Biology
Uthra Gowthaman, Maxim Ivanov, Isabel Schwarz, Heta P. Patel, Niels A. Mueller, Desire Garcia-Pichardo, Tineke L. Lenstra, Sebastian Marquardt
Summary: The study characterized the genetic architecture and molecular mechanism of DNC transcription in budding yeast, identifying the Hda1 histone deacetylase complex (Hda1C) as a repressor of DNC transcription. Hda1C contributes to decreased histone acetylation in DNC transcription regions to support DNC transcription repression, ensuring genome fidelity.
Article
Biochemistry & Molecular Biology
Anna Sawicka, Gabriel Villamil, Michael Lidschreiber, Xavier Darzacq, Claire Dugast-Darzacq, Bjoern Schwalb, Patrick Cramer
Summary: In human cells, shortening CTD by half does not affect pre-mRNA synthesis and processing, but it does impact Pol II pausing, enhancer element transcription, and transcription activation after MAP kinase pathway stimulation. This suggests that a long CTD is necessary for efficient recruitment of Pol II to target genes for rapid activation.
Article
Multidisciplinary Sciences
Michael Kronenberg, Michael F. Carey
Summary: Head-on (HO) collisions between the DNA replication machinery and RNA polymerase over R-loop forming sequences (RLFS) are genotoxic, leading to replication fork blockage and DNA breaks. This study explores the relationship between transcription and replication and suggests that HO collisions are avoided through transcriptional regulatory mechanisms.
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
Biochemistry & Molecular Biology
Leonid Serebreni, Lisa-Marie Pleyer, Vanja Haberle, Oliver Hendy, Anna Vlasova, Vincent Loubiere, Filip Nemcko, Katharina Bergauer, Elisabeth Roitinger, Karl Mechtler, Alexander Stark
Summary: Different classes of promoters have distinct mechanisms of transcription initiation, resulting in either focused or dispersed initiation patterns.
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
Multidisciplinary Sciences
Furqan M. Fazal, Daniel J. Koslover, Ben F. Luisi, Steven M. Block
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Editorial Material
Biochemistry & Molecular Biology
Furqan M. Fazal, Howard Y. Chang
Article
Multidisciplinary Sciences
Cong A. Meng, Furqan M. Fazal, Steven M. Block
NATURE COMMUNICATIONS
(2017)
Article
Biochemistry & Molecular Biology
Daniel J. Koslover, Furqan M. Fazal, Rachel A. Mooney, Robert Landick, Steven M. Block
JOURNAL OF MOLECULAR BIOLOGY
(2012)
Article
Optics
Furqan M. Fazal, Steven M. Block
Article
Multidisciplinary Sciences
Volker Schweikhard, Cong Meng, Kenji Murakami, Craig D. Kaplan, Roger D. Kornberg, Steven M. Block
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2014)
Article
Chemistry, Physical
Hongwei Xia, Junpeng Zhao, Cong Meng, Ying Wu, Yijie Lu, Jingxia Wang, Yanlin Song, Lei Jiang, Guangzhao Zhang
Article
Materials Science, Multidisciplinary
Yijie Lu, Cong Meng, Hongwei Xia, Guangzhao Zhang, Chi Wu
JOURNAL OF MATERIALS CHEMISTRY C
(2013)
Article
Biochemistry & Molecular Biology
Lei Sun, Furqan M. Fazal, Pan Li, James P. Broughton, Byron Lee, Lei Tang, Wenze Huang, Eric T. Kool, Howard Y. Chang, Qiangfeng Cliff Zhang
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Furqan M. Fazal, Shuo Han, Kevin R. Parker, Pornchai Kaewsapsak, Jin Xu, Alistair N. Boettiger, Howard Y. Chang, Alice Y. Ting
Article
Biochemistry & Molecular Biology
Kevin E. Wu, Kevin R. Parker, Furqan M. Fazal, Howard Y. Chang, James Zou
Article
Biochemistry & Molecular Biology
Kevin E. Wu, Furqan M. Fazal, Kevin R. Parker, James Zou, Howard Y. Chang
Article
Hematology
Kristina Maas-Bauer, Juliane K. Lohmeyer, Toshihito Hirai, Teresa Lopes Ramos, Furqan M. Fazal, Ulrike M. Litzenburger, Kathryn E. Yost, Jessica V. Ribado, Neeraja Kambham, Arielle S. Wenokur, Po-Yu Lin, Maite Alvarez, Melissa Mavers, Jeanette Baker, Ami S. Bhatt, Howard Y. Chang, Federico Simonetta, Robert S. Negrin
Summary: Different sublineages of iNKT cells exhibit distinct functions, with iNKT1 cells showing the highest antitumor activity against murine B-cell lymphoma cells, while iNKT2 and iNKT17 cells have immune-regulatory properties. These findings have important implications for the development of iNKT cell therapies in cancer immunotherapy and GVHD prevention and treatment.