Article
Multidisciplinary Sciences
Sandra Schilbach, Haibo Wang, Christian Dienemann, Patrick Cramer
Summary: This study presents an atomic model for the yeast preinitiation complex (PIC) with core mediator, revealing the molecular details of RNA polymerase II (Pol II) transcription initiation. The structure of the mediator middle module was optimized, and the missing subunit Med1 was identified. The study found that the flexible C-terminal repeat domain (CTD) of Pol II forms defined interactions with the mediator head and middle modules, as well as other regions of the mediator. The binding mode between the yeast mediator and Pol II differs from the human counterpart.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Maura Mittermeier, Bing Wang, Nelly Said, Daniela Gjorgjevikj, Markus C. Wahl, Irina Artsimovitch
Summary: Escherichia coli RfaH plays a role in abolishing Rho-mediated polarity in lipopolysaccharide core biosynthesis operons. A temperature-sensitive mutant rpoC397* was identified as a suppressor of SDS sensitivity, with 46 C-terminal residues of the RNA polymerase beta' subunit replaced by 23 residues carrying a net positive charge. The rpoC397* mutant mimics RfaH's resistance to Rho and exhibits similar responses to pause signals and Nus factors, while still binding to Rho and Nus factors in vivo.
MOLECULAR MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ahmet C. Berkyurek, Giulia Furlan, Lisa Lampersberger, Toni Beltran, Eva-Maria Weick, Emily Nischwitz, Isabela Cunha Navarro, Fabian Braukmann, Alper Akay, Jonathan Price, Falk Butter, Peter Sarkies, Eric A. Miska
Summary: PIWI-interacting RNAs (piRNAs) are small RNAs that regulate germ cell development in animals, and in the nematode Caenorhabditis elegans, the core subunit RPB-9 of RNA polymerase II (RNA Pol II) is identified as essential for piRNA-mediated gene silencing. RPB-9 is required for piRNA biogenesis by recruiting the Integrator complex at piRNA genes for transcriptional termination, suggesting the piRNA pathway has evolved to utilize a mechanism originally used for transcription fidelity.
Article
Biochemistry & Molecular Biology
Fiorella Scagnoli, Alessandro Palma, Annarita Favia, Claudio Scuoppo, Barbara Illi, Sergio Nasi
Summary: Deregulation of the MYC oncoprotein is a common event in cancer, and inhibiting its activity can restrain tumor development. This study shows that MYC regulates transcription termination by affecting a methylated target, R1810me2s, and Omomyc can counteract this effect. Omomyc also affects RNAPII elongation and reshapes gene expression, suggesting an MYC/PRMT5/RNAPII axis that contributes to altered gene expression in cancer.
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
Biochemistry & Molecular Biology
Yousra Yahia, Alexia Pigeot, Amal Zine El Aabidine, Nilay Shah, Nezih Karasu, Ignasi Forne, Stefan Krebs, Helmut Blum, Cyril Esnault, Tom Sexton, Axel Imhof, Dirk Eick, Jean-Christophe Andrau
Summary: This study shows that the largest subunit of RNA polymerase II (Pol II), known as the C-terminal domain (CTD), plays a crucial role in the transcriptional process. Using a CTD-& UDelta;5 mutant in human cells, it was found that this mutant can transcribe genes but has impaired termination. The mutant lacks interaction with the Mediator and Integrator complexes and does not affect the overall genomic organization.
Article
Biochemistry & Molecular Biology
Tianhe Wang, Friedrich C. Simmel
Summary: Regulatory RNA molecules have been explored as synthetic gene circuit components, offering advantages such as simple design, programmability, orthogonality, and low metabolic burden. This study developed riboswitch-inspired riboregulators in E. coli, combining TMSD with the switching principles of natural riboswitches for translational and transcriptional regulation. The design allows for translational activation or repression by changing the secondary structure of RNA, providing a new set of synthetic riboregulators for genetic sensors and circuits.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Seungha Hwang, Paul Dominic B. Olinares, Jimin Lee, Jinwoo Kim, Brian T. Chait, Rodney A. King, Jin Young Kang
Summary: In this study, the authors determined the structure of putRNA and its interaction with RNA polymerase using cryo-EM. They found that putRNA can inhibit pausing and termination during transcription, providing insights into the regulation of gene expression.
NATURE COMMUNICATIONS
(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
Craig J. Marshall, M. Zuhaib Qayyum, Julie E. Walker, Katsuhiko S. Murakami, Thomas J. Santangelo
Summary: Transcription termination is an important process in regulating gene expression, and the protein Eta has been identified as one of the factors involved in disrupting transcription elongation complexes. By studying the biochemical activities and crystal structure of Eta, researchers have gained insight into its role in transcription termination. The susceptibility of transcription elongation complexes to disruption by termination factors highlights the common features of transcription termination mechanisms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Matthew S. Verosloff, William K. Corcoran, Taylor B. Dolberg, David Z. Bushhouse, Joshua N. Leonard, Julius B. Lucks
Summary: Through the newly developed in cellulo Pol III transcription termination assay, it was found that efficient Pol III termination requires the cooperation of poly-U tracts, RNA sequence, and structural elements in nascent RNA. Different promoter types have different requirements for transcription termination.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemical Research Methods
Michael J. O'Brien, Katherine Gurdziel, Athar Ansari
Summary: Global Run-On sequencing is a reliable and widely used approach for monitoring nascent transcription on a genomewide scale. This article describes a GRO-seq protocol for studying transcription in budding yeast, Saccharomyces cerevisiae. The protocol involves permeabilization of yeast cells, bromo-UMP incorporation, cDNA library construction, deep sequencing, and mapping against the reference genome to identify transcriptionally active genes, elongation rate, termination defect, and promoter directionality. It is especially useful in identifying short-lived unstable transcripts.
Article
Multidisciplinary Sciences
Keyan Bao, Xueli Zhang, Dongyu Li, Wei Sun, Zhenzhao Sun, Jingfei Wang, Ping Zhu
Summary: By studying the structure of reovirus, we have identified the structures of its transcriptase complex in different states and proposed a transcriptional model with five states. Our findings reveal the key regulatory mechanisms during the transcription process of reovirus.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Araceli Gonzalez-Jimenez, Adrian Campos, Francisco Navarro, Andres Clemente-Blanco, Olga Calvo
Summary: Phosphorylation can regulate the function of RNA polymerases and affect the coordination with other nuclear processes. Apart from Rpb1-CTD, other RNAPII subunits are phosphorylated, but little is known about phosphorylation of RNAPI and RNAPIII. Different subunits of RNAPI and RNAPIII may be susceptible to phosphorylation, indicating a potential coordination mechanism among the three RNAPs.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Mengdi Li, Danhui Ma, Zhijie Chang
Summary: CREPT and p15RS are RPRD proteins that regulate cell proliferation and tumorigenesis, with opposite functions. Aberrant expression of both proteins is found in cancers. They both interact with RNA polymerase II, but CREPT also plays a key role in DNA damage repair.