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
Cell Biology
Xinxin Wang, Yilun Qi, Zhenning Wang, Li Wang, Aixia Song, Bolin Tao, Jiabei Li, Dan Zhao, Hongwei Zhang, Qianwei Jin, Yi-Zhou Jiang, Fei Xavier Chen, Yanhui Xu, Xizi Chen
Summary: This study identified a novel protein, RPAP2, which plays an important regulatory role in transcription initiation and DNA replication. RPAP2 inhibits the assembly of the pre-initiation complex (PIC) by preventing the interaction between Pol II and TFIIF, thereby limiting the transcription initiation of genes. Loss of RPAP2 leads to the accumulation of TFIIF and Pol II at the promoter regions, affecting gene expression.
Article
Multidisciplinary Sciences
Jiqin Wu, Xinyu Wang, Qiaojie Liu, Guoliang Lu, Peng Gong
Summary: This study presents crystal structures of the RNA-dependent RNA polymerase complex from dengue virus serotype 2, revealing a dramatic refolding of the priming element during elongation and confirming its essential interactions with the RNA duplex backbone for enzyme stability. Enzymology data further suggest that the critical refolding transition of the priming element likely occurs after the synthesis of a 4- to 5-nucleotide product.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Sanjay Dey, Claire Batisse, Jinal Shukla, Michael W. Webster, Maria Takacs, Charlotte Saint-Andre, Albert Weixlbaumer
Summary: This article investigates the regulatory mechanism of RNA in its own synthesis. Cryo-EM reconstructions reveal that U-rich RNA sequences can promote widening of the RNAP nucleic-acid-binding channel, facilitating transcript dissociation. These findings contribute to the understanding of RNA-mediated intrinsic transcription termination.
Article
Physics, Fluids & Plasmas
Jin Qian, David Dunlap, Laura Finzi
Summary: In this study, a thermodynamic model of transcriptional pausing is proposed to describe the kinetics of different types of pauses based on the thermal energy of transcription bubbles and nascent RNA structures. The model can accurately predict experimentally detected pauses and the effects of tension and transcription factors on pausing.
Article
Multidisciplinary Sciences
Brian A. Lewis, Subhendu Kumar Das, Rajiv Kumar Jha, David Levens
Summary: This study reveals the existence of dense and transcriptionally active biomolecular condensates (BMCs) in the nucleus, which can represent the physiological nuclear environment. This finding is crucial for further understanding transcriptional regulation mechanisms.
Article
Multidisciplinary Sciences
Sirui Zhang, Miaowei Mao, Yuesheng Lv, Yingqun Yang, Weijing He, Yongmei Song, Yongbo Wang, Yun Yang, Muthana Al Abo, Jennifer A. Freedman, Steven R. Patierno, Yang Wang, Zefeng Wang
Summary: Dysregulation of alternative splicing, particularly involving short exons, is a common feature in cancer. Short exons that are mis-spliced in cancers are more conserved and likely to encode functional low-complexity peptides. A CASE-based panel has been developed as reliable cancer stratification markers and strong predictors for survival.
Article
Microbiology
Rachel Nelson-Rigg, Sean P. Fagan, William J. Jaremko, Janice D. Pata
Summary: The emergence and spread of antibiotic resistance is a serious threat to public health. In this study, the inhibition of PolC DNA polymerase from Staphylococcus aureus by ME-EMAU was characterized using transient-state kinetic methods. The tight binding of ME-EMAU to S. aureus PolC and its slow dissociation rate suggest that it could be an effective inhibitor to prevent the replication and spread of resistant bacteria.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Biochemistry & Molecular Biology
Zhitai Hao, Vitaly Epshtein, Kelly H. Kim, Sergey Proshkin, Vladimir Svetlov, Venu Kamarthapu, Binod Bharati, Alexander Mironov, Thomas Walz, Evgeny Nudler
Summary: Rho is a crucial factor in transcription termination in bacteria, forming a pre-termination complex with RNAP and elongation factors to stabilize the process. RNA interacts with NusA before entering the central channel of Rho, highlighting the critical role of these interactions in termination. The study supports a mechanism where the formation of a persistent pre-termination complex is essential for the termination process.
Article
Plant Sciences
Nan Zhang, Kai Xu, Shengyi Liu, Rong Yan, Ziguang Liu, Ying Wu, Yifang Peng, Xiaoxu Zhang, Yasushi Yukawa, Juan Wu
Summary: Hypocotyl elongation is regulated by light, darkness, and the plant hormone abscisic acid. Long non-coding RNAs (lncRNAs) BoNR8 and AtR8 play a role in this regulation and are affected by light and ABA. These lncRNAs act together with genes involved in light signaling and ABA response, such as PHYB, COP1, HY5, PIF4, ABI3, and ABI5, to control hypocotyl elongation.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yi-Zhou Wang, Cuifang Liu, Jicheng Zhao, Juan Yu, Anfeng Luo, Xue Xiao, Shuo-Xing Dou, Lu Ma, Peng-Ye Wang, Ming Li, Guohong Li, Jianbin Yan, Ping Chen, Wei Li
Summary: This study reveals how H2A ubiquitination regulates the dual functions of the histone chaperone FACT in nucleosome assembly and disassembly. H2A ubiquitination restricts FACT binding on nucleosome and inhibits nucleosome disassembly, while deubiquitination of ubH2A rescues these functions to activate gene transcription.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Shu-Hao Liou, Sameer K. Singh, Robert H. Singer, Robert A. Coleman, Wei-Li Liu
Summary: Liou et al. report a 4.6 angstrom resolution structure of the human p53/RNA polymerase II assembly, using single particle cryoelectron microscopy. This study suggests that p53's functional domains regulate the DNA binding activity of RNA polymerase II, providing insights into p53-regulated gene expression.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Eunho Song, Seungha Hwang, Palinda Ruvan Munasingha, Yeon-Soo Seo, Jin Young Kang, Changwon Kang, Sungchul Hohng
Summary: In this study on bacterial Rho factor-dependent terminators, it was found that the three Rho-dependent termination routes operate compatibly and their efficiency depends on the termination pauses. The most abundant route involves Rho catching up with a paused RNA polymerase, leading to simultaneous release of transcript RNA and template DNA. The fastest route results in RNA-only release and recycling of RNAP, while the slowest route facilitates simultaneous releases. The termination efficiency of stand-by Rho positively correlates with pause duration, contrary to previous speculation.
NUCLEIC ACIDS RESEARCH
(2023)
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.
Article
Biochemistry & Molecular Biology
Inwha Baek, Larry J. Friedman, Jeff Gelles, Stephen Buratowski
Summary: Research shows that in activator-dependent PIC assembly, RNA Pol II, TFIIF, and TFIIE can preassemble on enhancer-bound activators, and multiple RNA Pol II complexes can simultaneously bind to form a localized cluster, while TFIIH binding is unique and depends on the basal promoter.