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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)
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Biochemistry & Molecular Biology
Margaret L. Rodgers, Yunsheng Sun, Sarah A. Woodson
Summary: During transcription, ribosomal subunits begin assembly by folding rRNA and associating it with ribosomal proteins (RPs). The initial recognition of properly folded rRNA by primary assembly proteins, like S4, is delayed due to the variable folding of rRNA during transcription. Late-binding RP S12 promotes the association of S4 with pre-16S rRNA, accelerating ribosome assembly.
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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.
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Biochemistry & Molecular Biology
Yi Zeng, Benjamin J. Fair, Huilin Zeng, Aiswarya Krishnamohan, Yichen Hou, Johnathon M. Hall, Alexander J. Ruthenburg, Yang Li, Jonathan P. Staley
Summary: Previous studies suggested that most vertebrate genes require exon definition for splicing, where spliceosome assembly occurs on exons rather than introns. However, our research found that 90% of introns, including long introns, can splice before the transcription of a downstream exon, indicating that exon definition is not necessary for most human introns. Additionally, splicing timing varies greatly among introns and is influenced by various genetic elements.
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Microbiology
Mengxue Wang, Jinghua Li, Yong Wang, Hang Fu, Haoning Qiu, Yanying Li, Ming Li, Ying Lu, Yu Vincent Fu
Summary: In this study, it was found that Hmo1, but not Hho1, is involved in chromatin assembly and compaction in budding yeast. Furthermore, Hmo1 can form condensates via reversible phase separation. Our findings provide insights into the functionality and evolution of linker histone H1 in Saccharomyces cerevisiae.
Editorial Material
Biochemistry & Molecular Biology
Nusrat S. Qureshi, Olivier Duss
Summary: This review provides a mechanistic overview of the co-transcriptional protein-RNA complex assembly, including processes such as co-transcriptional RNA folding, processing, modification, and assembly within biomolecular condensates. These tightly coupled processes cooperate to achieve efficient and spatial-temporally regulated assembly.
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Biochemistry & Molecular Biology
Achim P. Popp, Johannes Hettich, J. Christof M. Gebhardt
Summary: Research has shown that the binding of transcription factors (TF) primarily affects the frequency of transcriptional bursts, with variations in TF residence time having a stronger influence than variations in concentration. TF binding triggers multiple successive steps before the gene transitions to an active state, with actual mRNA synthesis decoupled from TF presence. Quantification of all transition times of TF and the gene provides detailed kinetic insight for a bottom-up understanding of gene regulation.
NUCLEIC ACIDS RESEARCH
(2021)
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Multidisciplinary Sciences
Adrien Chauvier, Patrick St-Pierre, Jean-Francois Nadon, Elsa D. M. Hien, Cibran Perez-Gonzalez, Sebastien H. Eschbach, Anne-Marie Lamontagne, J. Carlos Penedo, Daniel A. Lafontaine
Summary: The researchers presented a new approach for site-specific labeling and smFRET studies of kilobase-length transcripts within native bacterial complexes, revealing the relationship between RNA folding and gene regulation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Muchen Pan, Ana L. Alvarez-Cabrera, Joon S. Kang, Lihua Wang, Chunhai Fan, Z. Hong Zhou
Summary: The authors presented a 3.3 angstrom cryo-EM asymmetric reconstruction of transcribing MRV, revealing molecular interactions among virion proteins and genomic and messenger RNA. The study helps to understand the molecular mechanisms involved in virus assembly and RNA transcription by elucidating different interactions among molecules.
NATURE COMMUNICATIONS
(2021)
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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.
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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.
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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
Timothy T. Harden, Ben J. Vincent, Angela H. DePace
Summary: Combinatorial regulation of gene expression by transcription factors involves the kinetic synergy, where TFs play distinct kinetic roles. In this study, live imaging was used to determine the kinetic roles of three TFs (Zelda, Bicoid, and Stat92E) in activating transcription in Drosophila embryos. These TFs influence different sets of kinetic parameters, and their influence can change over time. Understanding the kinetic roles of TFs is important for elucidating the composition and flexibility of regulatory DNA sequences and the biochemical function of TFs.
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Oncology
Catherine E. Scull, Guy Twa, Yinfeng Zhang, Naiheng J. Yang, Robert N. Hunter III, Corinne E. Augelli-szafran, David A. Schneider
Summary: A newly identified ribosome biogenesis inhibitor, RBI2, has been shown to inhibit multiple types of cancer cells by inducing rapid polyadenylation and degradation of ribosomal RNA. This mechanism of action is distinct from previously described compounds and offers a potential novel pathway for cancer therapeutics targeting ribosome synthesis. This study reveals the importance of ribosome biogenesis in cancer cell growth and highlights the potential of RBI2 as a promising cancer therapeutic.
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Cell Biology
Mattia Marenda, Elena Lazarova, Sebastian van de Linde, Nick Gilbert, Davide Michieletto
Summary: Understanding biological function involves identifying and characterizing complex patterns of molecules, which can be quantitatively measured by single-molecule localization microscopy. Interconnected protein clusters are common within nuclear proteins, suggesting an important role in genome organization and function, while absent in ceramides located in the plasma membrane.
JOURNAL OF CELL BIOLOGY
(2021)