Article
Biochemistry & Molecular Biology
Guangna Chen, Hongliang Hu, Xinhui Chen, Jialuo Chen, Siyi Wang, He Ning, Cheng Zhu, Su Yang
Summary: TFIIB is a general transcription factor that plays a crucial role in RNA polymerase II activity. In plants, the TFIIB-related protein family, including BRP5/PTF2, has expanded greatly. This study revealed the essential role of BRP5/PTF2 in pollen germination and embryogenesis in Arabidopsis and its impact on pollen development and grain formation in rice. These findings highlight the importance of BRP5/PTF2 in plant sexual reproduction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Vu Q. Nguyen, Anand Ranjan, Sheng Liu, Xiaona Tang, Yick Hin Ling, Jan Wisniewski, Gaku Mizuguchi, Kai Yu Li, Vivian Jou, Qinsi Zheng, Luke D. Lavis, Timothee Lionnet, Carl Wu
Summary: The study reveals that transcription initiation by RNA Pol II at gene promoters requires formation of the PIC, with a key role played by the Mediator complex. On chromatin, TFIID/TBP, Mediator, and RNA Pol II efficiently assemble into a short-lived PIC within seconds. Nucleosome exclusion of PIC highlights the importance of chromatin remodeling in regulating promoter accessibility.
Article
Biochemistry & Molecular Biology
Sophie Terrone, Jessica Valat, Nicolas Fontrodona, Guillaume Giraud, Jean-Baptiste Claude, Emmanuel Combe, Audrey Lapendry, Helene Polveche, Lamya Ben Ameur, Arnaud Duvermy, Laurent Modolo, Pascal Bernard, Franck Mortreux, Didier Auboeuf, Cyril F. Bourgeois
Summary: DDX5 and DDX17 are RNA helicases that play important roles in regulating gene expression, particularly transcription and splicing. They are involved in the processing of RNA and have a significant impact on splicing and 3' end processing. The study also found that the genome organizing factor CTCF is involved in the regulation of DDX5/DDX17-dependent exons, which are characterized by high GC content and RNA Polymerase II density. Furthermore, it was discovered that local chromatin loops formed by DDX5/DDX17 connect regulated exons with their cognate promoter, providing evidence for gene looping modifying alternative splicing and polyadenylation. These findings highlight the importance of DDX5/DDX17-dependent chromatin folding in pre-messenger RNA processing.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Michael J. O'Brien, Athar Ansari
Summary: Viral infections depend on host transcription and translation machinery to replicate viral genes and express proteins, with the transcription factor TFIIB frequently targeted by viruses. Direct interactions between viral transcriptional regulators and host TFIIB may offer potential for antiviral therapies.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biology
Rachael Emily Turner, Paul F. Harrison, Angavai Swaminathan, Calvin A. Kraupner-Taylor, Belinda J. Goldie, Michael See, Amanda L. Peterson, Ralf B. Schittenhelm, David R. Powell, Darren J. Creek, Bernhard Dichtl, Traude H. Beilharz
Summary: This study investigates the regulation of mRNA function by 3' end formation factors, revealing that different drugs can impact the selection of poly(A) addition sites by influencing nucleotide levels and chromatin landscape to regulate alternative polyadenylation.
Article
Biochemistry & Molecular Biology
Debao Xie, Xiangdong Zhao, Lujie Ma, Le Wang, Pan Li, Hongqian Cheng, Zhaoying Li, Pei Zeng, Jing Zhang, Fanli Zeng
Summary: The proteins Rba50 and Gpn2 play important roles in the assembly of RNA polymerase. Their interaction is crucial for recruiting Rpb2, and the Rba50-Gpn2 complex has a similar role in the assembly of RNAPIII.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biology
Marzia Munafo, Victoria R. Lawless, Alessandro Passera, Serena MacMillan, Susanne Bornelov, Irmgard U. Haussmann, Matthias Soller, Gregory J. Hannon, Benjamin Czech
Summary: The nuclear pore complex (NPC) functions as a gateway between the nucleus and cytoplasm for exchange of macromolecular cargo. Specific nucleoporins within the NPC, such as Nup54 and Nup58, have essential roles in transposon silencing via the piRNA pathway in the Drosophila ovary, suggesting tissue-specific functions for certain NPC subunits. This study demonstrates that genomic loci under selective pressure can exploit NPC subunits to facilitate their expression, indicating additional functions beyond nuclear/cytoplasmic exchange for the NPC.
Article
Plant Sciences
Morgan Lee, Anna Dominguez-Ferreras, Ewon Kaliyadasa, Wei-Jie Huang, Edna Antony, Tracey Stevenson, Silke Lehmann, Patrick Schafer, Marc R. Knight, Vardis Ntoukakis, Heather Knight
Summary: This study revealed the roles of plant Mediator subunits MED16, MED14, and MED2 in regulating transcription in response to the phytohormone ABA and demonstrated their requirement for full transcriptional activation of promoters containing both ABRE and DRE elements. Furthermore, these subunits were shown to be essential for controlling water loss from leaves but not for ABA-dependent growth inhibition, indicating specificity in their functions. The experimental approach used in this study can be utilized to identify the functions of plant transcriptional regulator subunits.
FRONTIERS IN PLANT SCIENCE
(2021)
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)
Article
Biochemistry & Molecular Biology
Lujie Ma, Debao Xie, Xiangdong Zhao, Le Wang, Lifeng Hou, Xueqin Liu, Zhaoying Li, Hongqian Cheng, Jing Zhang, Mengdi Gao, Fanli Zeng
Summary: RNA polymerase II (RNAPII) is a crucial machinery in eukaryotes that controls mRNA synthesis and cell fate. Gpn3 and Npa3 directly participate in the assembly of RNAPII, and defects in Gpn3 disrupts the assembly, leading to cytoplasmic foci of RNAPII subunits. This study also reveals a new cellular rescue response called the "RNAPII assembly stress response".
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Plant Sciences
V. Miguel Palomar, Sarah Jaksich, Sho Fujii, Jan Kucinski, Andrzej T. Wierzbicki
Summary: In this study, the genome-wide pattern of plastid-encoded RNA polymerase (PEP) binding to chloroplast DNA was investigated using plastid chromatin immunoprecipitation-sequencing (ptChIP-seq) method. The results showed that PEP has a complex DNA binding pattern with preferential association at genes encoding rRNA, tRNA, and a subset of photosynthetic proteins in mature Arabidopsis thaliana chloroplasts. Sigma factors SIG2 and SIG6 were found to have effects on PEP binding to a subset of tRNA genes and throughout the rest of the genome. PEP binding was commonly enriched on gene promoters, around transcription start sites, and the levels of PEP binding to DNA were correlated with levels of RNA accumulation.
Article
Immunology
Michael D. Claiborne, Srona Sengupta, Liang Zhao, Matthew L. Arwood, Im-Meng Sun, Jiayu Wen, Elizabeth A. Thompson, Marisa Mitchell-Flack, Marikki Laiho, Jonathan D. Powell
Summary: Memory CD8(+) T cells exhibit longevity and rapid recall response. Metabolic reprogramming and mitochondrial function are important for their longevity, while the trifunctional enzyme CAD plays a critical role in promoting the rapid recall response. CAD-induced pyrimidine synthesis and ribosomal biogenesis are involved in this process.
SCIENCE IMMUNOLOGY
(2022)
Article
Biology
Jasmin van den Heuvel, Caroline Ashiono, Ludovic C. Gillet, Kerstin Dorner, Emanuel Wyler, Ivo Zemp, Ulrike Kutay
Summary: In this study, it was found that the ribosomal protein eS30 is synthesized with the ubiquitin-like protein FUBI in human cells, but FUBI is cleaved off during ribosomal subunit maturation. Deubiquitinase USP36 was identified as an enzyme involved in FUBI-eS30 processing, demonstrating its functional importance in ribosomal subunit maturation and identifying a novel protease in the process.
Article
Cell Biology
Catherine L. W. Miller, Fred Winston
Summary: Spt6 is an important histone chaperone that regulates chromatin accessibility and plays a role in DNA replication and genome stability. Depletion or mutation of Spt6 impairs DNA replication and makes the cells sensitive to DNA replication stress. This impairment is independent of its association with RNAPII, suggesting that Spt6 mutants have a transcription-independent defect in DNA replication.
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)
Article
Multidisciplinary Sciences
Scott Medler, Athar Ansari
SCIENTIFIC REPORTS
(2015)
Article
Genetics & Heredity
Neha Agarwal, Athar Ansari
Article
Multidisciplinary Sciences
Nadra Al-Husini, Ali Sharifi, Seyed Ahmad Mousavi, Hamidreza Chitsaz, Athar Ansari
SCIENTIFIC REPORTS
(2017)
Article
Multidisciplinary Sciences
Zuzer Dhoondia, Ricci Tarockoff, Nadra Alhusini, Scott Medler, Neha Agarwal, Athar Ansari
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2017)
Article
Biochemistry & Molecular Biology
Banupriya Mukundan, Athar Ansari
JOURNAL OF BIOLOGICAL CHEMISTRY
(2013)
Article
Multidisciplinary Sciences
Aboudi M. Moabbi, Neha Agarwal, Belal El Kaderi, Athar Ansari
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2012)
Article
Genetics & Heredity
Nadra Al Husini, Paul Kudla, Athar Ansari
Article
Biochemistry & Molecular Biology
Paula Allepuz-Fuster, Michael J. O'Brien, Noelia Gonzalez-Polo, Bianca Pereira, Zuzer Dhoondia, Athar Ansari, Olga Calvo
NUCLEIC ACIDS RESEARCH
(2019)
Review
Biochemistry & Molecular Biology
Nadra Al-Husini, Scott Medler, Athar Ansari
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2020)
Article
Biochemistry & Molecular Biology
Zuzer Dhoondia, Hesham Elewa, Marva Malik, Zahidur Arif, Roger Pique-Regi, Athar Ansari
Summary: The study reveals a novel role of Rat1 in mRNA splicing in budding yeast. Rat1 interacts with splicing factors such as Clf1, Isy1, Yju2, Prp43, and Sub2, and recruitment of these splicing factors on the intron is compromised in Rat1 mutants. Rat1 is not a general splicing factor and crosslinks to only long introns with an average length of 400 nucleotides.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Michael J. O'Brien, Athar Ansari
Summary: Viral infections depend on host transcription and translation machinery to replicate viral genes and express proteins, with the transcription factor TFIIB frequently targeted by viruses. Direct interactions between viral transcriptional regulators and host TFIIB may offer potential for antiviral therapies.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Katherine Dwyer, Neha Agarwal, Lori Pile, Athar Ansari
Summary: Introns play a crucial role in eukaryotic organisms by impacting various aspects of gene expression, including transcription. Studies in yeast have shown that introns contribute to the formation of multi-looped gene architecture, enhancing transcription through interactions like promoter-5 ' splice site, terminator-3 ' splice site, and promoter-terminator interactions. This splicing-facilitated changes in gene architecture may provide insight into transcriptional regulation in yeast and higher eukaryotes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Katherine Dwyer, Neha Agarwal, Alisa Gega, Athar Ansari
Summary: Introns play a conserved role in enhancing gene expression, with proximity to both the promoter and the terminator regions affecting their regulatory potential. While a promoter-proximal intron is most efficient in enhancing gene expression, a terminator-proximal intron can also positively influence transcription by affecting both the assembly of preinitiation complex and promoter directionality.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Genetics & Heredity
Michael J. O'Brien, Athar Ansari
Summary: The general transcription factor TFIIB is not only involved in transcription initiation, but also plays a role in transcription termination. It interacts with termination factors at the 3' end of genes, potentially leading to gene looping and providing promoter directionality. This pleiotropic role of TFIIB in the transcription cycle may explain why it is preferentially targeted by viruses and warrants further study in the context of viral pathogenesis.
Editorial Material
Biochemistry & Molecular Biology
Olga Calvo, Athar Ansari, Francisco Navarro
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)