Article
Biotechnology & Applied Microbiology
Trevor F. Freeman, Qiuxia Zhao, Agustian Surya, Reed Rothe, Elif Sarinay Cenik
Summary: This study investigates the impact of depleting the ribosome biogenesis components RPOA-2 and GRWD-1 on chromatin accessibility using ATAC-seq. The results show similar changes in chromatin accessibility for both perturbations, but a weak correlation with gene expression.
Article
Biochemistry & Molecular Biology
Marina Yu Mazina, Elena Kovalenko, Aleksandra A. Evdokimova, Maksim Erokhin, Darya Chetverina, Nadezhda E. Vorobyeva
Summary: This study investigated the recruitment and pausing mechanism of RNA polymerase II during Drosophila metamorphosis. The results indicate that, similar to mid-embryogenesis, promoters are bound by paused RNA polymerase II during metamorphosis, preparing for activation in later developmental stages.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Virology
Ashley N. Knox, Alice Mueller, Eva M. Medina, Eric T. Clambey, Linda F. van Dyk
Summary: This study investigated the regulation of pol III promoters and transcripts during gammaherpesvirus infection, revealing that lytic infection with gamma HV68 increased transcription from multiple host and viral pol III promoters. Additionally, induction of endogenous pol III-derived ncRNAs correlated tightly with viral gene expression, demonstrating how lytic gammaherpesvirus infection alters the transcriptional landscape of host cells to enhance host and viral noncoding RNA expression.
JOURNAL OF VIROLOGY
(2021)
Article
Cell Biology
Kevin M. Andre, Nathalie Giordanengo Aiach, Veronica Martinez-Fernandez, Leo Zeitler, Adriana Alberti, Arach Goldar, Michel Werner, Cyril Denby Wilkes, Julie Soutourina
Summary: Chromatin organization is crucial for transcriptional regulation. Mediator and RSC contribute to chromatin remodeling and transcriptional regulation by establishing physical contact and coordinating their functions.
Article
Multidisciplinary Sciences
Trevor van Eeuwen, Tao Li, Hee Jong Kim, Jose J. Gorbea Colon, Mitchell Parker, Roland L. Dunbrack, Benjamin A. Garcia, Kuang-Lei Tsai, Kenji Murakami
Summary: During transcription initiation, TFIIH marks RNA polymerase II by phosphorylating Ser5 of Rpb1's CTD, followed by modifications related to transcription elongation, mRNA processing, and histone dynamics. The structure of TFIIK helps extend the proposed model of the CTD path to TFIIH's active site.
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
Multidisciplinary Sciences
Jesus Garcia-Castillo, Francisca Alcaraz-Perez, Elena Martinez-Balsalobre, Diana Garcia-Moreno, Marlies P. Rossmann, Miriam Fernandez-Lajarin, Manuel Bernabe-Garcia, Ana B. Perez-Oliva, Virginia C. Rodriguez-Cortez, Clara Bueno, Isaac Adatto, Suneet Agarwal, Pablo Menendez, Leonard Zon, Victoriano Mulero, Maria L. Cayuela
Summary: Dyskeratosis congenita (DC) is a rare genetic syndrome caused by mutations in telomerase or telomeric proteins. Research shows that zebrafish terc plays a crucial role in regulating the expression of master myeloid genes, while mutations found in DC patients affect this process.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Diego Sanchez-Popoca, Isela Serrano-Fujarte, Marcos Fernandez-Mora, Edmundo Calva
Summary: LeuO is a transcriptional regulator in bacteria that plays a role in stress response and virulence. This article discusses four areas of research, including the diversity of the LeuO gene, the involvement of nucleoid-associated proteins in regulation processes, the effector-binding domain of LeuO, and the role of the CRISPR-Cas system in gene regulation in S. Typhi.
MOLECULAR MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Virtu Solano-Collado, Sofia Ruiz-Cruz, Fabian Lorenzo-Diaz, Radoslaw Pluta, Manuel Espinosa, Alicia Bravo
Summary: The study reveals the similarity of promoter recognition between SigA in Streptococcus pneumoniae and homologs in E. coli and Bacillus subtilis, showing the versatility of SigA in recognizing promoters from different sources. Results also demonstrate that SigA can direct RNA polymerase to transcribe genes involved in plasmid pMV158 replication and conjugative mobilization, indicating its critical role in the promiscuity of the plasmid.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
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
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.
Article
Microbiology
Alistair D. Middlemiss, Emily A. Warman, David Forrest, James R. J. Haycocks, David C. Grainger
Summary: Transcription of DNA into RNA, the first step of gene expression, is believed to occur in a specific direction. However, recent research has shown that many prokaryotic promoters can drive divergent transcription. This study used global transcription start site mapping to determine the prevalence of bidirectional promoters in Salmonella Typhimurium. Surprisingly, bidirectional promoters occur more frequently in plasmid components of the genome compared to chromosomal DNA. The implications for promoter sequence evolution are also discussed.
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
Biochemistry & Molecular Biology
Raphael Forquet, William Nasser, Sylvie Reverchon, Sam Meyer
Summary: DNA supercoiling acts as a global transcriptional regulator in bacteria. A thermodynamic model based on DNA elasticity is developed to predict the relative activation of promoters with different spacer lengths. The model is validated through in vitro and in vivo expression assays and genome-scale analysis in Escherichia coli, demonstrating the significant effect of spacer length on genomic expression after superhelical variations.
NUCLEIC ACIDS RESEARCH
(2022)
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
Jeremy Sandoz, Zita Nagy, Philippe Catez, Gizem Caliskan, Sylvain Geny, Jean-Baptiste Renaud, Jean-Paul Concordet, Arnaud Poterszman, Laszlo Tora, Jean-Marc Egly, Nicolas Le May, Frederic Coin
NATURE COMMUNICATIONS
(2019)
Article
Biochemistry & Molecular Biology
M. Semer, B. Bidon, A. Larnicol, G. Caliskan, P. Catez, J. M. Egly, F. Coin, N. Le May
NATURE CHEMICAL BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Corina Gsell, Holger Richly, Frederic Coin, Hanspeter Naegeli
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Alexey Epanchintsev, Marc-Alexander Rauschendorf, Federico Costanzo, Nadege Calmels, Cathy Obringer, Alain Sarasin, Frederic Coin, Vincent Laugel, Jean-Marc Egly
SCIENTIFIC REPORTS
(2020)
Editorial Material
Biochemistry & Molecular Biology
Samar Kabbara, Baptiste Bidon, Jaafar Kilani, Marwan Osman, Monzer Hamze, Ann M. Stock, Nicolas Papon
Article
Genetics & Heredity
Sarah Baer, Nicolas Tuzin, Peter B. Kang, Shehla Mohammed, Masaya Kubota, Yvette van Ierland, Tiffany Busa, Massimiliano Rossi, Godelieve Morel, Caroline Michot, Genevieve Baujat, Myriam Durand, Cathy Obringer, Nicolas Le May, Nadege Calmels, Vincent Laugel
Summary: Cockayne syndrome (CS) is a multisystem degenerative disorder with 3 subtypes, including CS2 as the most severe form. Growth failure and difficulties are common features, emphasizing the need for specific growth charts. Retrospective study on CS1 and CS2 patients highlights the importance of specific growth charts for improving nutrition management in these patients.
EUROPEAN JOURNAL OF MEDICAL GENETICS
(2021)
Article
Microbiology
Marwan Osman, Baptiste Bidon, Cynthia Abboud, Ayate Zakaria, Baraa Hamze, Marcel El Achcar, Hassan Mallat, Eric Dannaoui, Fouad Dabboussi, Nicolas Papon, Jean-Philippe Bouchara, Monzer Hamze
Summary: The study revealed that Aspergillus niger is the most common species among the isolates in Lebanon, with highest overall drug resistance to amphotericin B. Mutations in the CYP51A gene were not the primary cause of resistance to all azole antifungal drugs among these isolates.
FUTURE MICROBIOLOGY
(2021)
Review
Cell Biology
Baptiste Bidon, Samar Kabbara, Vincent Courdavault, Gaelle Glevarec, Audrey Oudin, Francois Hericourt, Sabine Carpin, Lukas Spichal, Brad M. Binder, J. Mark Cock, Nicolas Papon
Article
Genetics & Heredity
M. A. Spitz, F. Severac, C. Obringer, S. Baer, N. Le May, N. Calmels, V. Laugel
Summary: Cockayne syndrome is a progressive multisystem genetic disorder with a wide spectrum of clinical severity levels. Diagnostic and severity scores were established using clinical, imaging, and genetic data from 69 confirmed CS patients. The severity score successfully differentiated classical predefined subtypes of CS and reflected the disease's natural course over time.
ORPHANET JOURNAL OF RARE DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Pietro Berico, Max Cigrang, Guillaume Davidson, Cathy Braun, Jeremy Sandoz, Stephanie Legras, Bujamin Hektor Vokshi, Nevena Slovic, Francois Peyresaubes, Carlos Mario Gene Robles, Jean-Marc Egly, Emmanuel Compe, Irwin Davidson, Frederic Coin
Summary: The chronic inhibition of CDK7 drives melanoma cells to switch from differentiated melanocytic-type to undifferentiated mesenchymal-like cells, leading to tolerance to targeted therapies. Additionally, a GATA6-dependent gene expression program is activated, contributing to melanoma survival and targeted drug tolerance. These findings highlight the importance of CDK7 in regulating the expression of key transcription factors and genes involved in melanoma progression and resistance to treatment.
Article
Genetics & Heredity
Rayanne Damaj-Fourcade, Nicolas Meyer, Cathy Obringer, Nicolas Le May, Nadege Calmels, Vincent Laugel
Summary: This study aimed to investigate the genotype-phenotype correlation in Cockayne syndrome and found that the number of downstream mutations is associated with clinical expression, but further research is needed to understand the exact relationship.
FRONTIERS IN GENETICS
(2022)
Article
Medicine, Research & Experimental
Federico Costanzo, Marta Martinez Diez, Gema Santamaria Nunez, Juan Ignacio Diaz-Hernandez, Carlos Mario Genes Robles, Javier Diez Perez, Emmanuel Compe, Romeo Ricci, Tsai-Kun Li, Frederic Coin, Juan Fernando Martinez Leal, Eva Maria Garrido-Martin, Jean Marc Egly
Summary: This article focuses on the neuroendocrine subtypes of small-cell lung cancer (SCLC), SCLC-A and SCLC-N, and highlights the transcription addiction driven by ASCL1 and NEUROD1 transcription factors. The study reveals that lurbinectedin, a marine agent, effectively targets the CpG islands downstream of the transcription start site, inhibiting gene expression and suppressing the tumorigenic properties and neuroendocrine features of SCLC.
EMBO MOLECULAR MEDICINE
(2022)
Article
Multidisciplinary Sciences
Emmanuel Compe, Evanthia Pangou, Nicolas Le May, Clemence Elly, Cathy Braun, Ji-Hyun Hwang, Frederic Coin, Izabela Sumara, Kwang-Wook Choi, Jean-Marc Egly
Summary: The helicase XPD can localize with the motor protein Eg5 to mitotic spindles and the midbodies of human cells independently of other TFIIH subunits. The partnership between XPD and Eg5 is regulated by phosphorylation of Eg5/T926 by CDK1 and Eg5/S1033 by NEK6. This phosphorylation is required for Eg5 localization, checkpoint activation, and chromosome segregation in mitosis.
Article
Multidisciplinary Sciences
Jeremy Sandoz, Max Cigrang, Amelie Zachayus, Philippe Catez, Lise-Marie Donnio, Clemence Elly, Jadwiga Nieminuszczy, Pietro Berico, Cathy Braun, Sergey Alekseev, Jean-Marc Egly, Wojciech Niedzwiedz, Giuseppina Giglia-Mari, Emmanuel Compe, Frederic Coin
Summary: The exonuclease EXD2 plays a role in the recovery of class II gene transcription after UV irradiation. It moves from mitochondria to the nucleus where it interacts with RNA Pol II and degrades newly synthesized mRNA, allowing transcription to resume after DNA repair. Lack of EXD2 impairs mRNA synthesis recovery and reduces cell survival after UV irradiation, but does not affect DNA repair. Overexpression of wild-type EXD2 restores mRNA synthesis recovery and cell survival. EXD2 is relocated from mitochondria to the nucleus upon UV irradiation, where it interacts transiently with chromatin-bound RNA Pol II to promote the degradation of nascent mRNAs. In vitro experiments show that EXD2 primarily interacts with elongation-blocked RNA Pol II and efficiently degrades mRNA. Overall, this study highlights the crucial role of EXD2 in the transcriptional response to genotoxic attack, where it interacts with elongation-stalled RNA Pol II on chromatin to potentially degrade the associated nascent mRNA, allowing transcription restart after DNA repair.
NATURE COMMUNICATIONS
(2023)